The Interactive Fly

Zygotically transcribed genes

RNA polymerase and general transcription factors

Factors involved in function of RNA polymerase II

How does messenger RNA synthesis take place?

Evolution of general transcription factors

Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation

The same transcriptional activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter

TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription

Structures of three distinct activator-TFIID complexes

Architecture of an RNA polymerase II transcription pre-initiation complex

Association of the winged helix motif of the TFIIEalpha subunit of TFIIE with either the TFIIEbeta subunit or TFIIB distinguishes its functions in transcription

dTAF10- and dTAF10b-containing complexes are required for ecdysone-driven larval-pupal morphogenesis in Drosophila melanogaster

Identification of regions in the Spt5 subunit of DSIF that are involved in promoter proximal pausing

Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition

Proteins involved in messenger RNA synthesis

General Transcription Factors, as the protein factors involved in messenger RNA synthesis are known, are conserved across species as diverse as Saccharomyces cerevisiae, Drosophila and humans. TF stands for transcription factor; they were named in chronological order of their discovery. The entire set of General Transcription Factors is composed of about 30 subunits. Although the model below assumes that the factors are assembled by stages, there is some reason to believe that all thirty are also found assembled in a holoenzyme (Orphanides, 1996 and references).

Note: General Transcription Factors are listed below in order of recruitment to the promoter.


TFIID is multiprotein complex containing the TATA box binding protein (TBP) and (in Drosophila) at least seven other proteins known as TAFs or TBP associated factors. The first protein recruited to the promoter is TBP, which serves to induce a bend in the DNA. The 240 kD subunit (TAF250kd) contains an HMG-box, bromodomains, a serine kinase, and histone acetyltransferase activity. The smaller subunits are similar in structure to histones. Drosophila TBP-associated factor 60kD (also known as dTAFII62) and TBP-associated factor 40kD (also know as dTAFII42) are homologous to human hTAFII80 and hTAFII31 respectively; Drosophila and human proteins are homologous to histone H3 and histone H4, respectively. Both Drosophila and human TFIID also contain dTAFII30 alpha and hTAFII20 that are putatitive histone H2B homologues. In solution and in the crystalline state, the dTAFII42/dTAFII62 complex exists as a heterotetramer, resembling the (H3/H4)2 heterotetrameric core of the histone octamer, suggesting that TFIID contains a histone octamer-like substructure. TBP participates in TFIID function even in promoters lacking a TATA box (Xie, 1996).
     Drosophila                        FlyBase ID       Human homologs        Yeast homologs

     -----------------                 ----------       --------------------  --------------     


     TATA binding protein              FBgn0003687      TATA binding protein  TATA binding protein

     Tbp-related factor (Trf-1)        FBgn0010287      unknown

     Trf2                              FBgn0026758      TLF/TRF2

     TBP-associated factor (TAF) 250kD FBgn0010355      TAFII250              p130

     Bip2  (TAFII155)                  FBgn0026262      TAFII140               yTAFII47   

     TBP-associated factor 150kD       FBgn0011836      Not characterized     p150   

     TBP-associated factor 110kD       FBgn0010280      TAFII135              not characterized
     No hitter (testis specific)       FBgn0041103      

     TBP-associated factor 80kD        FBgn0010356      TAFII85               p90
     Cannonball (testis specific)      FBgn0011569      

     Cabeza                            FBgn0011571      TAFII68               

     TBP-associated factor 60kD        FBgn0010417      TAFII80               p60

     Taf55                             FBgn0024909      TAFII55               TAFII67

     TBP-associated factor  40kD       FBgn0011302      TAFII31               not characterized 

     TAF 30kD subunit alpha            FBgn0011290      hTAFII20              not characterized          

     TAF 30kD subunit beta             FBgn0011291      hTAFII28              p40          

     TATA binding protein associated 
               factor 24kD subunit     FBgn0028398      TAFII30

     Taf18                             FBgn0026324      TAFII18               TAFII19

     TBP-associated factor 16          FBgn0026324      TAFII60

     ENL/AF9                           FBgn0026441      TAFII60               TAFII30

TFIIB associates with TBP on the opposite side of the DNA helix. The TFIIB-TBP-DNA ternary complex is formed by TFIIB
clamping the acidic C-terminal stirrup of TBP in its basic cleft, and interacting with the phosphoribose backbone
upstream and downstream of the center of the TATA element.

TFIIB physically links TFIID at the promoter with the pol II/TFIIF complex.

     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------         

     Transcription factor IIB          FBgn0004915      TFIIB

Required for activation of transcription
     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------    

     Transcription factor IIA S        FBgn0013347      TFIIA gamma     

     Transcription factor IIA L        FBgn0011289      TFIIA alpha and beta     

TFIIE contains a zinc-binding domain and is involved in promoter melting. TFIIE recruits TFIIH to the promoter.
     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------         

     Transcription factor IIEalpha     FBgn0015828      TFIIEalpha (56 kD)    

     Transcription factor IIEbeta      FBgn0015829      TFIIEbeta (34 kD)     

TFIIF is the homolog of bacterial sigma subunit. Polymerase II cannot stably associate with the TFIID and TFIIB assembly at
the promoter and must be escorted to the promoter by TFIIF. TFIIF stimulates elongation.

     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------    

     Transcription factor TFIIFalpha   FBgn0010282      TFIIF RAP74    

     Transcription factor TFIIFbeta    FBgn0010421      TFIIF RAP30     

RNA polymerase
For RNA polymerase II, the transition from initiation to elongation is accompanied by covalent modification of an unusual
structure at the carboxy terminus of its largest subunit. This evolutionarily conserved structure consists of multiple
tandem repeats of a heptapeptide, the RNA pol II carboxy-terminal domain (CTD). The number of times this sequence is
repeated varies from 26 in yeast to 52 in humans and seems to be directly related to genome complexity. The
phosphorylation of the CTD is central to the transcription mechanism of pol II. The unphosphorylated form of pol II is the
form recruited to the initiation complex. During initiation of RNA synthesis, the CTD becomes extensively phosphorylated
on serine and threonine residues.
     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       -----------------

     RNA polymerase II 215kD subunit   FBgn0003277      RNA polymerase II large subunit   

     RNA polymerase II 140kD subunit   FBgn0003276      RNA polymerase II small subunit      

TFIIH is a multisubunit factor with 3'-5' helicase activity. The Drosophila TFIIH consists of 8 subunits (two listed here)
similar to their human counterparts. Besides the helicase activity, there is present RNA polII C-terminal domain kinase
activity (CDK7) and a cyclin partner for the kinase (Cyclin H). Cyclin H forms a ternary complex with CDK7 and MAT1.
This tripartite Cdk-activating kinase occurs in a free form and in association with 'core' TFIIH.
     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------          

     Transcription factor IIH          FBgn0015830      TFIIH (ERCC3)

     Cyclin-dependent kinase 7         FBgn0015617      CDK7  

A dimer of Cdk9 and Cyclin T that targets RNA polymerase II C-terminal domain.
Functions to overcome promoter-proximal pausing and premature termination -
promotes polymerase entry into productive elongation.
     Drosophila                        FlyBase ID       Human homologs

     -----------------                 ----------       ------------------          

     Cyclin dependent kinase 9         FBgn0019949      Cdk9

     Cyclin T                          FBgn0025455      Cyclin T  

critical for efficient release of stalled RNA Pol II from intrinsic stop sites in promoter regions -
promotes transcriptional elongation and decreases pausing
Drosophila                                  FlyBase ID       Human homologs

-----------------                           ----------       ------------------          

RNA polymerase II elongation factor         FBgn0010422      TfIIS

Factors involved in function of RNA polymerase II

Factors involved in function of RNA polymerase III

Paf1 complex (coordinates histone modifications and changes in nucleosome structure with transcription activation and Pol II elongation)

How does messenger RNA synthesis take place?

The conventional model for formation of a preinitiation complex and ordered transcription by RNA polymerase II (pol II) is characterized by a distinct series of events: (1) recognition of core promoter elements by TFIID (containing TBP and several other protein subunits), (2) recognition of and binding to the TFIID-promoter complex by TFIIB, (3) recruitment of a TFIIE/pol II complex by TFIIB, (4) binding of TFIIE (related to bacterial sigma) and TFIIH (containing a helicase required for promoter melting) to complete the preinitiation complex, (5) promoter melting and formation of an "open" initiation complex, (6) synthesis of the first phosphodiester bond of the nascent mRNA transcript, (7) release of pol II contacts with the promoter (promoter clearance, and (8) elongation of the RNA transcript. TFIIA can join the complex at any stage after TFIID binding and stabilizes the initiation complex. TFIID can remain bound to the core promoter supporting reinitiation of transcription. (Orphanides, 1996 and Nikolov, 1997).

This model has been further refined to incorporate known alterations in the level of phosphorylation of the carboxy-terminal domain (CTD) of RNA polymerase II (Cho, 1999). Stable association of RNAPII with promoter sequences requires TFIID (or TBP), TFIIB, and TFIIF. However, the RNAPII transcription system is unique because, after the polymerase has stably associated with promoter sequences, two additional factors, TFIIE and TFIIH, are necessary for transcription. This requirement is likely related to a unique structure found at the carboxyl terminus of the largest subunit of RNAPII known as the carboxy-terminal domain (CTD). This conserved structure consists of multiple tandem repeats of the heptapeptide Tyr-Ser-Pro-Thr-Ser-Pro-Ser, which serves as a substrate for a number of protein kinases. At least two forms of RNAPII have been detected in cells. The most abundant form contains a phosphorylated CTD (RNAPIIO). A second form contains an unphosphorylated CTD and is known as RNAPIIA. The phosphorylation of the CTD has been correlated with function. It was found that the nonphosphorylated form of RNAPII is recruited to the initiation complex, whereas the elongating polymerase is found with a phosphorylated CTD. TFIIH contains a CTD kinase activity and this activity is efficient after RNAPII has associated with promoter sequences. A 150-kD polypeptide termed FCP1 has now been isolated. Together with RNAPII, FCP1 reconstitutes a highly specific CTD phosphatase activity. Functional analysis demonstrates that the CTD phosphatase allows recycling of RNAPII. Upon reaching termination sequences, the CTD becomes dephosphorylated by the FCP1 phosphatase within the ternary complex (consisting of DNA, polymerase and phosphatase) or immediately after the release of RNAPII from the DNA template. The phosphatase dephosphorylates the CTD allowing efficient recycling of RNAPII into transcription initiation complexes, which result in increased transcription. The phosphatase is found to stimulate elongation by RNAPII; however, this function is independent of its catalytic activity (Cho, 1999 and references).

A model is presented detailing the role of cycling of CTD phosphorylation in the function of RNAPII. After the termination of the previous transciption cycle, TBP remains bound to the TATA motif and provides the foundation for association of TFIIB. RNAPII, through its interactions with TFIIF, recognizes the TBP-TFIIB complex association with the TATA motif. Because TFIIF has been found to interact with both the phosphorylated and nonphosphorylated forms of RNAPII and FCP1 and to stimulate FCP1 activity, its association with RNAPII prior to association with the TB complex may be important in attaining an RNAPII that is fully dephosphorylated. The association of RNAPII with promoter sequences provides the foundation for the entry of TFIIE and allows the association of TFIIH, resulting in the formation of a fully competent transcription initiation complex. During the process of initiation and prior to the formation of a fully competent elongation complex, the CTD becomes phosphorylated in a TFIIH-dependent manner. Phosphorylation of the CTD does not affect elongation efficiency, but allows RNAPII to disengage from the promoter and from transcription initiation factors. In the presence of the ribonucleoside triphosphates, the transcription initiation complex disassembles with the release of TFIIB, TFIIE, and TFIIH. CTD phosphorylation provides a foundation for the association of factors involved in RNA processing, such as the capping enzyme, splicing factors, and factors involved in 3'-end formation. Upon transcription of termination/polyadenylation signals, the elongating complex is altered, resulting in the release of RNAPII from the template by an unknown process. It is possible that RNAPII is converted to the nonphosphorylated form prior to, or concomitant with, its release from the DNA template. This possibility is supported by studies demonstrating that FCP1 is capable of dephosphorylating the CTD of RNAPII not only in solution prior to incorporation into transcription initiation complexes, but also in active ternary elongation complexes stalled as a result of nucleotide starvation. The finding that FCP1 also stimulates elongation by RNAPII, independent of its phosphatase activity, suggests that FCP1 may remain associated with RNAPII during elongation. The finding that FCP1 is active in ternary complexes has implications for the mechanism of transcription termination as well as for the down-regulation of RNA processing. Similar to the signal imposed on phosphorylation of the CTD (disengagement of RNAPII from the promoter and from interaction with initiation factors), dephosphorylation of the CTD may result in a signal that releases factors from RNAPII that are involved in RNA maturation (Cho, 1999 and references).

Evolution of general transcription factors

How have the factors required for transcription initiation (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II [pol II]) evolved to accommodate the elaborate transcriptional programs required for growth, differentiation, and development of multicellular organisms? Analysis of the complete Drosophila genome sequence, as well as those of C. elegans, Saccharomyces cerevisiae, and humans sheds light on this well studied question in eukaryotic biology. All four organisms encode single isoforms of RNA pol II, TFIIB, TFIIE, TFIIF, and TFIIH components, but multiple, sequence-related isoforms of TFIID components. In addition, Drosophila and humans encode multiple isoforms of TFIIA components. Current evidence indicates that tissue- and cell type-specific transcription is directed by differentially expressed TFIID and possibly TFIIA isoforms. Thus, in accord with experimental data, this analysis points to TFIIA and TFIID as the factors that help generate the broad transcriptional repertoire of multicellular organisms. The identification of the complete set of TFIIA and TFIID components in a genetically and biochemically tractable organism like Drosophila is an important step toward understanding the mechanisms governing developmentally regulated transcription not only in Drosophila but also in humans (Aoyagia, 2000 and references therein).

Biochemical fractionation of Drosophila embryos, human cells, and yeast cells has defined a set of multiprotein complexes termed general transcription factors (GTFs; TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH) required for mRNA transcription initiation in vitro. Transcription is initiated by recognition of core promoter elements by TFIID and sequential or concerted assembly of the other GTFs and RNA pol II to form the preinitiation complex (PIC). Although GTFs play essential roles during transcription initiation, it is the factors that regulate the ability of the GTFs to assemble and stably bind a core promoter that are probably major determinants of gene-specific transcription levels. For example, activators and coactivators are thought to stimulate transcription by recruiting GTFs to a promoter, thereby accelerating PIC assembly (Aoyagia, 2000 and references therein).

The GTF TFIID is composed of TATA-binding protein (TBP) and coactivator subunits termed TBP-associated factors (TAFIIs). TAFIIs not only function as 'conventional' coactivators by serving as physical links between DNA-binding activator proteins and the PIC but also possess enzymatic or promoter recognition activities that presumably enhance the efficiency of PIC assembly. TFIIA has also been described as a coactivator and displays a number of TAFII-like properties: it binds to TBP and TAFIIs; it interacts with specific transcriptional activators; it is generally required for activated transcription in vitro; and it contributes to promoter selectivity (Aoyagia, 2000 and references therein).

Inactivation of individual TAFIIs in Drosophila , mammalian, and yeast cells has demonstrated that TAFIIs are not required for the transcription of all RNA pol II genes, and in fact there is great variation in regard to the identity and number of gene targets for individual TAFIIs. Furthermore, different domains within a single TAFII can play gene-specific roles in transcription. The isolation of a human B cell-specific isoform of TAFII130 (TAFII105) raises the possibility that substoichiometric subunits of TFIID mediate tissue- or cell type-specific transcription and that additional components of TFIID may have escaped detection because of their low abundance. These possibilities have been born out in Drosophila where isoforms of TAFII110 and TAFII80 (No hitter [Nht] and Cannonball [Can], respectively) are expressed exclusively in testis and regulate transcription of a subset of genes required for spermatogenesis, and isoforms of TBP (TBP-related factors [TRF1 and TRF2]) are expressed in a tissue-specific manner and bind different genes in salivary gland cells. Similarly, analysis of the human TFIIA-L isoform ALF (TFIIAalpha/ß-like factor) reveals that its expression is restricted to the testis; however, it remains to be determined if it is used for the transcription of testis-specific genes. In Drosophila , TFIIA-S is expressed in a dynamic pattern during eye development and is transiently upregulated in photoreceptor precursor cells before their fate is determined. Therefore, the role of TFIIA and TFIID in transcription initiation is governed by the expression patterns and activities of their varied components (Aoyagia, 2000 and references therein).

Finally, it is critical to note that analysis of the function of TAFIIs is complicated by the fact that they are components of at least two other complexes that lack TBP: p300/CBP-associated factor (PCAF) and TBP-free TAFII-containing complex (TFTC). The human PCAF histone acetyltransferase (HAT) complex contains three TAFIIs that are shared with TFIID (TAFII31/32, TAFII20/15, and TAFII30) and three TAFII isoforms (PCAF-associated factor 65ß [PAF65ß], PAF65alpha, and SPT3) related to TAFII100, TAFII70/80, and TAFII18, respectively. Yeast possess an analogous complex, Spr-Ada-Gcn5-acetyltransferase (SAGA), containing TFIID TAFIIs and the Gcn5 HAT, and Drosophila may also, since it contains a Gcn5/PCAF homolog that interacts with TAFII24 (Aoyagia, 2000 and references therein).

Searches of the completed Drosophila, C. elegans, and yeast genomes and the partial human genome for sequence homologs of biochemically identified components of the general transcription machinery have led to the following conclusions: (1) all of the components of RNA pol II, TFIIB, TFIIE, TFIIF, and TFIIH are encoded by single copy genes in Drosophila , C. elegans, and yeast;(2) multiple isoforms of TFIID components are encoded in Drosophila , C. elegans, humans, and yeast, and multiple isoforms of TFIIA components are encoded in Drosophila and humans; (3) each organism encodes isoforms of different sets of TFIIA and TFIID components, some which are unique to a particular organism (Aoyagia, 2000 and references therein).

Sequence comparisons uncovered Drosophila homologs of TAFIIs previously identified in yeast or humans by biochemical means but which had not been described in Drosophila (yeast TAFII67/human TAFII55, yeast TAFII30/ human ENL/AF-9, and yeast TAFII19/human TAFII18). Thus, all TAFIIs present in both yeast and humans are present in Drosophila , as well as C. elegans. In contrast, yeast TAFII47 and TAFII65 are absent from Drosophila, C. elegans, and apparently from humans, suggesting that these TAFIIs perform a yeast-specific role, such as serving as coactivators for DNA-binding activators that are not present in metazoans. Finally, there are TAFIIs present in Drosophila, C. elegans, and humans that are absent from yeast (human TAFII68/Drosophila Cabeza and multiple TAFII isoforms). In addition to Can and Nht, there are alternatively spliced forms of TAFII30alpha, two genes (TAFII24 and TAFII16) that encode Drosophila homologs of human TAFII30, and TAFII60 and TAF30alpha isoforms (TAFII60-2 and TAF30alpha-2, respectively). TFIIA-S and TFIIA-L are the only other GTF components in Drosophila and humans, respectively, that are expressed in multiple isoforms. The fact that these proteins are unique to multicellular organisms suggests that they play cell-specific roles (Aoyagia, 2000 and references therein).

A number of TAFIIs contain a common structural motif called the histone fold that was originally shown to drive folding and association of each of the core histones (H2A, H2B, H3, and H4) and subsequently shown to play a similar role in association of TAFIIs. TAFII pairs, such as Drosophila TAFII40 and TAFII60, form heterotetramers, analogous to H3 and H4, and numerous other TAFII-TAFII and TAFII-nonTAFII interactions have been shown to involve histone fold motifs. The demonstrated histone fold interaction of human TAFII135 and TAFII20, predicts that Drosophila isoforms of these proteins, Nht and TAFII30alpha-2, respectively, may heterodimerize and hints at the existence of a human TAFII20 isoform that would heterodimerize with the TAFII135 isoform, TAFII105. B cell-specific expression of the hypothetical TAFII20 isoform may explain why TAFII105 associates with TFIID in B cells but not in other cell types (Aoyagia, 2000 and references therein).

In addition to the TAFIIs indicated above, other Drosophila transcription factors contain histone fold motifs, including Prodos, NF-YC-like (CG3075), CG11301, CHRAC-14 (CG13399), CHRAC-16 (CG15736), Dr1 (CG4185), NC2alpha (CG10318), and BIP2 (CG2009). It is interesting to speculate that these factors may be unidentified TAFII components of TFIID or binding partners for known TAFIIs in complexes that lack TBP (Aoyagia, 2000 and references therein).

Analysis of eukaryotic genomes has defined sets of proteins that are similar in sequence to known components of TFIIA and TFIID. Since known components of TFIIA and TFIID have been shown to play key roles in developmentally regulated transcription, it is exciting to speculate that the newly identified genes will play similar roles and that TFIIA and TFIID components have evolved to support tissue- or cell type-specific transcriptional requirements of individual eukaryotic organisms. The challenge now is to determine if TAFIIs that have been identified on the basis of their sequence are components of TBP-containing complexes or other TAFII-containing complexes, whether TAFIIs and TFIIA isoforms are differentially expressed during development, and how differentially expressed TBP, TAFII, and TFIIA isoforms function in concert with the ubiquitously expressed form of TFIID and TFIIA to regulate gene expression. The subunit composition of human PCAF complex leads to the prediction that Drosophila TAFII60-2 and Can and C. elegans Y37E11AL.c are components of PCAF/SAGA and not TFIID. However, protein isoforms that are unique to a particular organism, such as Drosophila TAFII30alpha-2 and C. elegans F54F7.1 and K10D3.3, may be tissue- or cell type-specific components of TFIID and not of PCAF/SAGA. Drosophila may be the most appropriate organism for these studies since the biochemical activities of these factors can be determined using established TFIIA and TFIID purification schemes and in vitro transcription systems, and developmental requirements for these factors can be determined using existing mutants or mutants generated by traditional mutagenesis schemes, P-element insertion, RNA interference (RNAi), or homologous recombination (Aoyagia, 2000 and references therein).

Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation

The presence of general transcription factors and other coactivators at the Drosophila hsp70 gene promoter in vivo has been examined by polytene chromosome immunofluorescence and chromatin immunoprecipitation at endogenous heat-shock loci or at a hsp70 promoter-containing transgene. These studies indicate that the hsp70 promoter is already occupied by TATA-binding protein (TBP) and several TBP-associated factors (TAFs), TFIIB, TFIIF (RAP30), TFIIH (XPB), TBP-free/TAF-containg complex (GCN5 and TRRAP), and the Mediator complex subunit 13 before heat shock. After heat shock, there is a significant recruitment of the heat-shock transcription factor, RNA polymerase II, XPD, GCN5, TRRAP, or Mediator complex 13 to the hsp70 promoter. Surprisingly, upon heat shock, there is a marked diminution in the occupancy of TBP, six different TAFs, TFIIB, and TFIIF, whereas there is no change in the occupancy of these factors at ecdysone-induced loci under the same conditions. Hence, these findings reveal a distinct mechanism of transcriptional induction at the hsp70 promoters, and further indicate that the apparent promoter occupancy of the general transcriptional factors does not necessarily reflect the transcriptional state of a gene (Lebedeva. 2005; full text of article).

An inverse correlation was observed between factor occupancy and transcriptional activation. In the absence of heat shock, it was found that TBP, TAFs, TFIIB, TFIIF, TFIIH, TFTC, and Mediator are present at the hsp70 promoter region. These results are similar to previous observations in which the basal factors have been found to be present at transcriptionally inactive promoters. Surprisingly, however, the apparent occupancy of TBP, several TAFs, TFIIB, and TFIIF significantly decreases upon transcriptional activation. These results could be due to some of the following scenarios: (1) upon activation, the undetected factors are present but adopt a conformation that renders them refractory to polytene chromosome staining and to ChIP analysis; (2) the factors that are not detected are indeed absent and do not participate in the ongoing transcription of the genes; or (3) the factors are present only transiently at the actively transcribed promoter and thus exhibit lower average occupancy upon polytene chromosome staining and ChIP analysis (Lebedeva. 2005).

The first scenario requires that TBP, several TAFs, TFIIB, and TFIIF simultaneously become essentially invisible to polytene immunostaining as well as to ChIP analysis upon transcriptional activation of hsp70 and other heat-shock genes. The observed effects are not a consequence of the heat shock treatment, because these factors are observed at ecdysone-responsive genes that have been subjected to heat shock. Moreover, for several factors (TBP, TAF1, and TAF10), the immunostaining was repeated with two different polyclonal antibodies that were raised against different epitopes, and identical results were obtained after heat-shock treatment. Furthermore, histone H3 K14 acetylation was detected at the hsp70 promoter after heat shock. Thus, the conditions allow the access of antibodies to proteins that are in close proximity to hsp70 promoter DNA. Thus, given that these experiments involve the use of many highly specific polyclonal antibodies and that the effect is observed with multiple polypeptides and is not a consequence of the heat-shock treatment, the first model appears to be unlikely (Lebedeva. 2005).

In the second scenario, TBP, several TAFs, TFIIB, and TFIIF do not participate in the ongoing transcription of heat-shock genes after heat induction. For instance, the factors required for transcription reinitiation may be a subset of those that participate in the first round of transcription. In fact, biochemical studies in yeast have shown that some, but not all, GTFs remain at the promoter after initiation and form a platform for the assembly of subsequent reinitiation complexes. This subset of factors includes TBP, TAF5, TFIIA, TFIIH, TFIIE, and Mediator, but not TFIIB or TFIIF. In accord with those results, this stydy found that TFIIH (XPB subunit) and Mediator (MED13), but not TFIIB or TFIIF remain at the hsp70 promoter after heat induction. In contrast, the apparent occupancy of TFIID (TBP, TAF1, and several other TAFs) is significantly reduced upon heat shock. Thus, for the second scenario to be correct, TBP and several TAFs must be dispensable for transcription reinitiation from heat-induced hsp70 promoters (Lebedeva. 2005).

In the third scenario, the average occupancy of the basal transcription factors at the hsp70 promoters is higher in the inactive gene than in the transcriptionally induced gene. This situation could occur if the basal transcription factors are in a static complex at the inactive hsp70 promoter and in a rapid cycling state of preinitiation-complex assembly and disassembly at the transcriptionally active hsp70 promoter. More specifically, in vivo data in the context of the third scenario suggest that TBP, several TAFs, TFIIB, and TFIIF make a transition from a static state to a rapidly cycling state upon heat-shock induction (Lebedeva. 2005).

It should be considered that the latter two scenarios might appear to be inconsistent with in vivo KMnO4 footprinting data, which suggest that TFIID binds to the Drosophila hsp70 promoters both before and after heat shock. In this regard, it should be noted that ChIP (as well as immunofluorescence) and footprinting experiments yield distinct types of information. ChIP provides data regarding the occupancy of a particular factor at a specific DNA sequence but does not indicate how the factor interacts with DNA or if the factor is biochemically active. Moreover, in some instances, specific DNA-bound factors may not be detectable by ChIP (although, as discussed above, it is unlikely that multiple subunits of a protein complex, such as TFIID, would be invisible in a ChIP assay with multiple polyclonal antibodies). In vivo footprinting, however, shows that a factor is bound to a specific DNA sequence but does not indicate exactly what factor is bound to that sequence. Therefore, the models and data are not necessarily contradictory. For example, it is possible that the factor that is responsible for the TATA footprint in the induced gene is not TBP or TFIID but rather another protein, such as a TBP-related factor, or a TFTC/STAGA-type complex. Alternatively, an induced hsp70 promoter might not contain the complete TFIID complex but rather only a subcomplex or TBP alone that is in a ChIP-invisible state, possibly hidden under other proteins, such as the polymerase. At the present time, however, the resolution of these issues will require the development of more sophisticated assays for the analysis of the functions of transcription factors in vivo (Lebedeva. 2005).

Thus, a model for the activation of hsp70 genes is as follows. First, the inactive gene contains many GTFs (such as TFIIB, TFIID, TFIIF, and TFIIH) as well as the downstream paused RNA Pol II. Upon heat induction, HSF binds to the promoter and recruits coactivators, such as Mediator and SAGA complexes, and these factors promote the release of the paused polymerase and the assembly of a new transcription preinitiation complex. After initiation, the transcription complex might partially disassemble, at which point factors such as TFIIB and TFIID (or many TFIID subunits) dissociate from the template DNA. (TFIIF may remain associated with the elongating polymerase and thus depart the promoter region.) Then, in subsequent rounds of initiation (i.e., reinitiation), the reassociation of TFIIB and TFIID with the template may be fleeting with a low residence time at the promoter (the third scenario described above). Alternatively, TFIIB and TFIID may be dispensable for reinitiation (the second scenario described above). TFIIH, in contrast, is needed to unwind the template DNA for every new round of transcription; thus, the average occupancy of TFIIH at the promoter increases along with the polymerase in proportion to the number of transcription reinitiation events. Thus, upon heat induction, an increase would be observed in HSF, Mediator, SAGA/TFTC, TFIIH, and RNA Pol II as well as a decrease in TFIIB, TFIID (or many TFIID subunits), and TFIIF at the promoter (Lebedeva. 2005).

The specific mechanism of transcriptional activation by HSF at heat shock genes is likely to be one of multiple mechanisms of regulation that are used in vivo. For example, in contrast to what is seen at the hsp70 promoters, the apparent occupancy of TBP, TFIIB, and several TAFs at ecdysone-responsive promoters does not decrease upon transcriptional induction, even if the cells are also subjected to heat shock (Lebedeva. 2005).

In conclusion, these results with the hsp70 promoters provide an example of a transcriptional mechanism wherein the apparent occupancy of TBP, several TAFs, TFIIB, and TFIIF decreases upon gene activation. Therefore, the extent of the apparent occupancy of these factors at a given promoter does not necessarily reflect the transcriptional activity of that promoter. The discovery and analysis of distinct transcriptional mechanisms is a key step toward the ultimate goal of understanding all of many strategies that are used by the cell to control gene activity (Lebedeva. 2005).

The same transcriptional activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter

Cells often fine-tune gene expression at the level of transcription to generate the appropriate response to a given environmental or developmental stimulus. Both positive and negative influences on gene expression must be balanced to produce the correct level of mRNA synthesis. To this end, the cell uses several classes of regulatory coactivator complexes including two central players, TFIID and Mediator (MED), in potentiating activated transcription. Both of these complexes integrate activator signals and convey them to the basal apparatus. Interestingly, many promoters require both regulatory complexes, although at first glance they may seem to be redundant. RNA interference (RNAi) was used in Drosophila cells to selectively deplete subunits of the MED and TFIID complexes to dissect the contribution of each of these complexes in modulating activated transcription. The robust response of the metallothionein genes to heavy metal was used as a model for transcriptional activation by analyzing direct factor recruitment in both heterogeneous cell populations and at the single-cell level. Intriguingly, it was found that MED and TFIID interact functionally to modulate transcriptional response to metal. The metal response element-binding transcription factor-1 (MTF-1) recruits TFIID, which then binds promoter DNA, setting up a 'checkpoint complex' for the initiation of transcription that is subsequently activated upon recruitment of the MED complex. The appropriate expression level of the endogenous metallothionein genes is achieved only when the activities of these two coactivators are balanced. Surprisingly, it was found that the same activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter. Finally, the stability of multi-subunit coactivator complexes can be compromised by loss of a single subunit, underscoring the potential for combinatorial control of transcription activation (Marr, 2006).

There are four known metallothionein genes in Drosophila: MtnA, MtnB, MtnC, and MtnD. Of these, the best characterized is the MtnA gene, which produces a transcript of ~600 bases in length, bearing one intron. All of the regulatory elements required for robust response to heavy metals, including copper, lie within 500 bp of the transcription start site. The gene is controlled by a single activator, metal response element-binding transcription factor 1 (MTF-1), which binds two adjacent metal response elements (MRE) 50 bp upstream of the TATA-box (Zhang, 2001). Quantitative PCR (qPCR) analysis of the endogenous gene in Drosophila S2 cells shows that the gene is highly induced (~250-fold) after a short exposure to copper. The total amount of stable MtnA mRNA approximates the level of the abundant transcript for the ribosomal subunit Rp49. Primer extension analysis confirms that transcriptional activation of the endogenous MtnA gene originates from a unique start site overlapping the core promoter. The transcript accumulates linearly for ~12 h, thus measurements in this time window likely reflect relative levels of transcription of the MtnA gene. Importantly, induction at the endogenous chromosomal locus is easily assayed in order to measure physiologically relevant transcriptional activation in the context of native chromatin. Taken together, these properties establish the endogenous MtnA gene as a useful model for studying transcriptional mechanisms governing an inducible gene (Marr, 2006).

Using chromatin immunoprecipitation (ChIP), it was found that the sequence-specific DNA-binding protein MTF-1 is specifically recruited to the MtnA promoter region in response to copper. Curiously, the ChIP of the promoter region was compared to a region 1 kb downstream, a significant amount of MTF-1 was found to be present on the promoter even in the absence of added copper. Under these conditions, little transcription is detected from this gene. As a preliminary experiment to investigate a potential functional interaction between TFIID and MED, it was first asked whether the two complexes are both recruited in a signal-dependent manner to the MtnA gene. Using ChIP, it was found that both TBP and the TAFs are efficiently recruited to the promoter region in response to copper. In addition, the MED17, MED24, MED26, and MED27 subunits of MED are all recruited to the promoter region in response to copper treatment. Consistent with the high level of induction, RNAPII occupancy at the MtnA promoter is also increased in response to heavy metal treatment. Thus, both core coactivator complexes and RNAPII are efficiently recruited to the promoter region upon induction and resultant binding of MTF-1 to the MREs (Marr, 2006).

Because the ChIP assay is limited to measuring response in a heterogeneous population of cells, a transgenic model system was extablished in Drosophila S2 cells in order to visualize the response at the single-cell level. Such an approach has proved useful in understanding transcription factor dynamics in vivo. By selecting for stably transfected MtnA firefly luciferase reporters, a concatenated transgenic locus was generated in a clonal line of S2 cells. The transgenic locus was assayed for dependence on copper using a luciferase assay. Importantly, transcription initiates a unique site that maps to the correct start site of the MtnA core promoter. With this substantial increase in gene number (~2000) at the integrated transgenic locus, it should now be possible to visualize direct recruitment of specific transcription factors to the MtnA promoter within a single cell (Marr, 2006).

As expected, in the absence of heavy metal, MTF-1 is predominantly cytoplasmic; however, in agreement with ChIP data, some MTF-1 can be detected at the transgenic cluster even in the absence of a metal stimulus. Thus, antibody labeling of MTF-1 provides a useful marker for the subnuclear location of the transgene cluster in both induced and uninduced cells. Notably, the locus is not undergoing transcription (as detected by RNA FISH) in the absence of heavy metal induction despite the presence of some MTF-1 at the transgene cluster. Upon copper induction, MTF-1 vacates the cytoplasm and accumulates selectively at the transgenic locus. Under these same conditions, TBP is also actively recruited to this cluster. Consistent with not only TBP but holo-TFIID complex recruitment, it was found that TAF2 also accumulates at the transgene. Likewise MED components recruited to the transgene were detected using antibodies against MED26. As expected, RNAPII is recruited to the cluster in a copper-dependent manner consistent with the transcriptional induction of the transgene under these conditions. In contrast, TBP-related factor 1 (TRF1), a subunit known to be a key component of the RNA polymerase III core promoter recognition complex, is not recruited to the transgene. This negative control helps rule out the possibility that the tandemly reiterated transgene is simply nonspecifically attracting transcription factors (Marr, 2006).

Having established by two independent methods that both TFIID and MED complexes are recruited to the MtnA promoter in an activator-dependent manner, their role in potentiating transcriptional activation of the endogenous MtnA gene was investigated. The efficient technique of RNAi in Drosophila S2 cells was used to knock down expression of TFIID and MED subunits. In addition, the activator MTF-1 was knocked down to ascertain the extent of the activator’s role in induction. After treatment with copper, total RNA was purified from dsRNA treated and untreated S2 cells and then they were assayed by two independent methods. First, a primer extension analysis was used on equivalent amounts of total RNA. This assay revealed that an accurate transcription is detected from one distinct core promoter start site. Next, qPCR normalized to the Rp49 mRNA was used, to confirm that there is little or no global disturbance of RNAPII transcription (Marr, 2006).

Not surprisingly, depletion of MTF-1 severely reduced transcriptional activation from the MtnA promoter, confirming the central role of this activator. RNAi directed against TBP also had a dramatic inhibitory effect. The MtnA promoter is <10% as active when TBP levels are severely depleted. Surprisingly, knockdown of multiple TAFs had little apparent effect on the ability of MTF-1 to activate MtnA. Indeed, depletion of the TAFs actually stimulated (1.5- to 2-fold) production of RNA. With the exception of TAF11, a reduction of individual TAFs resulted in a remarkably uniform response. The reason for this uniformity became apparent when the stability of the TFIID complex was examined in the RNAi-treated cells. The overall stability of the holo-TFIID complex appears to be coupled to the stability of certain individual TAFs. In the most dramatic example, RNAi-targeted reduction of TAF4 leads to the concomitant loss of TAF1, TAF5, TAF6, and TAF9, as well as a detectable reduction in TBP. Interestingly, TAF2 and TAF11 are largely unaffected by depletion of TAF4. Similar results are observed for the other TAFs as well. When the transcript levels of the TAFs were measure after RNAi treatment, it is clear that the loss of stability occurs at the protein level, since the transcript levels for nontargeted TAFs are unaffected. For example, when TAF4 is targeted, only the TAF4 transcript is depleted (Marr, 2006).

In contrast to the TAFs, RNAi reduction of MED subunits gave striking but variable effects on the ability of MTF-1 to activate transcription from the MtnA promoter. Unlike TFIID, the response is far from uniform. For example, dsRNA directed against MED23 has little effect on induction of MtnA, while loss of MED17, the Drosophila SRB4 homolog, has a strong inhibitory effect. The lack of a uniform response in the MED RNAi led to a further investigation of the potential differential response upon depletion of MED subunits at related promoters activated by MTF-1. As discussed above, Drosophila has four metallothionein genes that respond to heavy metals. Three of these—MtnA, MtnB, and MtnD—are active in S2 cells. All three of these genes are specifically activated by the same factor, MTF-1. All three Mtn genes were examined in a single experiment using qPCR. First, it was confirmed that all three promoters, MtnA, MtnB, and MtnD, require MTF-1 for induction. Remarkably, distinct differential requirements were found for MED subunits depending on the promoter. For example, loss of MED13, a subunit of the larger MED complex (ARC-L) thought to play a repressive role in transcription, is not essential for MtnA induction. In contrast, MED13 was found to be important for both MtnB and MtnD activation by MTF-1. In contrast, the opposite specificity was seen with the MED26 subunit, a component of the smaller MED complex (CRSP), thought to play predominantly a coactivator role in transcription. Interestingly, MED26 is required for full induction of the MtnA promoter but is dispensable for MTF-1 activation of the MtnB and MtnD promoters. Thus, these experiments reveal a remarkable example of differential dependence on cofactor composition even though all three promoters tested use the same activator. Apparently, the precise role of individual MED subunits depends on the promoter context and structure, despite the absence of any evidence of direct binding of DNA by the MED complex (Marr, 2006).

To help rule out nonspecific effects on transcription such as a change in the concentration of free RNA polymerase, representative targets from TFIID and MED were tested in a transient transfection assay where the effect to a second promoter can be normalized. In these experiments, TAF4 and MED17 were chosed as representative targets, since TAF4 compromises much of the TFIID complex and MED 17 is likely a component of the core MED complex. The transient transfection data are largely consistent with the data generated at the endogenous locus and at the transgene (Marr, 2006).

The data presented above suggest that activation of the MtnA gene requires specific MED subunits, and at the same time the TAFs appear to be playing a potential negative regulatory role. Because it is clear that the TAFs are specifically recruited in S2 cells to the MtnA promoter in a copper-dependent manner by MTF-1, whether TFIID recruitment can occur in the absence of the MED complex was examined. To achieve this, RNAi directed against MED17 was used, which results in an almost complete loss of MED activity. Surprisingly, TFIID is still efficiently recruited to the MtnA gene. ChIP experiments confirmed that TBP and TAF2 are still actively (and likely directly) recruited to the endogenous MtnA gene by MTF-1 even when the gene is transcriptionally inactive as measured by qPCR analysis. The MtnA luciferase transgene system was used to investigate this relationship at the single-cell level. Without any RNAi, TBP, TAF2, and RNAPII were all recruited to the transgene. In agreement with the ChIP data above, even in the absence of MED activity, after MED17 depletion, TBP and TAF2 are nevertheless efficiently recruited to the transgene. In contrast, no RNAPII can be detected at the transgene consistent with the loss of transcription activation. Apparently, TFIID is recruited to the promoter, but the promoter is not active in supporting transcription. Importantly, recruitment of this 'inactive TFIID' is dependent on the activator MTF-1. In the absence of MTF-1, no TFIID or RNAPII is recruited to the transgene (Marr, 2006).

This perplexing result of recruiting an apparently 'inactive' TFIID prompted an examination of what happens when both TAFs and MEDs were depleted. Remarkably when both the TAFs and MED complex are depleted and 'removed' from the MtnA promoter, MTF-1-dependent activation of transcription is restored to ~95% the level of untreated cells, which is well above the inhibited level observed when the MEDs alone are depleted. In humans and Drosophila, TAFs can be subunits of other complexes such as TFTC and STAGA, so it is possible that the functional interaction analyzed is not TFIID-specific. To test this, specific subunits of these other complexes were targeted to determine if they would have a similar ability to rescue the MED knockdown. Unlike the TFIID subunits, RNAi against dAda2b, dGCN5, dSPT3, and dTRA1 was unable to rescue the loss of the MED subunits. These findings taken together suggest that most likely the functional relationship revealed by these experiments with the MtnA promoter, indeed, involve some regulatory transaction between TFIID and MED (Marr, 2006).

The requirement for coactivator complexes mediating transcriptional responses to activators has been well documented. However, by using an inducible Drosophila gene as a model system, a previously unknown functional interaction has been uncovered between two coactivator complexes, TFIID and MED. In the absence of TAFs, the cell responds inappropriately to a metal stimulus. The cell synthesizes 50%–200% more mRNA from the MtnA gene than it does in the presence of the TAFs. The data suggest that at this gene, TFIID is recruited in an inactive state, a state that impedes initiation of transcription. It is believed that this sets up a checkpoint early in the initiation process to meter the RNA synthesis. The MED complex must be recruited to get past this checkpoint. It is postulated that the MED complex likely modifies TFIID, converting it to an active state. This could be accomplished either through one of the known enzymatic activities of MED, phosphorylating (cdk8) or ubiquitylating (MED8) TFIID subunits, or through some, as yet undetected, chaperone-like function that remodels TFIID into an active conformation. Not surprisingly then, in the absence of MED subunits the cell cannot mount an appropriate response to environmental signals. In fact, depletions of many of the MED subunits lead to <20% of the normal amount of mRNA. Unlike the uniform response to depletion of TAFs, the response to depletion of MEDs is much less uniform. One possibility is that the MED complex is more functionally and structurally diverse than TFIID. Indeed, alternative subcomplexes of MED have been purified biochemically, whereas no such subcomplexes of TFIID have been reported (Marr, 2006).

By analysis of three different Mtn genes, all of which are dependent on the same single activator, it was found, surprisingly, that there is a differential requirement of specific MED subunits at the three Mtn promoters. This is taken as evidence that, depending on the precise arrangement of cis elements and promoter context, the same activator can require different mediator subunits or modules to transmit its signals to the basal apparatus (Marr, 2006).

Interestingly, the kinase module of the MED complex, previously linked with repression functions, is required for efficient activation at two of the promoters. This result, combined with the finding that at the MtnA promoter the TAFs have a repressive regulatory influence on transcription initiation, underscores the difficulty in assigning black and white functions to the coactivator complexes. It is likely that both TFIID and MED interpret multiple inputs from cellular signals and act either positively or negatively depending on the signals received as well as the specific promoter context. As such, the complexes may better be viewed as coregulators since they can play either a positive or negative role in the process of modulating gene expression. For example, only when both TFIID and MED are intact do Drosophila S2 cells produce the appropriate amounts of MtnA mRNA. In contrast, when either coactivator complex is disrupted, aberrant levels of transcription are seen. However, when both coactivator complexes are depleted, a significant level of metal inducible activation is actually restored. Presumably, in this 'stripped down' system, some portion of the remaining TBP pool can mediate transcription. Curiously, in the absence of TAFs but with a full complement of MEDs, there is also an aberrant level of transcription consistent with the notion that there is some finely tuned codependence between the TBP/TAF complex and the MED complex at this promoter (Marr, 2006).

The results also reinforce the notion that the activator is the primary determinant of the transcriptional response. The MTF-1 depletion experiments were the most detrimental to mRNA induction. In the absence of MTF-1, there is no detectable activation of the Mtn genes. In contrast, there is some residual transcription of MtnA even when either the MEDs or TBP are largely depleted from the Drosophila cells. This remaining activity could be due to incomplete depletion, or it could indicate alternative mechanisms of activation that are activator-dependent but can partially bypass the requirement for the coregulator complexes (Marr, 2006).

In the course of testing the requirement for TAFs in activated transcription, the codependent stability of the TFIID complex was discovered. Particularly striking is the finding that TAF4 depletion destabilizes most of the other TAFs and, to some extent, even TBP. Therefore, the TAF depletion experiments most likely reflect a loss of holo-TFIID rather than just the loss of individual subunits. It is worth noting that metazoan organisms contain multiple variants of TAF4: TAF4b in vertebrates and No-hitter in Drosophila. Both of these have been implicated in tissue-specific gene expression. It is conceivable that substitution of this keystone TAF can provide a mechanism to change the entire coregulator profile of TFIID (Marr, 2006).

One intriguing question this work raises is: Why would an activator recruit an inactive TFIID complex to the promoter? There are several previously described cases in which TFIID occupancy at a promoter does not strictly correlate with transcriptional activity. However, in most of these cases the genes being examined were either in a repressed or an unstimulated state. In contrast, the current studies were designed to specifically measure the role of coactivator complexes such as TFIID and MED in the context of an active gene MtnA upon metal stimulation. The ability to deplete MED activity under these conditions revealed the unexpected finding that although TFIID is dynamically recruited to the MtnA promoter, TFIID is mainly held in an 'inactive' state until the second cofactor complex, MED, is recruited. Perhaps this recruitment of an 'inactive' TFIID is a more common phenomenon that can only be detected in special circumstances and may represent a previously unappreciated control mechanism in transcription activation. If the activator first recruits TFIID, then subsequently recruits MED, and there is a requirement for additional factors to potentiate the secondary recruitment of coregulator assemblies, then this provides a potential checkpoint for fine-tuning the control of gene expression. Alternatively, since the cell invests a significant amount of energy in making a high level of transcript, requirement of continued stimulation (i.e., activator bound at the promoter) for mRNA production would provide the most economical use of resources (Marr, 2006).

TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription

The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter element (DPE). In this circuit, TBP activates TATA-dependent transcription and represses DPE-dependent transcription, whereas Mot1 and NC2 block TBP function and thus repress TATA-dependent transcription and activate DPE-dependent transcription. This regulatory circuit is likely to be one means by which biological networks can transmit transcriptional signals, such as those from DPE-specific and TATA-specific enhancers, via distinct pathways (Hsu, 2008).

The RNA polymerase II core promoter comprises the sequences that direct the initiation of transcription. Although it has often been presumed that the core promoter is a generic entity, current evidence indicates that there is considerable diversity in core promoter structure and function. Hence, the core promoter is a regulatory element (Hsu, 2008 and references therein).

This study focuses on the relation between two core promoter motifs: the downstream core promoter element (DPE) and the TATA box. The TATA box is the most ancient core promoter motif, as it is conserved from archaebacteria to humans. It has a consensus of TATAWAAR, where the upstream T nucleotide is typically located about -31 or -30 relative to the A + 1 in the Initiator (Inr) element. The DPE appears to be conserved among metazoans. It is strictly located from +28 to +33 relative to the A + 1 in the Inr, and has a consensus of RGWYVT in Drosophila (Hsu, 2008).

Both the TATA box and DPE are binding sites for the TFIID basal transcription factor, but TFIID appears to have distinct modes of binding to the two core promoter motifs. The TBP subunit of TFIID binds to the TATA box, whereas the TAF6 and TAF9 subunits of TFIID are in close proximity to the DPE. In addition, the DNase I footprinting patterns on TATA-containing versus DPE-containing promoters are different. In particular, TFIID footprints of DPE-dependent core promoters exhibit a periodic 10-bp DNase I digestion pattern that suggests an extended, close interaction of TFIID from the Inr through the DPE (Hsu, 2008 and references therein).

There are differences in the functional properties of DPE-dependent versus TATA-dependent core promoters. For instance, an enhancer-trapping analysis in Drosophila revealed the existence of DPE-specific as well as TATA-specific transcriptional enhancers. It was also found that a set of factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, RNA polymerase II, PC4, and Sp1) that is sufficient for transcription of promoters containing both TATA and DCE (downstream core element) motifs is not able to transcribe a DPE-dependent promoter. In that case, DPE-dependent transcription was additionally found to require casein kinase II (CKII) and Mediator. In other studies, NC2 (also known as Dr1-Drap1), which was originally identified as a repressor of TATA-dependent transcription, was found to activate transcription from five different DPE-dependent core promoters in reactions performed with a nuclear extract. With a purified transcription system, however, NC2 activation of a DPE-dependent core promoter was not observed (Hsu, 2008).

To determine the nature of the factors that promote DPE-dependent versus TATA-dependent transcription, the properties of key transcription factors was investigated by RNAi depletion, overexpression, and chromatin immunoprecipitation (ChIP) analyses with multiple DPE-dependent and TATA-dependent promoters. The new findings reveal a regulatory circuit that controls the balance between DPE-dependent versus TATA-dependent transcription (Hsu, 2008).

This study used cultured Drosophila cells as the experimental system to investigate DPE versus TATA function. Two sets of reporter constructs were created that contain either TATA or DPE motifs driving a luciferase reporter gene. The DPE-dependent and TATA-dependent promoters in each set were identical, except for the sequences at the positions of the DPE and TATA motifs, and had comparable transcriptional activities (Hsu, 2008).

The effects of several transcription factors were investigated upon DPE versus TATA transcription by RNAi depletion analysis. The transcription factors were selected on the basis of their fundamental importance as well as their potential role in DPE-dependent transcription. First RNAi depletion of each target factor was carried out, and then one-half of the cells was transfected with the DPE-dependent reporter construct and the other half of the cells with the TATA-dependent reporter. The resulting transcription levels were assessed by measurement of the luciferase activities relative to those in mock RNAi controls (Hsu, 2008).

Depletion of TBP sharply decreases TATA-dependent transcription, but has little effect on DPE-dependent transcription. This effect was observed with a distinct and independent set of DPE-dependent and TATA-dependent reporter constructs as well as with a different nonoverlapping dsRNA probe for TBP. Consistent with the ability of TFIIA to promote TBP binding to DNA, depletion of TFIIA reduces TATA transcription more than DPE transcription with two different sets of reporter constructs. In contrast, no differential DPE versus TATA effects were seen upon RNAi depletion of TAF4 (which is essential for the structural integrity of TFIID), TFIIB, CKIIα, a PC4-like protein, subunits of Mediator (Med17, Med24), or subunits of the SAGA/TFTC complex (Gcn5, Spt3, Ada2b) (Hsu, 2008).

Thus, these findings indicate that TBP and, to a lesser extent, TFIIA have a key role in discriminating between DPE- versus TATA-dependent transcription. The stronger effect of TBP relative to TFIIA is consistent with an auxiliary function of TFIIA, such as its ability to increase the binding of TBP to the TATA box. Because depletion of TBP did not adversely affect DPE-dependent transcription, the possibility was considered that DPE-dependent transcription might involve a factor, such as SAGA/TFTC, that lacks TBP. Therefore the effect of depletion of three SAGA/TFTC subunits (Gcn5, Spt3, and Ada2b) was tested, but no substantial decrease was seen in DPE-dependent transcription or any differential DPE versus TATA effects. Thus, it appears unlikely that SAGA/TFTC is important for DPE-dependent transcription. Lastly, upon depletion of CKII, Mediator, PC4-like, TAF4, and TFIIB, a decrease was observed in both DPE-dependent and TATA-dependent transcription. These results are consistent with a more general transcriptional function rather than a DPE-specific or TATA-specific activity for these factors (Hsu, 2008).

NC2 has been previously found to be a DPE-specific transcriptional activator. With a different biochemical system, however, NC2-mediated enhancement of DPE transcription was not observed. Therefore attempts were made to clarify these apparently contrasting results by RNAi analysis of NC2 with DPE versus TATA reporter gene systems. NC2 comprises two subunits, NC2α (Drap1) and NC2β (Dr1). Upon RNAi depletion of either NC2α or NC2β, a more substantial decrease was seen in DPE- relative to TATA-dependent transcription with two different sets of reporter genes as well as with two different dsRNAs. These results therefore indicate that NC2 promotes DPE-dependent transcription relative to TATA-dependent transcription in cultured cells (Hsu, 2008).

Next, the effects were tested of Mot1 (also known as BTAF1 and Hel89B) on DPE versus TATA transcription. Like NC2, Mot1 antagonizes TBP function. NC2 represses TATA-dependent transcription by blocking the association of TBP with other factors such as TFIIA and TFIIB. Mot1 is an ATPase that removes TBP from DNA by an ATP-dependent mechanism. Genetic studies in Saccharomyces cerevisiae suggest that NC2 and Mot1 have related functions. NC2 and Mot1 bind to overlapping regions in the yeast genome and form a complex with TBP and DNA. In addition, although NC2 and Mot1 are often thought to be repressive, a positive function for these factors has been observed in vitro and in vivo (Hsu, 2008 and references therein).

It was observed that RNAi depletion of Mot1 has a stronger detrimental effect on DPE-dependent than TATA-dependent transcription. This effect was seen with two different sets of reporter genes as well as with two independent nonoverlapping dsRNA fragments. Thus, like NC2, Mot1 promotes DPE- relative to TATA-dependent transcription (Hsu, 2008).

To investigate the relationship between TBP, NC2, and Mot1 in the regulation of core promoter activity, different combinations of these factors were codepleted and the resulting effects upon DPE versus TATA transcription were determined. Codepletion of both NC2α and Mot1 preferentially decreases DPE relative to TATA transcription to an extent that is similar to that seen upon depletion of either NC2α or Mot1 alone. These results suggest that NC2 and Mot1 promote DPE-dependent transcription via the same pathway. In contrast, when TBP + Mot1 or TBP + NC2α were codepleted, nearly the same effect on DPE versus TATA transcription was seen as that seen upon depletion of TBP alone. These findings suggest that TBP is downstream from NC2 and Mot1 in the pathway that regulates DPE versus TATA transcription. Thus, NC2 and Mot1 appear to modulate DPE versus TATA transcription by acting via TBP (Hsu, 2008).

To complement the RNAi depletion studies, the effects of overexpression of TBP, Mot1, or NC2 was investigated in S2 cells. In these experiments, TBP, Mot1, or NC2 expression vectors were cotransfected along with the DPE-dependent or TATA-dependent reporter constructs. Overexpression of TBP increases TATA-dependent transcription and decreases DPE-dependent transcription. Conversely, overexpression of Mot1 increases DPE-dependent transcription and decreases TATA-dependent transcription. Overexpression of both subunits of NC2 decreases TATA-dependent transcription, but has little effect on DPE-dependent transcription. Consistent with the two NC2 subunits functioning together in a complex, overexpression of NC2α alone or NC2β alone has no effect on DPE-dependent or TATA-dependent transcription. In addition, a parallel set of overexpression experiments was carried out with TBP, Mot1, and NC2 with a different set of DPE-dependent and TATA-dependent reporter genes, and nearly identical results were obtained. These findings further demonstrate that TBP favors TATA relative to DPE transcription, whereas Mot1 and NC2 favor DPE relative to TATA transcription (Hsu, 2008).

To examine the functions of TBP, Mot1, and NC2 in a more natural context, the effects of RNAi depletion of TBP, Mot1, or NC2 upon transcription of endogenous DPE- or TATA-containing genes was tested in Drosophila Kc cells. In these experiments, secondary/late ecdysone-responsive genes, that are activated upon ecdysone induction, were employed. In this manner, it was possible to characterize the requirements for TBP, Mot1, and NC2 for transcriptional activation (Hsu, 2008).

Many genes in Drosophila are activated by the steroid hormone 20-hydroxyecdysone (20HE). A list of genes was obtained that was induced by 20HE in Drosophila Kc cells. From this list, secondary/late-response genes were identified with DPE+Inr motifs (CG9511, CG16876, Glut1) or TATA + Inr motifs (Obp99c, CG4500) in their core promoters. The 20HE induction of these genes in Kc cells was confirmed by using real-time RT-PCR. In addition, the transcription start sites of each of these genes was verified by primer extension analysis of mRNA isolated from Kc cells (Hsu, 2008).

The RNAi analysis of the endogenous secondary/late-response genes was carried out as follows: TBP, TAF4, NC2α, and Mot1 were each individually depleted by RNAi in Kc cells for 4 d, and then the ecdysone-responsive genes were induced with 20HE for 24 h. The total RNA was isolated, and the transcript levels of the selected genes were determined by real-time RT-PCR. It was observed that depletion of TBP decreases transcription of the TATA-containing promoters and increases transcription of the DPE-containing promoters. Thus, these results suggest not only that TBP activates TATA-dependent promoters, but also that it represses DPE-dependent promoters. Conversely, it was found that depletion of Mot1 or NC2α decreases transcription of DPE-containing promoters and increases transcription of TATA-containing promoters. These findings suggest a positive function of Mot1 and NC2 at DPE-dependent promoters and a negative function at TATA-containing promoters. RNAi depletion of TAF4 causes a substantial decrease in transcription from both DPE-containing and TATA-containing promoters. These results further support the conclusion that TAF4 is required for both DPE-dependent and TATA-dependent transcription (Hsu, 2008).

The RNAi depletion analysis with the endogenous genes leads to nearly the same conclusions as the experiments with the transfected luciferase reporter genes. Both sets of experiments indicate that TBP favors TATA-dependent relative to DPE-dependent transcription, and that Mot1 and NC2 favor DPE-dependent relative to TATA-dependent transcription. However, it is useful to note the two distinctions. First, TBP depletion results in an increase in transcription from endogenous DPE-containing genes, but does not alter transcription from transfected DPE-dependent reporter genes. Second, depletion of Mot1 or NC2α causes an increase in transcription from endogenous TATA-containing genes, but results in a slight decrease in transcription from transfected TATA-dependent reporter genes. The analysis of the endogenous genes is likely to provide a more accurate representation of TBP, Mot1, and NC2 activity than the studies with the transfected genes, because the endogenous genes are in their natural context at the normal copy number and the experiments with the endogenous genes do not involve the extra transfection procedure. Thus, the findings from the analysis of the endogenous genes suggest a repressive function of TBP at DPE-dependent promoters as well as a repressive function of Mot1 and NC2 at TATA-dependent promoters (Hsu, 2008).

The secondary/late ecdysone-responsive genes were further characterized by ChIP analysis with TBP and RNA polymerase II (Rpb3 subunit), for which ChIP-quality antibodies were available. With the TATA-containing CG4500 promoter, there is increased ChIP signal for both TBP and Rpb3 in the promoter region upon 20HE induction. In the control/reference TATA-containing hsp70 promoter, an increase in ChIP of TBP and Rpb3 was also observed in the promoter region. By comparison, with the DPE-containing Glut1 and CG16876 promoters, there is increased ChIP of Rpb3 in the promoter region upon 20HE induction; however, the ChIP signal for TBP does not increase under the same conditions. The absence of an increased ChIP signal for TBP with the DPE-containing promoters does not necessarily indicate that TBP is not present at the promoter; for instance, it is possible that TBP may be in an altered configuration that masks the accessibility of the antibodies. Yet, whether or not TBP is in close proximity to the DPE-containing promoters, these results show that there are differences in the nature of the interaction of TBP with TATA-containing versus DPE-containing promoters (Hsu, 2008).

It is also relevant to note that secondary/late-response genes were chosen in these studies, because secondary/late genes are more likely than primary/early-response genes to be in a naïve state prior to ecdysone induction. To test this notion, RNAi depletion analyses was carried out with two primary/early-response genes, E74A and E75B, both of which contain DPE motifs. With these genes, no change was observed in transcription upon RNAi depletion of TBP, TAF4, Mot1, or NC2α. Moreover, ChIP analysis further revealed that both TBP and RNA polymerase II (Rpb3 subunit) are present at the promoters prior to ecdysone induction. Therefore, it appears likely that these primary/early-response genes exist in a preactivated state that does not require the subsequent action of factors such as TFIID, Mot1, or NC2 (Hsu, 2008).

The RNAi depletion and overexpression data reveal a regulatory circuit with the following properties: TBP activates TATA-dependent transcription and represses DPE-transcription; then, Mot1 and NC2 act to block both the activating and repressive functions of TBP. In this model, there are opposing forces that alter the balance between DPE versus TATA transcription. A decrease in TBP or an increase in Mot1/NC2 favors DPE transcription, whereas an increase in TBP or a decrease in Mot1/NC2 favors TATA transcription. Importantly, the functions of Mot1 and NC2 are dependent on TBP. In addition, the proposed circuit is consistent with the known antagonistic relationship between TBP and NC2 as well as between TBP and Mot1 (Hsu, 2008).

How might TBP repress DPE-dependent transcription? Two possible explanations are suggested. (1) In the absence of a TATA box, TBP might interfere with the proper assembly of the transcription initiation complex. (2) There may be an essential DPE-directed transcription factor that is inhibited by TBP. It is possible that DPE-mediated transcription does not directly involve TBP; there is substantial evidence of RNA polymerase II-mediated transcription occurring in the absence of TBP (Hsu, 2008 and references therein).

It was also considered whether either of the TBP-related factors, TRF1 and TRF2, are used instead of TBP at DPE-containing promoters. To this end, the effect of depleting TRF1 or TRF2 was examined upon the expression of DPE-containing versus TATA-containing endogenous genes. TRF1, which is largely involved in RNA polymerase III transcription in Drosophila, has little or no effect on transcription of DPE-containing or TATA-containing genes. TRF2 is important for both DPE-mediated and TATA-mediated transcription. The effect of TRF2 is similar to that of TAF4, which appears to contribute to both DPE-depentend and TATA-dependent transcription. Neither TRF1 nor TRF2 exhibit an opposite effect on DPE-mediated versus TATA-mediated transcription as do TBP, Mot1, and NC2. In addition, a genome-wide ChIP analysis of TRF2 did not reveal an association of TRF2 with DPE-containing genes. Thus, at the present time, there is no evidence suggesting a specific link between either TRF1 or TRF2 and DPE-mdidated or TATA-mediated transcription (Hsu, 2008).

In conclusion, the analysis of TBP, Mot1, and NC2 in the context of DPE-containing versus TATA-containing promoters has revealed a regulatory circuit that controls the balance between DPE-mediated versus TATA-mediated transcription. This circuit may be a key means by which DPE or TATA specificity of transcriptional enhancers is achieved. In the future, it will be interesting and important to build upon this core circuit to identify the connections and mechanisms by which biological networks use DPE and TATA specificity to increase the number of pathways by which signals can be transmitted (Hsu, 2008).

Structures of three distinct activator-TFIID complexes

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) was determined and their structures were compared as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, these results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation (Liu, 2009).

Three D density difference maps generated from reconstructions of the three independent activator/TFIID assemblies (i.e., p53-IID, Sp1-IID, and c-Jun-IID) and free holo-TFIID have served as a method to map the most likely contact sites of these activators within the native TBP-TAF complex. Remarkably, each activator contacts TFIID via select TAF interfaces within TFIID. The unique and localized arrangements of these three activators contacting different surfaces of TFIID could be indicative of the wide diversity of potential activator contact points within TFIID that would be dependent on both the specificity of activation domains as well as core promoter DNA sequences appended to target gene promoters. It is also possible, however, that these distinct activator-TFIID contacts can form a common scaffold when TFIID binds to the core promoter DNA (Liu, 2009).

It is well established that activators including p53, Sp1, and c-Jun frequently work synergistically with each other or other activators to potentiate selective gene expression programs in response to a variety of stimuli in vivo. Therefore, combinatorial mechanisms of promoter activation might favor distinct nonoverlapping activator-binding sites within TFIID, which can be achieved by specific interactions between selective TAF subunits and activators. Indeed, it was established that TAF1 and TAF4 serve as coactivators for Sp1, while TAF1, TAF6, and TAF 9 mediate p53-dependent transactivation and TAF1 and TAF7 subunits are thought to be coactivators for c-Jun. Since activators make sequence-specific contacts with the DNA template at various positions upstream of the core promoter, it is also plausible that activators bound to unique surfaces of TFIID can influence specific structures of a promoter as the DNA traverses along TFIID resulting in distinct activator/promoter DNA structures (Liu, 2009).

Activator mapping results also complement and structurally extend the functional relevance of previous biochemical and immunomapping studies of TFIID. For example, label transfer studies show that the N-terminal activation domain of p53 contacts TAF6, confirming previous biochemical evidence showing that amino acids 1-42 of p53 contact TAF6/9. In support of this observation, the p53-IID 3D structure indicates that p53 contacts TFIID at lobes A and C where TAF6/9 are located as determined by EM immunomapping. In addition, previous studies have shown that both TBP and TAF1 can directly contact p53 in the absence of additional TFIID subunits. Interestingly, body-labeled p53 cross-linked to TAF1, TAF5, and weakly to TBP, thus extending the immunomapping studies that determined the locations of TBP and the N terminus of TAF1 at lobe C. Thus, EM activator mapping studies show a significant interface between p53 and specific TAFs located at lobes A and C of TFIID. Likewise, Sp1 label transfer results confirmed previous biochemical data showing a direct interaction between TAF4 and the N-terminal glutamine-rich domains of Sp1. In addition to TAF4, TAF6 was identified as weakly cross-linked to Sp1, suggesting that TAF6 may also be in the vicinity but perhaps more distal to the N terminus of Sp1. The largest TFIID subunit, TAF1, was cross-linked when body-labeled Sp1 was used. This result was not entirely unexpected, since previous studies found that TAF1 is required for Sp1-dependent transactivation, possibly through a direct interaction between TAF1 and Sp1 (Liu, 2009).

In comparison with p53 and Sp1, body-labeled c-Jun was shown to contact TAF1 and TAF6 in label transfer studies with no subunits contacting the N-terminal activation domain of c-Jun. This N-terminal activation domain of c-Jun may be structurally flexible or predominantly unstructured and is apparently positioned away from TFIID contacts. Indeed, successful structural studies of c-Jun thus far have been limited to the C-terminal leucine zipper DNA-binding region when bound to DNA. Previous biochemical assays have shown that the C-terminal basic leucine zipper DNA-binding region also contacts the N terminus of TAF1 (Liu, 2009).

It is worth noting that the extra density representing c-Jun and the other activator polypeptides in EM studies may not reflect the full-expected size of the activators. This is due to the presence of large unstructured regions in these proteins that are averaged out during structural analysis. As activators contain multiple molten globular domains that likely interact with different partners, one would expect a high degree of structural disorder in the domains that are not in direct contact with TFIID. Thus, the extra density associated with each activator determined from the single-particle reconstructions likely only represents minimally the most stably associated portion of activators bound to TFIID. This common situation would invariably lead to underrepresenting the actual size of the activator in a manner not unlike crystal structures of domains with flexible loops that become 'invisible' in the crystal structure (Liu, 2009).

Based on EM immunomapping, there are two copies of TAF6 within TFIID, wherein one copy resides in lobe A and another in lobe B. Collectively, the current studies suggest that two distinct activators (p53 and c-Jun) strongly contact the two different TAF6 subunits that are each located in different lobes of TFIID. It is unknown how p53 or c-Jun discriminates between TAF6 on lobe A versus B when binding to TFIID. In the future, it will be interesting to investigate if these two activators can bind to a single TFIID molecule simultaneously and decipher 3D structures of TFIID assemblies bound to select endogenous promoter DNA sequences in the presence and absence of distinct activators that are engaged in synergistic transcriptional activation (Liu, 2009).

It is of note that unlike the radical, diverse, and global structural changes observed with CRSP/Mediator complexes upon activator binding, TFIID largely retains its overall architecture when bound by three different activators. Interestingly, this study found that two of the activator/IID structures, p53-IID and Sp1-IID assemblies appear to be more constricted around the central cavity with narrower ChB-D and ChA-B channels, while the third structure, c-Jun-IID, remains most similar to free holo-TFIID. In particular, the p53-IID structure more closely resembles the closed conformational state of the previous cryo-TFIID structure. To test if p53-bound TFIID mimics the most closed conformational form of holo-TFIID, 3D reconstructions were performed using either the most closed or 'open' cryo-TFIID structures as an initial reference volume for refinement. Interestingly, it was found that both newly refined 3D structures generated from either the closed or open reference volume are fairly similar, with possibly a partial occupancy of p53 on lobe A. These findings suggest that the overall p53-TFIID structure tends to move toward the closed conformation with moderate movement at the outer tips of lobes A and B, even though p53-IID is predominantly observed in an intermediate average conformational form between the most closed and open forms. Perhaps factors contacting lobe A or C can induce certain coordinated movements within lobes that lead to a closed conformation of TFIID (Liu, 2009).

Although TFIID largely retains its prototypic global architecture upon activator binding, several common localized structural changes induced upon activator binding were observed in the 3D reconstruction. For example, a prominent and consistent induced extra density protrusion located in lobe D was observed when each of the three different activators binds TFIID. Given that all these activators are represented by distinct densities with unique sizes and shapes within the bound TFIID structure, and the fact that it has been demonstrated that they each can target different subunits within TFIID by a number of independent biochemical assays, it seems reasonable to assign 'unique and significant' extra densities located at distinct sites as representing the different bound activators. In contrast, the common similarly sized extra density seen at lobe D of each activator-IID structure most likely represents a conserved conformational change induced by these three different activators. Interestingly, this protrusion in lobe D resides distal to each of the activator-binding sites, suggesting that these three activators may potentially induce a long-range internal conformational change within TFIID. It would be intriguing to identify which TAF subunits are located at the tip of lobe D and eventually determine the function, if any, of this extended lobe in activator-induced transcription initiation. However, despite the potential significance of these structural changes induced by activators, it is premature to speculate regarding their functional importance (Liu, 2009).

Architecture of an RNA polymerase II transcription pre-initiation complex

The protein density and arrangement of subunits of a complete, 32-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by means of cryogenic electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs) and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft (Murakami, 2013).

This study has revealed a central principle of the PIC: the association of promoter DNA only with the GTFs and not with pol II. Promoter DNA is suspended above the pol II cleft, contacting three GTFs -- TFIIB, TFIID (TBP subunit), and TFIIE -- at the upstream end of the cleft (TATA box) and contacting TFIIH (Ssl2 helicase subunit) at the downstream end. In between, the DNA is free and available for action of the helicase, which untwists the DNA to introduce negative superhelical strain and thereby promote melting at a distance (Murakami, 2013).

This principle of the PIC is a consequence of the rigidity of duplex DNA. The promoter duplex must follow a straight path, whereas bending through ~90° is required for binding in the pol II cleft. Only after melting can the DNA bend for entry in the cleft. Melting is thermally driven, induced by untwisting strain in the DNA above the cleft. A melted region is short-lived and must be captured by binding to pol II, which occurs rapidly enough because the DNA is positioned above the cleft. The GTFs therefore catalyze the formation of a stably melted region (transcription bubble) in two ways, by the introduction of untwisting strain (by the helicase) and by positioning promoter DNA (Murakami, 2013).

Untwisting strain is distributed throughout the DNA above the pol II cleft, so melting may occur at any point, but only a melted region adjacent to TFIIB is stabilized by binding to pol II. The reason is again the rigidity of duplex DNA, and the requirement for a sharp bend adjacent to TFIIB to penetrate the pol II cleft. A single strand of DNA must extend from the point of contact with TFIIB, ~13 bp downstream of the TATA box, through the binding site for the transcription bubble in pol II. TFIIB may also interact with the single strand to stabilize the bubble (Murakami, 2013).

These conclusions are based on results from both cryo-EM and XL-MS, which served to validate one another: Segmentation and labeling of electron density, based on fitting pol II and other known structures, was consistent with all but three of 266 cross-links observed. The PIC structure is also consistent with partial structural information from x-ray crystallography (pol II-TFIIB, pol II-TFIIS, TFIIA-TBP-TFIIB-DNA, and Tfb2-Tfb5), from nuclear magnetic resonance (Tfb1-Tfa1 and Tfa2-DNA), and from EM (core and holo TFIIH). This consistency provides cross-validation, both supporting this PIC structure and establishing the relevance of the partial structural information. Further consistency was found with the results of FeBABE cleavage mapping of complexes formed in yeast nuclear extract; the locations of proteins along the DNA in the PIC structure and those determined with FeBABE cleavage differ by no more than 5 bp. This PIC structure also agrees with results of protein-DNA cross-linking in a reconstituted human transcription system; positions of TFIIE and TFIIH differ between the two studies by ~20 and 10 bp. The location of Ssl2 in this structure, ~30 bp downstream from the TATA box, supports the proposal, made on the basis of previous DNA-protein cross-linking analysis, that helicase action torques the DNA to introduce untwisting strain and thereby to promote melting at a distance (Murakami, 2013).

Association of the winged helix motif of the TFIIEalpha subunit of TFIIE with either the TFIIEbeta subunit or TFIIB distinguishes its functions in transcription

In eukaryotes, the general transcription factor TFIIE consists of two subunits, alpha and beta, and plays essential roles in transcription. Structure-function studies indicate that TFIIE has three-winged helix (WH) motifs, with one in TFIIEα and two in TFIIEβ. Recent studies suggested that, by binding to the clamp region of RNA polymerase II, TFIIEα-WH promotes the conformational change that transforms the promoter-bound inactive preinitiation complex to the active complex. To elucidate its roles in transcription, functional analyses of point-mutated human TFIIEα-WH proteins were carried out. In vitro transcription analyses identified two classes of mutants. One class was defective in transcription initiation, and the other was defective in the transition from initiation to elongation. Analyses of the binding of this motif to other general transcription factors showed that the former class was defective in binding to the basic helix-loop-helix motif of TFIIEβ and the latter class was defective in binding to the N-terminal cyclin homology region of TFIIB. Furthermore, TFIIEα-WH bound to the TFIIH XPB subunit at a third distinct region. Therefore, these results provide further insights into the mechanisms underlying RNA polymerase II activation at the initial stages of transcription (Tanaka, 2015).

dTAF10- and dTAF10b-containing complexes are required for ecdysone-driven larval-pupal morphogenesis in Drosophila melanogaster

In eukaryotes the TFIID complex is required for preinitiation complex assembly which positions RNA polymerase II around transcription start sites. Histone acetyltransferase complexes including SAGA and ATAC, modulate transcription at several steps through modification of specific core histone residues. This study investigated the function of Drosophila proteins TAF10 and TAF10b, which are subunits of dTFIID and dSAGA, respectively. The simultaneous deletion of both dTaf10 genes impaired the recruitment of the dTFIID subunit dTAF5 to polytene chromosomes, while binding of other TFIID subunits,

Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II; see Drosophila Pol II). A "step-wise" preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, this study established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Real-time measurements were performed of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, it was found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB-promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II-TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions (Zhang, 2016).

Identification of regions in the Spt5 subunit of DSIF that are involved in promoter proximal pausing

DRB-sensitivity inducing factor (DSIF2, or Spt4/5) is a conserved transcription elongation factor that both inhibits and stimulates transcription elongation in metazoans. In Drosophila and vertebrates, DSIF together with negative elongation factor (NELF) associates with RNA polymerase II (Pol II) during early elongation and causes Pol II to pause in the promoter proximal region of genes. The mechanism of how DSIF establishes pausing is not known. This study constructed Spt5 mutant forms of DSIF and tested their capacity to restore promoter proximal pausing to DSIF-depleted Drosophila nuclear extracts. The C-terminal repeats (CTR) region of Spt5, which has been implicated in both inhibition and stimulation of elongation, is dispensable for promoter proximal pausing. A region encompassing KOW4 and KOW5 of Spt5 is essential for pausing, and mutations in KOW5 specifically shift the location of the pause. RNA crosslinking analysis reveals that KOW5 directly contacts the nascent transcript and deletion of KOW5 disrupts this interaction. These results suggest that KOW5 is involved in promoter proximal pausing through contact with the nascent RNA (Qiu, 2017).

Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition

The general transcription factor TBP (TATA-box binding protein) and its associated factors (TAFs) together form the TFIID complex, which directs transcription initiation. Through RNAi and mutant analysis, this study identified a specific TBP family protein, TRF2, and a set of TAFs that regulate lipid droplet (LD) size in the Drosophila larval fat body. Among the three Drosophila TBP genes, trf2, tbp and trf1, only loss of function of trf2 results in increased LD size. Moreover, TRF2 and TAF9 regulate fatty acid composition of several classes of phospholipids. Through RNA profiling, TRF2 and TAF9 were found to affect the transcription of a common set of genes, including peroxisomal fatty acid beta-oxidation-related genes that affect phospholipid fatty acid composition. Knockdown of several TRF2 and TAF9 target genes results in large LDs, a phenotype which is similar to that of trf2 mutants. Together, these findings provide new insights into the specific role of the general transcription machinery in lipid homeostasis (Fan, 2017).

This study reveals a rather specific role of TRF2 and TAFs, which are general transcription factors, in regulating LD size. In addition, TRF2 and TAF9 affect phospholipid fatty acid composition, most likely through ACOX genes which mediate peroxisomal fatty acid β-oxidation (Fan, 2017).

By binding to their responsive elements in target genes, specific transcription factors like SREBP (see Drosophila Srebp), PPARs and NHR49, play important roles in lipid metabolism. It is interesting to find that the general transcription machineries, in this case TRF2 and core TAFs, also exhibit specificity in regulating lipid metabolism. In the Drosophila late 3rd instar larval fat body, defects in trf2 cause increased LD size, whereas mutation of the other two homologous genes, tbp and trf1, have no obvious effects on lipid storage. Inactivation of taf genes causes a similar phenotype to trf2 mutation, suggesting that TRF2 may associate with these TAF proteins to direct transcription of specific target genes. Moreover, trf2 mutants have large LDs at both 2nd and early 3rd instar larval stages, suggesting that general transcription factors are also required at early developmental stages for LD size regulation. Interestingly, taf9 mutants have no obvious phenotype at these stages. It is possible that TAF9 may act as an accessory factor compared to promoter-binding TRF2. This is consistent with the fact that less genes are affected in taf9 mutants than trf2 mutants in RNA-seq analysis. It was also found that knockdown of trf2 in larval and adult fat body leads to different LD phenotype. This may be due to different lipid storage status or different LD size regulatory mechanisms between larval and adult stages (Fan, 2017).

The finding of this study adds to the growing evidence supporting a specific role of general transcription factors in lipid homeostasis. For example, knockdown of RNA Pol II subunits such as RpII140 and RpII33 leads to small and dispersed LDs in Drosophila S2 cells. Mutation in DNA polymerase δ (POLD1) leads to lipodystrophy with a progressive loss of subcutaneous fat. Furthermore, TAF8 and TAF7L were reported to be involved in adipocyte differentiation. Moreover, previous studies showed that several subunits of the Mediator complex interact with specific transcription factors and play important roles in lipid metabolism. Added together, these lines of evidence strongly support essential and specific roles of the core/basal transcriptional machinery components in lipid metabolism (Fan, 2017).

Using RNA-seq analysis, rescue experiments and ChIP-qPCR, identified several target genes regulated by TRF2 and TAF9. It is possible that other genes may regulate LD size but were missed in the RNA-seq analysis and RNAi screening assay because of either insufficient alterations in genes expression (lower than the twofold threshold) or low efficiency of RNAi. Among all the verified target genes of TRF2 and TAF9,CG10315, which strongly rescues the trf2G0071 mutant phenotype when overexpressed and encodes the eukaryotic translation initiation factor eIF2B-δ, may be a good candidate for further study. Although they are best known for their molecular functions in mRNA translation regulation, eIFs have been implicated in several other processes, including cancer and metabolism. For example, in yeast, eIF2B physically interacts with the VLCFA synthesis enzyme YBR159W. In adipocytes, eIF2α activity is correlated with the anti-lipolytic and adipogenesis inhibitory effects of the AMPK activator AICAR. In addition, given the evidence that some eIFs, such as eIF4G and eIF-4a, localize on LDsand knockdown of some eIFs, including eIF-1A, eIF-2β, eIF3ga, eIF3-S8 and eIF3-S9, results in large LDs in Drosophila S2 cells, it is important to further explore the specific mechanisms of these eIFs in LD size regulation (Fan, 2017).

Although TRF2 exists widely in metazoans and shares sequence homology in its core domain with TBP, it recognizes sequence elements distinct from the TATA-box. A previous study has investigated TRF2- and TBP-bound promoters throughout the Drosophila genome in S2 cells and revealed that some sequence elements, such as DRE, are strongly associated with TRF2 occupancy while the TATA-box is strongly associated with TBP occupancy (Isogai, 2007). This study also identified that DRE is significantly enriched in extended promoters of the 181 target genes. The distribution of TATA-boxes in the core promoters of the 181 target genes compared with all genes was further explored, and it was found that the TATA-box is not enriched in the core promoters of TRF2 target genes. The proportion of TATA-box is 0.155 (75 of 484 isoforms) for the 181 target genes while the proportion is 0.217 (7849 of 36099 isoforms) for all genes as the background. These results suggest that TRF2 and TAF9 may regulate the expression of a subset of genes by recognizing specific sequence elements such as DRE but not the TATA-box (Fan, 2017).

This study shows that expression of peroxisomal fatty acid β-oxidation pathway genes, including two acyl-CoA oxidase (ACOX) genes, CG4586 and CG9527, the β-ketoacyl-CoA thiolase gene CG9149, and the enoyl-CoA hydratase gene CG9577, is regulated by TRF2 and TAF9. Lipidomic analysis indicates that in the fat body of trf2 and taf9 RNAi, many phospholipids, such as PA, PC, PG and PI, contain more long chain fatty acids. Furthermore, knockdown of CG4586 and CG9527 in the fat body also causes similar changes.

These results coincide with the function of ACOX, which is implicated in the peroxisomal fatty acid β-oxidation pathway for catabolizing very long chain fatty acids and some long chain fatty acids. Similar to these findings, a previous study found that defective peroxisomal fatty acid β-oxidation resulted in enlarged LDs in C. elegans and blocked catabolism of LCFAs, such as vaccenic acid, which probably contributed to LD expansion in mutant worms. Since overexpressing CG4586 or CG9527 only marginally rescues the enlarged LD phenotype of trf2 mutants, it remains to be determined whether the increased level of long chain fatty acid-containing phospholipids contributes to LD size. Regarding the regulation of fatty acid chain length in phospholipids, a recent study reported that there was increased acyl chain length in phospholipids of lung squamous cell carcinoma accompanied by significant changes in the expression of fatty acid elongases (ELOVLs) compared to matched normal tissues. A functional screen followed by phospholipidomic analysis revealed that ELOVL6 is mainly responsible for phospholipid acyl chain elongation in cancer cells. The current findings provide new clues about the regulation of fatty acid chain length in phospholipids. ELOVL and the peroxisomal fatty acid β-oxidation pathway may represent two opposing regulators in determining fatty acid chain length in vivo (Fan, 2017).

Previous studies have shown that TRF2 is involved in specific biological processes including embryonic development, metamorphosis, germ cell differentiation and spermiogenesis. The current results reveal a novel function of TRF2 in the regulation of specialized transcriptional programs involved in LD size control and phospholipid fatty acid composition. Since TRF2 is conserved among metazoans, its role in the regulation of lipid metabolism may be of considerable relevance to various organisms including mammals. These findings may provide new insights into both the regulation of lipid metabolism and the physiological functions of TRF2 (Fan, 2017).

list of proteins involved in messenger RNA synthesis


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date revised: 26 December 2016

Zygotically transcribed genes

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