Chromatin remodelling during development (original) (raw)
Kornberg, R. D. Chromatin structure: a repeating unit of histones and DNA. Science184, 868–871 (1974). ADSPubMedCAS Google Scholar
Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet.9, 465–476 (2008). ArticlePubMedCAS Google Scholar
Wang, Y. et al. Linking covalent histone modifications to epigenetics: the rigidity and plasticity of the marks. Cold Spring Harb. Symp. Quant. Biol.69, 161–169 (2004). ArticlePubMedCAS Google Scholar
Cote, J., Quinn, J., Workman, J. L. & Peterson, C. L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science265, 53–60 (1994). ArticleADSPubMedCAS Google Scholar
Schones, D. & Zhao, K. Genome-wide approaches to studying chromatin modifications. Nature Rev. Genet.9, 179–191 (2008). ArticlePubMedCAS Google Scholar
Deuring, R. et al. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo.Mol. Cell5, 355–365 (2000). ArticlePubMedCAS Google Scholar
Morrison, A. J. & Shen, X. Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. Nature Rev. Mol. Cell Biol.10, 373–384 (2009). ArticleCAS Google Scholar
Chi, T. Sequential roles of Brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity19, 169–182 (2003). ArticlePubMedCAS Google Scholar
Stankunas, K. et al. Endocardial Brg1 represses ADAMTS1 to maintain the microenvironment for myocardial morphogenesis. Dev. Cell14, 298–311 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Wu, J. et al. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron56, 94–108 (2007). ArticlePubMedCAS Google Scholar
Voncken, J. W. et al. Rnf2 (Ring1b) deficiency causes gastrulation arrest and cell cycle inhibition. Proc. Natl Acad. Sci. USA100, 2468–2473 (2003). ArticleADSPubMedCASPubMed Central Google Scholar
Kennison, J. A. & Tamkun, J. W. Dosage-dependent modifiers of polycomb and antennapedia mutations in Drosophila . Proc. Natl Acad. Sci. USA85, 8136–8140 (1988). ArticleADSPubMedCASPubMed Central Google Scholar
Chalkley, G. E. et al. The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex. Mol. Cell. Biol.28, 2920–2929 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Dingwall, A. K. et al. The Drosophila snr1 and brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. Mol. Biol. Cell6, 777–791 (1995). ArticlePubMedPubMed CentralCAS Google Scholar
Armstrong, J. A. et al. The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J.21, 5245–5254 (2002). ArticlePubMedPubMed CentralCAS Google Scholar
Shao, Z. et al. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell98, 37–46 (1999). ArticlePubMedCAS Google Scholar
Brown, E., Malakar, S. & Krebs, J. E. How many remodelers does it take to make a brain? Diverse and cooperative roles of ATP-dependent chromatin-remodeling complexes in development. Biochem. Cell Biol.85, 444–462 (2007). ArticlePubMedCAS Google Scholar
Wang, W. et al. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev.10, 2117–2130 (1996). ArticlePubMedCAS Google Scholar
Lessard, J. et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron55, 201–215 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Bultman, S. et al. A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol. Cell6, 1287–1295 (2000). ArticlePubMedCAS Google Scholar
Reyes, J. C. et al. Altered control of cellular proliferation in the absence of mammalian brahma (SNF2α). EMBO J.17, 6979–6991 (1998). ArticlePubMedPubMed CentralCAS Google Scholar
Yan, Z. et al. BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells26, 1155–1165 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl Acad. Sci. USA106, 5181–5186 (2009). ArticleADSPubMedPubMed Central Google Scholar
Kidder, B. L., Palmer, S. & Knott, J. G. SWI/SNF–Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. Stem Cells27, 317–328 (2008). ArticleCAS Google Scholar
Gao, X. et al. ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proc. Natl Acad. Sci. USA105, 6656–6661 (2008). ArticleADSPubMedPubMed Central Google Scholar
Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc. Natl Acad. Sci. USA106, 5187–5191 (2009). ArticleADSPubMedPubMed Central Google Scholar
Hansis, C., Barreto, G., Maltry, N. & Niehrs, C. Nuclear reprogramming of human somatic cells by Xenopus egg extract requires BRG1. Curr. Biol.14, 1475–1480 (2004). ArticlePubMedCAS Google Scholar
Klochendler-Yeivin, A. et al. The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression. EMBO Rep.1, 500–506 (2000). ArticlePubMedPubMed CentralCAS Google Scholar
Kim, J. K. et al. Srg3, a mouse homolog of yeast SWI3, is essential for early embryogenesis and involved in brain development. Mol. Cell Biol.21, 7787–7795 (2001). ArticlePubMedPubMed CentralCAS Google Scholar
Schaniel, C. et al. Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells doi:10.1002/stem.223 (25 September 2009). ArticlePubMedPubMed CentralCAS Google Scholar
Parrish, J. Z., Kim, M. D., Jan, L. Y. & Jan, Y. N. Genome-wide analyses identify transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites. Genes Dev.20, 820–835 (2006). ArticlePubMedPubMed CentralCAS Google Scholar
Yoo, A. S., Staahl, B. T., Chen, L. & Crabtree, G. R. MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature460, 642–646 (2009). ArticleADSPubMedPubMed CentralCAS Google Scholar
Lange, M. et al. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev.22, 2370–2384 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Lickert, H. et al. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature432, 107–112 (2004). ArticleADSPubMedCAS Google Scholar
Takeuchi, J. K. et al. Baf60c is a nuclear Notch signaling component required for the establishment of left–right asymmetry. Proc. Natl Acad. Sci. USA104, 846–851 (2007). ArticleADSPubMedCASPubMed Central Google Scholar
Takeuchi, J. K. & Bruneau, B. G. Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors. Nature459, 708–711 (2009). This study showed that BAF60C, together with two cardiogenic transcription factors (GATA4 and TBX5), is sufficient to direct heart formation in non-cardiogenic tissues in developing embyros, demonstrating that chromatin remodelling by specific BAF complexes can be both necessary and sufficient for specific fate induction. ArticleADSPubMedPubMed CentralCAS Google Scholar
Huang, X., Gao, X., Diaz-Trelles, R., Ruiz-Lozano, P. & Wang, Z. Coronary development is regulated by ATP-dependent SWI/SNF chromatin remodeling component BAF180. Dev. Biol.319, 258–266 (2008). ArticlePubMedCAS Google Scholar
Sawada, S., Scarborough, J. D., Killeen, N. & Littman, D. R. A lineage-specific transcriptional silencer regulates CD4 gene expression during T lymphocyte development. Cell77, 917–929 (1994). ArticlePubMedCAS Google Scholar
Wan, M. et al. Molecular basis of CD4 repression by the Swi/Snf-like BAF chromatin remodeling complex. Eur. J. Immunol.39, 580–588 (2009). ArticlePubMedPubMed CentralCAS Google Scholar
Chi, T. H. et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature418, 195–199 (2002). ArticleADSPubMedCAS Google Scholar
Cosma, M. P., Tanaka, T. & Nasmyth, K. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell97, 299–311 (1999). ArticlePubMedCAS Google Scholar
Khavari, P. A., Peterson, C. L., Tamkun, J. W., Mendel, D. B. & Crabtree, G. R. BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription. Nature366, 170–174 (1993). ArticleADSPubMedCAS Google Scholar
de la Serna, I. L., Carlson, K. A. & Imbalzano, A. N. Mammalian SWI/SNF complexes promote MyoD-mediated muscle differentiation. Nature Genet.27, 187–190 (2001). ArticlePubMedCAS Google Scholar
Dirscherl, S. S. & Krebs, J. E. Functional diversity of ISWI complexes. Biochem. Cell Biol.82, 482–489 (2004). ArticlePubMedCAS Google Scholar
Siriaco, G., Deuring, R., Chioda, M., Becker, P. B. & Tamkun, J. W. Drosophila ISWI regulates the association of histone H1 with interphase chromosomes in vivo.Genetics182, 661–669 (2009). ArticlePubMedPubMed CentralCAS Google Scholar
Xi, R. & Xie, T. Stem cell self-renewal controlled by chromatin remodeling factors. Science310, 1487–1489 (2005). ArticleADSPubMedCAS Google Scholar
Badenhorst, P., Voas, M., Rebay, I. & Wu, C. Biological functions of the ISWI chromatin remodeling complex NURF. Genes Dev.16, 3186–3198 (2002). ArticlePubMedPubMed CentralCAS Google Scholar
Landry, J. et al. Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet.4, e1000241 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Banting, G. S. et al. CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L. Hum. Mol. Genet.14, 513–524 (2005). ArticlePubMedCAS Google Scholar
Stopka, T. & Skoultchi, A. I. The, ISWI ATPase Snf2h is required for early mouse development. Proc. Natl Acad. Sci. USA100, 14097–14102 (2003). ArticleADSPubMedCASPubMed Central Google Scholar
Francke, U. Williams–Beuren syndrome: genes and mechanisms. Hum. Mol. Genet.8, 1947–1954 (1999). ArticlePubMedCAS Google Scholar
Yoshimura, K. et al. Distinct function of 2 chromatin remodeling complexes that share a common subunit, Williams syndrome transcription factor (WSTF). Proc. Natl Acad. Sci. USA106, 9280–9285 (2009). ArticleADSPubMedPubMed Central Google Scholar
Hall, J. A. & Georgel, P. T. CHD proteins: a diverse family with strong ties. Biochem. Cell Biol.85, 463–476 (2007). ArticlePubMedCAS Google Scholar
Flanagan, J. F. et al. Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature438, 1181–1185 (2005). ArticleADSPubMedCAS Google Scholar
Sims, R. J. et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell28, 665–676 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
McDaniel, I. E., Lee, J. M., Berger, M. S., Hanagami, C. K. & Armstrong, J. A. Investigations of CHD1 function in transcription and development of Drosophila melanogaster . Genetics178, 583–587 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Konev, A. Y. et al. CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo.Science317, 1087–1090 (2007). This was the first study to show the ability of CHD1 to incorporate H3.3 into paternal chromatin, rendering it competent for post-fertilization mitosis, possibly explaining the sterility of CHD1-deficientD. melanogaster. ArticleADSPubMedPubMed CentralCAS Google Scholar
Hödl, M. & Basler, K. Transcription in the absence of histone H3.3. Curr. Biol.19, 1221–1226 (2009). ArticlePubMedCAS Google Scholar
Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature460, 802–803 (2009). ArticleCAS Google Scholar
Zhang, Y., LeRoy, G., Seelig, H. P., Lane, W. S. & Reinberg, D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell95, 279–289 (1998). ArticlePubMedCAS Google Scholar
Bowen, N. J., Fujita, N., Kajita, M. & Wade, P. A. Mi-2/NuRD: multiple complexes for many purposes. Biochim. Biophys. Acta1677, 52–57 (2004). ArticlePubMedCAS Google Scholar
Feng, Q. & Zhang, Y. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes. Genes Dev.15, 827–832 (2001). PubMedPubMed CentralCAS Google Scholar
Denslow, S. A. & Wade, P. A. The human Mi-2/NuRD complex and gene regulation. Oncogene26, 5433–5438 (2007). ArticlePubMedCAS Google Scholar
Kaji, K., Nichols, J. & Hendrich, B. Mbd3, a component of the NuRD co-repressor complex, is required for development of pluripotent cells. Development134, 1123–1132 (2007). ArticlePubMedCAS Google Scholar
Kaji, K. et al. The NuRD component Mbd3 is required for pluripotency of embryonic stem cells. Nature Cell Biol.8, 285–292 (2006). ArticlePubMedCAS Google Scholar
Williams, C. J. et al. The chromatin remodeler Mi-2β is required for CD4 expression and T cell development. Immunity20, 719–733 (2004). ArticlePubMedCAS Google Scholar
Yoshida, T. et al. The role of the chromatin remodeler Mi-2β in hematopoietic stem cell self-renewal and multilineage differentiation. Genes Dev.22, 1174–1189 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Vissers, L. E. et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nature Genet.36, 955–957 (2004). ArticlePubMedCAS Google Scholar
Hurd, E. A. et al. Loss of Chd7 function in gene-trapped reporter mice is embryonic lethal and associated with severe defects in multiple developing tissues. Mamm. Genome18, 94–104 (2007). ArticlePubMedCAS Google Scholar
Srinivasan, S., Dorighi, K. M. & Tamkun, J. W. Drosophila Kismet regulates histone H3 lysine 27 methylation and early elongation by RNA polymerase II. PLoS Genet.4, e1000217 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Mizuguchi, G. et al. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science303, 343–348 (2004). ArticleADSPubMedCAS Google Scholar
Ruhl, D. D. et al. Purification of a human SRCAP complex that remodels chromatin by incorporating the histone variant H2A.Z into nucleosomes. Biochemistry45, 5671–5677 (2006). ArticlePubMedCAS Google Scholar
Wong, M. M., Cox, L. K. & Chrivia, J. C. The chromatin remodeling protein, SRCAP, is critical for deposition of the histone variant H2A.Z at promoters. J. Biol. Chem.282, 26132–26139 (2007). ArticlePubMedCAS Google Scholar
Creyghton, M. P. et al. H2AZ is enriched at Polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell135, 649–661 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Sapountzi, V., Logan, I. R. & Robson, C. N. Cellular functions of TIP60. Int. J. Biochem. Cell Biol.38, 1496–1509 (2006). ArticlePubMedCAS Google Scholar
Herceg, Z. et al. Disruption of Trrap causes early embryonic lethality and defects in cell cycle progression. Nature Genet.29, 206–211 (2001). ArticlePubMedCAS Google Scholar
Fazzio, T. G., Huff, J. T. & Panning, B. An RNAi screen of chromatin proteins identifies Tip60−p400 as a regulator of embryonic stem cell identity. Cell134, 162–174 (2008). This paper reports an RNAi screen of mouse ESCs for chromatin proteins that are crucial for pluripotency and self-renewal. Two major classes of remodeller, TIP60-p400 and BAF complexes, were found to be essential. ArticlePubMedPubMed CentralCAS Google Scholar
Lanctot, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Rev. Genet.8, 104–115 (2007). ArticlePubMedCAS Google Scholar
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science295, 1306–1311 (2002). ArticleADSPubMedCAS Google Scholar
de La Serna, I. L., Ohkawa, Y. & Imbalzano, A. N. Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers. Nature Rev. Genet.7, 461–473 (2006). ArticlePubMedCAS Google Scholar
Pedersen, T. A., Kowenz- Leutz, E., Leutz, A. & Nerlov, C. Cooperation between C/EBPα TBP/TFIIB and SWI/SNF recruiting domains is required for adipocyte differentiation. Genes Dev.15, 3208–3216 (2001). ArticlePubMedPubMed CentralCAS Google Scholar
Bultman, S. J., Gebuhr, T. C. & Magnuson, T. A Brg1 mutation that uncouples ATPase activity from chromatin remodeling reveals an essential role for SWI/SNF-related complexes in β-globin expression and erythroid development. Genes Dev.19, 2849–2861 (2005). ArticlePubMedPubMed CentralCAS Google Scholar
Kaeser, M. D., Aslanian, A., Dong, M. Q., Yates, J. R. & Emerson, B. M. BRD7, a novel PBAF-specific SWI/SNF subunit, is required for target gene activation and repression in embryonic stem cells. J. Biol. Chem.283, 32254–32263 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Marfella, C. G. et al. Mutation of the SNF2 family member Chd2 affects mouse development and survival. J. Cell. Physiol.209, 162–171 (2006). ArticlePubMedCAS Google Scholar
White, P. S. et al. Definition and characterization of a region of 1p36.3 consistently deleted in neuroblastoma. Oncogene24, 2684–2694 (2005). ArticlePubMedCAS Google Scholar
Layman, W. S. et al. Defects in neural stem cell proliferation and olfaction in Chd7 deficient mice indicate a mechanism for hyposmia in human CHARGE syndrome. Hum. Mol. Genet.18, 1909–1923 (2009). ArticlePubMedPubMed CentralCAS Google Scholar
Shur, I., Socher, R.,& Benayahu, D. In vivo association of CReMM/CHD9 with promoters in osteogenic cells. J. Cell. Physiol.207, 374–378 (2006). ArticlePubMedCAS Google Scholar
Toh, Y. & Nicolson, G. L. The role of the MTA family and their encoded proteins in human cancers: molecular functions and clinical implications. Clin. Exp. Metastasis26, 215–227 (2009). ArticlePubMedCAS Google Scholar