Chromatin assembly factor 1 subunit


p55 is observed mainly in the nuclei of syncytial blastoderm embryos (nuclear cycle 13) in both S or M phases. After cellularization, p55 appears to be nuclear except during M phase, in which it is present throughout the cell, possibly as a consequence of the partial breakdown of the nuclear envelope during mitosis. The level of p55 is highest during early embryogenesis and then decreases by a factor of approximately 10 in larvae, pupae, and adults. The amount of protein present in early embryos corresponds to about 220,000 molecules per nucleus, based on an estimated average of 12,000 nuclei per embryo. Thus p55 is a relatively abundant protein (Tyler, 1996).

Effects of Mutation or RNAI

Many proteins have been proposed to be involved in retinoblastoma protein (pRB)-mediated repression, but it is largely uncertain which cofactors are essential for pRB to repress endogenous E2F-regulated promoters. Advantage was taken of the stream-lined Drosophila dE2F/RBF pathway, which has only two E2Fs (dE2F1 and dE2F2), and two pRB family members (RBF1 and RBF2). With RNA interference (RNAi), potential corepressors were depleted and the elevated expression of groups of E2F target genes that are known to be directly regulated by RBF1 and RBF2 was sought. Previous studies have implicated histone deacetylase (HDAC) and SWI/SNF chromatin-modifying complexes in pRB-mediated repression. However, the results fail to support the idea that the SWI/SNF proteins are required for RBF-mediated repression and suggest that a requirement for HDAC activities is likely to be limited to a subset of targets. The chromatin assembly factor p55/dCAF-1 is essential for the repression of dE2F2-regulated targets. The removal of p55 deregulates the expression of E2F targets that are normally repressed by dE2F2/RBF1 and dE2F2/RBF2 complexes in a cell cycle-independent manner but has no effect on the expression of E2F targets that are normally coupled with cell proliferation. The results indicate that the mechanisms of RBF regulation at these two types of E2F targets are different and suggest that p55, and perhaps p55's mammalian orthologs RbAp46 and RbAp48, have a conserved function in repression by pRB-related proteins (Taylor-Harding, 2004).

Caf1 was identified in a genome-wide analyses for transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites

Dendrite arborization patterns are critical determinants of neuronal function. To explore the basis of transcriptional regulation in dendrite pattern formation, RNA interference (RNAi) was used to screen 730 transcriptional regulators and 78 genes involved in patterning the stereotyped dendritic arbors of class I da neurons were identified in Drosophila. Most of these transcriptional regulators affect dendrite morphology without altering the number of class I dendrite arborization (da) neurons and fall primarily into three groups. Group A genes control both primary dendrite extension and lateral branching, hence the overall dendritic field. Nineteen genes within group A act to increase arborization, whereas 20 other genes restrict dendritic coverage. Group B genes appear to balance dendritic outgrowth and branching. Nineteen group B genes function to promote branching rather than outgrowth, and two others have the opposite effects. Finally, 10 group C genes are critical for the routing of the dendritic arbors of individual class I da neurons. Thus, multiple genetic programs operate to calibrate dendritic coverage, to coordinate the elaboration of primary versus secondary branches, and to lay out these dendritic branches in the proper orientation (Parrish, 2006; Full text of article).

To assay for the stereotyped dendrite arborization pattern of class I da neurons (hereafter referred to as class I neurons) in RNAi-based analysis of dendrite development, a Gal4 enhancer trap line (Gal4221) was used that is highly expressed in class I neurons and weakly expressed in class IV neurons during embryogenesis. Because of the simple and stereotyped dendritic arborization patterns of the dorsally located ddaD and ddaE, the studies of dendrite development focused on these two dorsally located class I neurons (Parrish, 2006).

To establish that RNAi is an efficient method to systematically study dendrite development in the Drosophila embryonic PNS, it was demonstrated that injecting embryos with double-stranded RNA (dsRNA) for green fluorescent protein (gfp) is sufficient to attenuate Gal-4221-driven expression of an mCD8::GFP fusion protein as measured by confocal microscopy. Next whether RNAi could efficiently phenocopy loss-of-function mutants known to affect dendrite development was tested. Similar to the mutant phenotype of short stop (shot), which encodes an actin/microtubule cross-linking protein, shot(RNAi) caused routing defects, dorsal overextension, and a reduction in lateral branching of dorsally extended primary dendrites. Likewise, RNAi of sequoia or flamingo resulted in overextension of ddaD and ddaE, RNAi of hamlet resulted in supernumerary class I neurons, and RNAi of tumbleweed resulted in supernumerary class I neurons and a range of arborization defects, consistent with the reported mutant phenotypes. Thus, RNAi is effective in generating reduction of function phenotypes in embryonic class I dendrites (Parrish, 2006).

RNAi of the Polycomb group (PcG) genes Su(z)12, E(z), esc, or Caf1 similarly caused an increase in branch number and an expansion of the receptive field of class I neurons. Consistent with the similar RNAi phenotypes for these genes, Su(z)12, E(z), esc, and Caf1 are components of the multiprotein esc/E(z) polycomb repressor complex. One critical role for PcG-mediated gene silencing is the regulation of hox gene expression. Therefore, Polycomb-mediated regulation of hox gene expression likely contributes to arborization of class I neurons (Parrish, 2006).

The biological function of the WD40 repeat-containing protein p55/Caf1 in Drosophila

The p55 family WD40 repeat-containing histone chaperone proteins are components of several chromatin regulatory complexes (such as PRC2, NURF and CAF-1) and interact with histone H4, yet their functional relevance in vivo is unclear. This study used Drosophila as a genetic model to dissect the function of p55/Caf1 during development. In agree with a recent report, this study found that p55 is essential for Drosophila development and is required for cell proliferation and viability. However, the data further demonstrate that histone H3K27 di-/tri-methylation and PRC2-mediated gene silencing still occur normally when p55 is missing. p55 is also implicated in bridging chromatin regulatory complexes to the chromatin by binding to histone H4, but it was found that a transgene of p55 whose binding pocket is disrupted could still functionally substitute the wild-type p55 for survival. These studies suggest that p55 is not crucial for PRC2-mediated gene silencing in vivo, and the vital function of p55 is probably not dependent on its interaction with histone H4 (Wen, 2012).


Anderson, A. E., et al. (2011). The enhancer of trithorax and polycomb gene Caf1/p55 is essential for cell survival and patterning in Drosophila development. Development 138: 1957-1966. PubMed Citation: 21558377

Bannister, A. J. and Kouzarides, T. (1996). The CBP co-activator is a histone acetyltransferase. Nature 384 (6610): 641-643. PubMed Citation: 8967953

Beall, E. L., et al. (2007). Discovery of tMAC: a Drosophila testis-specific meiotic arrest complex paralogous to Myb-Muv B. Genes Dev. 21: 904-919. Medline abstract: 17403774

Blanco, J. C. G., et al. (1998). The histone acetylase PCAF is a nuclear receptor coactivator. Genes Dev. 12: 1638-1651. PubMed Citation: 9620851

Brownell, J. E., et al. (1996). Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84: 843-851. PubMed Citation: 8601308

Bulger, M., et al. (1995). Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein. Proc Natl Acad Sci 92: 11726-11730. PubMed Citation: 8524837

Candau, R., et al. (1997). Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo. EMBO J 16 (3): 555-565. PubMed Citation: 9034338

Chang, L., et al. (1997). Histones in transit: cytosolic histone complexes and diacetylation of H4 during nucleosome assembly in human cells. Biochemistry 36 (3): 469-480. PubMed Citation: 9012662

Chiang, Y. C., et al. (1996). ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J Biol Chem 271 (50): 32359-32365. PubMed Citation: 8943299

Czermin, B., et al. (2002). Drosophila Enhancer of Zeste/Esc complexes have a histone H3 methyltransferase activity that marks chromosomal polycomb sites. Cell 111: 185-196. 12408863

Dhalluin, C., et al. (1999). Structure and ligand of a histone acetyltransferase bromodomain. Nature 398(6735): 491-6. PubMed Citation: 10365964

Dutnall, R. N., et al. (1998). Structure of the histone acetyltransferase Hat1: a paradigm for the GCN5-related N-acetyltransferase superfamily. Cell 94(4): 427-438. PubMed Citation: 9727486

Enomoto, S., et al. (1997). RLF2, a subunit of yeast chromatin assembly factor-I, is required for telomeric chromatin function in vivo. Genes Dev 11 (3): 358-370. PubMed Citation: 9030688

Enomoto, S. and Berman, J. (1998). Chromatin assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Genes Dev. 12: 219-232. PubMed Citation: 9436982

Furuyama, T., Tie, F. and Harte, P. J. (2003). Polycomb group proteins ESC and E(Z) are present in multiple distinct complexes that undergo dynamic changes during development. Genesis 35(2): 114-24. 12533794

Furuyama, T., Dalal, Y. and Henikoff, S. (2006a). Chaperone-mediated assembly of centromeric chromatin in vitro. Proc. Natl. Acad. Sci. 103(16): 6172-7. Medline abstract: 16601098

Furuyama, T. and Henikoff, S. (2006b). Biotin-tag affinity purification of a centromeric nucleosome assembly complex. Cell Cycle 5(12): 1269-74. Medline abstract: 16775420

Gaillard, P. H., et al. (1996). Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86 (6): 887-896. PubMed Citation: 8808624

Herrera, J. E., et al. (1997). The histone acetyltransferase activity of human GCN5 and PCAF is stabilized by coenzymes. J. Biol. Chem. 272(43): 27253-27258. PubMed Citation: 9341171

Hochheimer, A., et al. (2002). TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420(6914): 439-45. 12459787

Ito, T., et al. (1997). ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90(1): 145-155. PubMed Citation: 9230310

Ito, T., et al. (1999). ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13: 1529-1539. PubMed Citation: 10385622

Jin, S. G., Jiang, C. L., Rauch, T., Li, H. and Pfeifer, G. P. (2005). MBD3L2 interacts with MBD3 and components of the NuRD complex and can oppose MBD2-MeCP1-mediated methylation silencing. J. Biol. Chem. 280(13): 12700-9. 15701600

Kamakaka, R. T., et al. (1996). Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol. Cell. Biol. 16: 810-817. PubMed Citation: 8622682

Kaufman, P. D., et al. (1995). The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell 81: 1105-1114. PubMed Citation: 7600578

Kaufman, P. D (1996). Nucleosome assembly: the CAF and the HAT. Curr Opin Cell Biol 8 (3): 369-373. PubMed Citation: 8743889

Kaufman, P. D., Kobayashi, R. and Stillman, B. (1997). Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev. 11 (3): 345-357. PubMed Citation: 9030687

Ketel, C. S., et al. (2005). Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes. Mol. Cell. Biol. 25: 6857-6868. 16055700

Kleff, S., et al. (1995). Identification of a gene encoding a yeast histone H4 acetyltransferase. J. Biol. Chem. 270: 24674-77. PubMed Citation: 7559580

Korenjak, M., et al. (2004). Native E2F/RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes. Cell 119(2): 181-93. 15479636

Krude, T. and Knippers, R. (1993). Nucleosome assembly during complementary DNA strand synthesis in extracts from mammalian cells. J Biol Chem 268: 14432-42

Krude, T. (1995). Chromatin assembly factor 1 (CAF-1) colocalizes with replication foci in HeLa cell nuclei. Exp Cell Res 220 (2): 304-311

Krude, T. (1995). Chromatin. Nucleosome assembly during DNA replication. Curr Biol 5: 1232-1234

Kuo, M. H., et al. (1996). Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature 383 (6597): 269-272

Kuzmichev, A., et al. (2002). Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16: 2893-2905. 12435631

Li-Kroeger, D., Witt, L. M., Grimes, H. L., Cook, T. A. and Gebelein, B. (2008). Hox and senseless antagonism functions as a molecular switch to regulate EGF secretion in the Drosophila PNS. Dev. Cell 15(2): 298-308. PubMed Citation: 18694568

Marheineke, K. and Krude, T. (1998). Nucleosome assembly activity and intracellular localization of human CAF-1 changes during the cell division cycle. J Biol Chem 273(24): 15279-86

Martinez-Balbás, M. A., Tsukiyama, T., Gdula, D., Wu, C. (1998). Drosophila NURF-55, a WD repeat protein involved in histone metabolism. Proc. Natl. Acad. Sci. 95(1): 132-137. 9419341

Mizzen, C. A., et al. (1996). The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell 87 (7): 1261-1270

Monson, E. K., de Bruin, D. and Zakian, V. A. (1997). The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc. Natl. Acad. Sci. 94(24): 13081-6

Munshi, N., et al. (1998). Acetylation of HMG I(Y) by CBP turns off IFN beta expression by disrupting the enhanceosome. Mol. Cell 2(4): 457-67

Nekrasov, M., Wild, B. and Müller, J. (2005). Nucleosome binding and histone methyltransferase activity of Drosophila PRC2. EMBO Rep. 6(4): 348-53. PubMed Citation: 15776017

Ogryzko, V. V., et al. (1996). The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87 (5): 953-959

Parrish, J. Z., Kim, M. D., Jan, L. Y. and Jan, Y. N. (2006). Genome-wide analyses identify transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites. Genes Dev. 20(7): 820-35. Medline abstract: 16547170

Parthun, M. R., Widom, J. and Gottschling, D. E. (1996). The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism. Cell 87 (1): 85-94

Ray-Gallet, D., Woolfe, A., Vassias, I., Pellentz, C., Lacoste, N., Puri, A., Schultz, D. C., Pchelintsev, N. A., Adams, P. D., Jansen, L. E. and Almouzni, G. (2011). Dynamics of histone H3 deposition in vivo reveal a nucleosome gap-filling mechanism for H3.3 to maintain chromatin integrity. Mol Cell 44: 928-941. PubMed ID: 22195966

Richman, R., et al. (1998). Micronuclei and the cytoplasm of growing Tetrahymena contain a histone acetylase activity which is highly specific for free histone H4. J. Cell Biol. 106(4): 1017-26. 88198345

Reid, J. L., et al. (1998). E1A directly binds and regulates the P/CAF acetyltransferase. EMBO J. 17: 4469-4477. 9687513

Roth, S. Y. and Allis, C. D. (1996). Histone acetylation and chromatin assembly: a single escort, multiple dances? Cell 87: 5-8

Schmitges, F. W., et al. (2011). Histone methylation by PRC2 is inhibited by active chromatin marks. Mol. Cell 42(3): 330-41. PubMed Citation: 21549310

Sharp, J. A., et al. (2001). Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr. Biol. 11: 463-473

Shibahara, K. and Stillman, B. (1999). Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell 96(4): 575-85

Smith, S. and Stillman, G. (1991). Stepwise assembly of chromatin during DNA replication in vitro. EMBO J 10: 971-80

Sobel, R. E., Cook, R. G. and Allis, C. D. (1994). Non-random acetylation of histone H4 by a cytoplasmic histone acetyltransferase as determined by a novel methodology. J. Biol. Chem. 269: 18576-82

Sobel, R. E., et al. (1995). Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl. Acad. Sci. 92: 1237-41

Solari, F. and Ahringer, J. (2000). NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans. Curr. Biol. 10(4): 223-6.

Song, J. J., Garlick, J. D. and Kingston, R. E. (2008). Structural basis of histone H4 recognition by p55. Genes Dev. 22: 1313-1318. PubMed Citation: 18443147

Stephens, G. E., Xiao, H., Lankenau, D. H., Wu, C. and Elgin, S. C. (2006). Heterochromatin protein 2 interacts with Nap-1 and NURF: a link between heterochromatin-induced gene silencing and the chromatin remodeling machinery in Drosophila. Biochemistry 45: 14990-14999. PubMed ID: 17154536

Taunton, J., Hassig, C. A. and Schreiber, S. L. (1996). A mammalian histone deacetylase related to the yeast transcriptional regulator Rpb3p. Science 272: 408-411

Tie, F., et al. (2001). The Drosophila Polycomb Group proteins ESC and E(Z) are present in a complex containing the histone-binding protein p55 and the histone deacetylase RPD3. Development 128: 275-286. 11124122

Taylor-Harding, B., Binne, U. K., Korenjak, M., Brehm, A. and Dyson, N. J. (2004). p55, the Drosophila ortholog of RbAp46/RbAp48, is required for the repression of dE2F2/RBF-related genes. Mol. Cell. Biol. 24: 9124-9136. 15456884

Tursun, B., Patel, T., Kratsios, P. and Hobert, O. (2011). Direct conversion of C. elegans germ cells into specific neuron types. Science 331: 304-308. Pubmed: 21148348

Tyler, J. K., et al. (1996). The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase-associated protein. Mol Cell Biol 16 (11): 6149-6159. PubMed Citation: 8887645

Tyler, J. K., et al. (1999). The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402: 555-560. 10591219

Tyler, J. K., et al. (2001). Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol. Cell. Bio. 21: 6574-6584. 11533245

Vermaak, D., et al. (1999). Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol. Cell Biol. 19(9): 5847-60

Verreault, A., et al. (1996). Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87 (1): 95-104

Verreault, A., et al. (1998). Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr. Biol. 8(2): 96-108. 98089172

Wang, L., et al. (1997). Histone acetyltransferase activity is conserved between yeast and human GCN5 and is required for complementation of growth and transcriptional activation. Mol Cell Biol 17 (1): 519-527. PubMed ID: 8972232

Wen, P., Quan, Z. and Xi, R. (2012). The biological function of the WD40 repeat-containing protein p55/Caf1 in Drosophila. Dev Dyn 241: 455-464. PubMed ID: 22241697

Xu, W., Edmondson, D. G. and Roth, S. Y. (1998). Mammalian GCN5 and P/CAF acetyltransferases have homologous amino-terminal domains important for recognition of nucleosomal substrates. Mol. Cell. Biol. 18(10): 5659-5669. PubMed ID: 9742083

Zhang, Y., et al. (1998). SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex. Mol. Cell 1(7): 1021-31. PubMed ID: 9651585

Zhang, Z., Shibahara, K. and Stillman, B. (2000). PCNA connects DNA replication to epigenetic inheritance in yeast. Nature 408(6809): 221-5. PubMed ID: 11089978

Chromatin assembly factor 1 subunit: Biological Overview | Evolutionary Homologs | Regulation | Developmental Biology | Effects of RNAi

date revised: 10 August 2013 

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