E(spl) region transcript m4
The functional relationships have been investigated among three loci that are required for multiple alternative cell fate decisions during
adult peripheral neurogenesis in Drosophila: Notch (N), which encodes a transmembrane receptor protein; Suppressor of Hairless
[Su(H)], which encodes a DNA-binding transcription factor, and the Enhancer of split gene complex [E(spl)-C], which includes seven
transcription units that encode basic helix-loop-helix (bHLH) repressor proteins. Several lines of evidence are described establishing
that Su(H) directly activates transcription of E(spl)-C genes in response to N receptor activity. Expression of an activated form of the
N receptor leads to elevated and ectopic E(spl)-C transcript accumulation and promoter activity in imaginal discs. The
proximal upstream regions of three E(spl)-C genes, including m4, contain multiple specific binding sites for Su(H). The integrity of these sites, as well
as Su(H) gene activity, are required not only for normal levels of expression of E(spl)-C genes in imaginal disc proneural clusters, but
also for their transcriptional response to hyperactivity of the N receptor. Under Su(H) minus conditions, both the endogenous m4 gene and the 51-bp m4 promoter fragment exhibit strong expression in PNS proneural clusters; in the latter case at least, the expression is dependent on the integrity of two E-box binding sites for proneural activators. These results establish Su(H) as a direct regulatory link between
N receptor activity and the expression of E(spl)-C genes, extending the known linear structure of the N cell-cell signaling pathway (Bailey, 1995 and Nellesen, 1999).
In Drosophila, genes of the Enhancer of split Complex [E(spl)-C] are important components of the Notch (N) cell-cell signaling pathway, which is utilized in
imaginal discs to effect a series of cell fate decisions during adult peripheral nervous system development. Seven genes in the complex encode basic
helix-loop-helix (bHLH) transcriptional repressors, while four others encode members of the Bearded family of small proteins. A striking diversity is observed
in the imaginal disc expression patterns of the various E(spl)-C genes, suggestive of a diversity of function, but the mechanistic basis of this variety has not
been elucidated. Strong evidence is presented from promoter-reporter transgene experiments that regulation at the transcriptional level is primarily
responsible. Certain E(spl)-C genes are known to be direct targets of transcriptional activation both by the N-signal-dependent activator
Suppressor of Hairless [Su(H)] and by the proneural bHLH proteins achaete and scute. Extensive sequence analysis of the promoter-proximal upstream
regions of 12 transcription units in the E(spl)-C reveals that such dual transcriptional activation is likely to be the rule for at least 10 of the 12 genes. The very different wing imaginal disc expression patterns of E(spl)m4 and E(spl)mgamma are a property of small (200-300 bp), evolutionarily
conserved transcriptional enhancer elements, which can confer these distinct patterns on a heterologous promoter despite their considerable structural similarity
[each having three Su(H) and two proneural protein binding sites]. As originally defined by its structure in m4, m8 and mgamma, the Su(H) paired site (SPS) configuration consists of two high-affinity (YGTGRGAAM; M denotes A or C) Su(H) binding sites in an inerted repeat arrangement, with 300 bp between the first G of the two sites. In addition, the 'Y' of the upstream site is T, while that of the downstream site is C. Finally, the sequence between the two Su(H) sites includes the hexamer GAAAGT or its complement ACTTTC. The SPS motifs of m4 and mgamma in Drosophila hydei are remarkably conserved. A 43-nt block in m4 SPS contains the entire SPS motif and shows only a single varient position. Also all four bHLH activator binding sites in the two genes are conserved. A putative bHLH repressor binding site defined by the N box consensus sequence CACNAG does not appear to be as conserved as sites defined by CACGYG that have been shown to bind these proteins with high affinity. Thus of four distinct CACGYG sites (one in mgamma and three in m4 ), two are conserved, while apparently only one of seven distinct N box sites (three in mgamma and four in m4) is conserved. Conserved transcription factor binding sites are often accompanied by strongly conserved flanking sequences. It is concluded that the distinctive expression patterns of
E(spl)-C genes in imaginal tissues depend to a significant degree on the capacity of their transcriptional cis-regulatory apparatus to respond selectively to direct
proneural- and Su(H)-mediated activation, often in only a subset of the territories and cells in which these modes of regulation are operative (Nellesen, 1999).
The neurogenic genes of Drosophila are required for correct separation of neural and epidermal progenitor cells during early embryogenesis.
Results from genetic analyses indicate that the neurogenic genes are functionally related. The spatial distribution of RNA from the neurogenic
genes Dl, neu, and m4, m5, m7 and E(spl) [four genes of the Enhancer of split complex] has been studied in various neurogenic mutant embryos by in situ hybridization. An
abnormal distribution of RNA from certain of the genes is found in neurogenic mutants, suggesting that at least some of the functional interactions inferred
from genetic data take place at the transcriptional level (Godt, 1991).
Transcriptional expression
of some E(spl)-C genes encoding bHLH transcription
factors is activated in response to Notch signaling. In order to elucidate whether there are additional Notch responsive genes
among the newly characterized genes,
all bHLH and non-bHLH genes in the E(spl) locus
were systematically compared for their Notch responsiveness. Truncation of the extracellular
domain of Notch results in a constitutively activated
Notch receptor. Such an activated Notch receptor
(N intra) was expressed in a zebra pattern employing
the Gal4/UAS system. These
embryos were subsequently hybridized with probes specific
for the particular genes of the E(spl) locus. If the
transcription of the respective gene is dependent on the
Notch signal, it should be expressed in a striped pattern.
All genes within the E(spl) locus
except m1 and m6 are activated in seven stripes,
indicating that these genes are regulated by the Notch
pathway during embryogenesis. From this it is concluded
that the E(spl)-C comprises three different classes of
Notch responsive genes: the seven bHLH genes; malpha/m4, and
m2 (Wurmbach, 1999).
The transcription factor Su(H) seems to provide a direct
link between the activated Notch receptor and Notch target
genes. In accordance, the promoter regions of the E(spl)-C
genes mdelta, mgamma, m4, m5 and m8 contain respective Su(H)
protein binding sites. An
investigation was carried out to see whether this is also true for malpha and m2.
Embryos homozygous mutant for Su(H) were derived
from germ-line clones. These Su(H) mutant embryos were
hybridized in situ with probes for m2, malpha, and m4 (as control),
respectively, and compared with the heterozygous siblings
that bear one Su(H) zygotic copy and, thus, develop
normally. malpha and m4 transcripts are nearly absent in the neuro-ectoderm
of the mutant embryos. This result is very similar
to that observed for E(spl) bHLH genes. In accordance, the malpha promoter
region contains two putative Su(H) binding sites that fit
exactly the consensus sequence [(C/T)GTG(G/A)GAA(C/
A)], and two potential sites that differ in their last position
(T instead of C/A at position 9), a variation observed
before for a genuine Su(H) binding site in the md promoter. Similarly, the promoter region of m4
contains three perfect Su(H) binding sites (Bailey, 1995 and Wurmbach, 1999).
In contrast to m4 and malpha, a considerable amount of m2
transcript is found in Su(H) mutant embryos especially in
the dorsal ectoderm, although at a reduced level.
Apparently, Su(H) is not strictly required for the initiation of
m2 transcription, but seems to augment it. Only at later
stages of development, m2 transcripts disappear, suggesting
that Su(H) is essential for the maintenance of m2 transcription.
The m2 promoter region contains a single divergent
Su(H) binding site that differs at two positions, the fifth
and the ninth, from the consensus. Similarly divergent
Su(H) binding sites have been shown to bind the Su(H)
protein in vitro (Wurmbach, 1999).
The transcriptional effect of m4/alpha is observed in
S2 cultured cells, where two different luciferase
reporter genes, one driven by a promoter fragment of E(spl)-
mgamma and one by a promoter fragment of E(spl)-m8 were tested. These
promoters are induced to 6x and 12x, respectively, after
cotransfection with plasmids expressing Su(H) and an intra-cellular activated form of Notch (RICN). Addition of
expression plasmid for m4 or malpha gives a small yet consistent
~2x repression of both reporters. In contrast, m4/alpha
has no effect on an unrelated luciferase reporter gene driven
by the achaete proximal promoter. A specific repressive effect of m4/alpha is thus observed on E(spl)bHLH
transcription both in imaginal discs and in cultured cells.
The ability of m4/alpha to downregulate E(spl)bHLH levels,
could account for their promotion of SOP fate. If this is the
sole activity of m4/alpha proteins, then restoring the expression
of E(spl)bHLH genes should abolish the m4/alpha gain-of-function (GOF) phenotype. Scutellum specific GAL4
lines were used to ectopically co-express m4 or malpha with one of the
E(spl)bHLH genes. Whereas m4/alpha alone produces
6+/-13 scutellar bristles, coexpression of E(spl)bHLH eliminates scutellars, a phenotype indistinguishable from the
gain-of-function phenotype of E(spl)bHLH alone. This
epistatic relation of UAS-E(spl) over UAS-m4/alpha led to
the conclusion that m4/alpha cannot antagonize E(spl) bHLH
factors at the protein level; rather, they must act upstream of E(spl) bHLH
accumulation. Consistent with this conclusion, no interactions is observed for m4 or malpha with a number of E(spl) bHLH or with their co-repressor Groucho in a yeast
two-hybrid assay. Furthermore, m4/alpha does not
interact with the proneural proteins Da, Ac, Sc or Ato. In
fact m4 appears to be a cytoplasmic protein, at least as far as
can be judged from the subcellular localization of an m4-
green fluorescent protein (GFP) fusion, making
interaction with these nuclear factors unlikely (Apidianakis, 1999).
During the development of the Drosophila adult peripheral nervous system (PNS), inhibitory cell-cell interactions mediated by the Notch receptor are essential
for proper specification of sensory organ cell fates. The 3' untranslated regions (UTRs) of many genes involved in Notch signaling, including Bearded (Brd) and the genes of the Enhancer of
split Complex (E(spl)-C), contain (often in multiple copies) two novel heptanucleotide sequence motifs: the Brd box (AGCTTTA) and the GY box
(GTCTTCC). Moreover, the molecular lesion associated with a strong gain-of-function mutant of Brd suggests that the loss of these sequence elements from
its 3' UTR might be responsible for the hyperactivity of the mutant gene. The wild-type Brd 3' UTR confers negative regulatory activity on
heterologous transcripts in vivo and this activity requires its three Brd box elements and, to a lesser extent, its GY box. Brd box-mediated
regulation decreases both transcript and protein levels, and the results suggest that deadenylation or inhibition of polyadenylation is a component of this
regulation. Though Brd and the E(spl)-C genes are expressed in spatially restricted patterns in both embryos and imaginal discs, the regulatory
activity that functions through the Brd box is both temporally and spatially general. A Brd genomic DNA transgene with specific mutations in its Brd and GY
boxes exhibits hypermorphic activity that results in characteristic defects in PNS development, demonstrating that Brd is normally regulated by these motifs. Brd boxes and GY boxes in the E(spl)m4 gene are specifically conserved between two distantly related Drosophila species, strongly
suggesting that E(spl)-C genes are regulated by these elements as well (Lai, 1998a).
Most E(spl)-C genes contain a novel sequence motif, the K box (TGTGAT), in their 3' untranslated regions (3' UTRs). Three lines of
evidence are presented that demonstrate the importance of this element in the post-transcriptional regulation of E(spl)-C genes. (1) K box sequences are specifically
conserved in the orthologs of two structurally distinct E(spl)-C genes (m4 and m8) from a distantly related Drosophila species; (2) the wild-type m8 3'
UTR strongly reduces accumulation of heterologous transcripts in vivo, an activity that requires its K box sequences, and (3) m8 genomic DNA transgenes
lacking these motifs cause mild gain-of-function PNS defects and can partially phenocopy the genetic interaction of E(spl)D with Notchspl. Although E(spl)-C
genes are expressed in temporally and spatially specific patterns, K box-mediated regulation is ubiquitous, implying that other targets of this
activity may exist. In support of this, sequence analyses are presented that implicate genes of the Iroquois Complex (Iro-C) and engrailed as additional targets of
K box-mediated regulation (Lai, 1998b).
Micro RNAs are a large family of noncoding RNAs of 21-22 nucleotides whose functions are generally unknown. A large subset of Drosophila RNAs has been shown to be perfectly complementary to several classes of sequence motif previously
demonstrated to mediate negative post-transcriptional regulation.
These findings suggest a more general role for micro RNAs in gene
regulation through the formation of RNA duplexes (Lai, 2002).
A new strategy of gene regulation was defined by the activities of Caenorhabditis elegans let-7 and lin-4. These RNA molecules of 21-22 nt are complementary to the 3' untranslated regions (UTRs) of target transcripts and mediate negative post-transcriptional regulation through RNA duplex formation. Several recent reports now reveal that a large family of RNAs of 21-22 nt, collectively termed micro RNAs (miRNAs), exists in organisms as diverse as worms, flies and humans. Although it was presumed that many of these new miRNAs would also act in post-transcriptional gene regulation, initial searches did not reveal obvious targets based on sequence complementarity (Lai, 2002).
In Drosophila, two 3'-UTR sequence motifs, the K box (cUGUGAUa) and the Brd box (AGCUUUA) mediate negative post-transcriptional regulation. Although originally identified in the 3' UTRs of Notch pathway target genes encoding basic helix-loop-helix (bHLH) repressors and Bearded family proteins, modes of regulation mediated by both motifs are spatially and temporally ubiquitous. This suggests that at least some of the many other Drosophila transcripts that contain K boxes or Brd boxes in their 3' UTRs are also actively regulated by these motifs. Since RNA-binding proteins typically show relatively relaxed binding specificities, it was hypothesized that an RNA component might be involved in recognition of these highly constrained motifs. This was bolstered by the finding that another motif common to the 3' UTRs of many of the same Notch pathway target genes, the GY box (uGUCUUCC), is complementary to and mediates RNA duplex formation through the proneural box (AUGGAAGACAAU), a motif located in the 3' UTRs of transcripts encoding proneural bHLH activators, (Lai, 2002).
Drosophila miRNAs encoded by 11 of 21 distinct genomic miRNA loci are complementary to the K box at their 5' end, with all but miR-11 having a perfect (8/8) antisense match to the extended K box consensus (UAUCACAG). Notably, the most 5' nucleotide of miR-11 is a cytosine residue, making it complementary to the second most common nucleotide at this position in identified K boxes. In addition, perfect antisense matches to the Brd box and GY box were found at the 5' ends of fly miR-4 and fly miR-7, respectively. The precise complementarity of these miRNAs to K box, Brd box and GY box motifs suggests that they bind these sequences in 3' UTRs and, in the case of the former two motifs, mediate negative post-transcriptional regulation. Complementarity between miRNAs and 3' UTRs extends beyond core sequence motifs in many cases, providing additional support for the existence of the proposed RNA duplexes. Examples exist of extended miRNA complementarity to 3' UTRs containing K boxes, Brd boxes and GY boxes. Complements to all three sequence motifs are located exclusively at the 5' ends of miRNA, suggesting that some aspect of regulation may be shared by these different miRNAs. For example, a common factor might be involved in the recognition or stabilization of these short miRNA-3' UTR duplexes (Lai, 2002).
Several miRNAs complementary to K boxes (miR-11 and the miR-2b and miR-13 subfamilies) are broadly expressed throughout Drosophila development, consistent with their proposed involvement in temporally ubiquitous regulation mediated by K boxes; the GY box-complementary miRNA miR-7 is similarly broadly expressed during development. The expression of the single identified Brd box-complementary miRNA miR-4 is restricted to embryogenesis. However, since the search for miRNAs has not yet been saturating, other miRNAs complementary to Brd boxes that are expressed later in development might yet be found (Lai, 2002).
The regulatory role of the K box and Brd box in other organisms has not yet been tested. Nevertheless, the presence of their complements in worm and human miRNAs suggests that these modes of regulation have potentially been conserved. Notably, the complements to these motifs are also located specifically at the 5' ends of miRNA. The restricted location of complements in these different species further suggests that the regulatory targets of many other miRNAs will be determined by the sequence of their 5' ends. In agreement with this idea, most of the known lin-4 and let-7 target sequences also involve perfect complements with the 5' ends of these miRNAs. Systematic searches for the complements of other 5' miRNA ends in 3' UTRs may therefore identify new post-transcriptional regulatory sequence elements. It should be noted, however, that despite the existence of three conserved sites in the lin-14 3' UTR that include perfect complements to lin-4, normal regulation of lin-14 actually depends on variant lin-4 binding sites containing a bulged nucleotide in the 5' complementary region. Thus, this rule is probably not absolute (Lai, 2002).
Initially, miRNAs are transcribed as RNAs of approximately 70 nt containing a stem-loop structure; these are cleaved by the RNAse III enzyme Dicer to generate the mature miRNA. Curiously, only a single strand of the duplex precursor stem structure is generally stable and is recovered as miRNA. The model proposed here may help to explain this phenomenon, since the strand that is complementary to these identified 3' UTR motifs is nearly exclusively the one that is isolated as miRNA. The single exception is miR-5, whose sequence contains a K box. Notably, miR-5 and the K box-complementary miRNAs miR-6-1,2,3 (whose loci are incidentally located next to each other in the genome) are complementary at 20 of 21 continuous nucleotide positions. This suggests that miR-5 might influence or possibly interfere with the ability of miR-6-1,2,3 to interact with 3' UTRs that contain K boxes (Lai, 2002).
Negative regulation by K box- and Brd box-complementary miRNA must differ from lin-4-mediated regulation, because K boxes and Brd boxes have significant, though distinct, effects on both transcript stability and translational efficiency, whereas lin-4 is thought to act at a step following translational initiation. The GY box does not seem to have a strong effect at the cis-regulatory level. Other miRNAs may show additional regulatory capacities; efforts are underway to understand the different molecular mechanisms of regulation mediated by miRNA-3' UTR RNA duplexes (Lai, 2002).
The possibility of protein-protein interactions between m4/alpha and a
number of potential cytoplasmic partners was tested using the yeast
two-hybrid system. Both Hairless and Su(H) are found in both
nucleus and the cytoplasm,
making such interactions feasible in vivo, yet neither one is
able to interact with either m4 or malpha in yeast.
No interactions were observed, not with an intracellular
fragment of Notch, NICN1, nor with the cytoplasmic factor Dx.
Another possibility tested was whether m4/alpha might interact with one another or with Brd. Brd LOF alleles do not
modify the overexpression phenotype of m4/alpha.
Furthermore, there is no synergy in bristle induction when
m4 is co-expressed with malpha; rather the number of ectopic
bristles is the same as with two copies of UAS-m4. Consistent with this is the inability of m4 and malpha to homo- or hetero-dimerize among themselves in the two-hybrid assay. Therefore, there is no genetic or molecular
evidence for interactions among M4, Malpha and Brd (Apidianakis, 1999).
Home page: The Interactive Fly © 1997 Thomas B. Brody, Ph.D.
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E(spl) region transcript m4:
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