The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Chromatin dynamics: Interplay between remodeling enzymes and histone modifications
Open accessAbstract
Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure and ligand of a histone acetyltransferase bromodomain
Dhalluin, C., Carlson, J. E., Zeng, L., He, C., Aggarwal, A. K., Zhou, M.-M., & Zhou, M.-M. (1999) · Nature · doi:10.1038/20974 · Cited by 1,732
Zhang, Y., Ng, H.-H., Erdjument-Bromage, H., Tempst, P., Bird, A., & Reinberg, D. (1999) · Genes & Development · doi:10.1101/gad.13.15.1924 · Cited by 1,103
Regulation of nucleosome dynamics by histone modifications
Zentner, G. E., & Henikoff, S. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2470 · Cited by 923 · cited 6×
“Common modifications include lysine acetylation, the mono-, di-, or trimethylation of lysines, mono- or di-methylation of arginines, the phosphorylation of serines, threonines, or tyrosines, as well as lysine ubiquitylation and SUMOylation [6].”
BackgroundMethodInfluentialChromatin deacetylation by an ATP-dependent nucleosome remodelling complex
Tong, J. K., Hassig, C. A., Schnitzler, G. R., Kingston, R. E., & Schreiber, S. L. (1998) · Nature · doi:10.1038/27699 · Cited by 692
Chromatin Higher-order Structure and Dynamics
Woodcock, C. L., & Ghosh, R. P. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000596 · Cited by 384
Screen for DNA‐damage‐responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells
Tjeertes, J. V., Miller, K. M., & Jackson, S. P. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.119 · Cited by 347
Rufiange, A., Jacques, P.-É., Bhat, W., Robert, F., & Nourani, A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.011 · Cited by 313
Cell cycle-regulated histone acetylation required for expression of the yeast HO gene
Krebs, J. E., Kuo, M.-H., Allis, C. D., & Peterson, C. L. (1999) · Genes & Development · doi:10.1101/gad.13.11.1412 · Cited by 275
Self-citationChromatin and Transcription in Yeast
Rando, O. J., & Winston, F. (2012) · Genetics · doi:10.1534/genetics.111.132266 · Cited by 269
Reynolds, N., Latos, P., Hynes-Allen, A., Loos, R., Leaford, D., O'Shaughnessy, A., Mosaku, O., Signolet, J., Brennecke, P., Kalkan, T., et al. (2012) · Cell Stem Cell · doi:10.1016/j.stem.2012.02.020 · Cited by 236 · cited 1×
“For example, the DrosophilaNuRD complex is recruited by the hunchback (Hb) repressor to repress HOX gene transcription [71], and mammalian NuRD complexes interact with a variety of transcriptional repressors to regulate lineage commitment and differentiation of specific cell types [72–74].”
Background
Research works printed but not linked: 137
- Hargreaves, 2011, ATP-dependent chromatin remodeling: genetics, genomics and mechanisms, Cell Res., 21, 396, 10.1038/cr.2011.32 · DOI · Paper page
- Luger, 1997, Crystal structure of the nucleosome core particle at 2.8Å resolution, Nature, 389, 251, 10.1038/38444 · DOI · Paper page
- Shogren-Knaak, 2006, Histone H4-K16 acetylation controls chromatin structure and protein interactions, Science, 311, 844, 10.1126/science.1124000 · DOI · Paper page
- Fierz, 2011, Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction, Nat. Chem. Biol., 7, 1, 10.1038/nchembio.501 · DOI · Paper page
- Patel, 2013, Readout of epigenetic modifications, Annu. Rev. Biochem., 82, 81, 10.1146/annurev-biochem-072711-165700 · DOI · Paper page
- Papamichos-Chronakis, 2013, Chromatin and the genome integrity network, Nat. Rev. Genet., 14, 62, 10.1038/nrg3345 · DOI · Paper page
- Clapier, 2009, The biology of chromatin remodeling complexes, Annu. Rev. Biochem., 78, 273, 10.1146/annurev.biochem.77.062706.153223 · DOI · Paper page
- Boyer, 2000, Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes, J. Biol. Chem., 275, 18864, 10.1074/jbc.M002810200 · DOI
- Allfrey, 1964, Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis, Proc. Natl. Acad. Sci. U. S. A., 51, 786, 10.1073/pnas.51.5.786 · DOI · Paper page
- Pogo, 1966, RNA synthesis and histone acetylation during the course of gene activation in lymphocytes, Proc. Natl. Acad. Sci. U. S. A., 55, 805, 10.1073/pnas.55.4.805 · DOI · Paper page
- Vidali, 1978, Butyrate suppression of histone deacetylation leads to accumulation of multiacetylated forms of histones H3 and H4 and increased DNase I sensitivity of the associated DNA sequences, Proc. Natl. Acad. Sci. U. S. A., 75, 2239, 10.1073/pnas.75.5.2239 · DOI · Paper page
- Tse, 1998, Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA Polymerase III, Mol. Cell. Biol., 18, 4629, 10.1128/MCB.18.8.4629 · DOI · Paper page
- Ferreira, 2007, Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms, J. Mol. Biol., 374, 563, 10.1016/j.jmb.2007.09.059 · DOI
- Watanabe, 2010, Structural characterization of H3K56Q nucleosomes and nucleosomal arrays, Biochim. Biophys. Acta, 1799, 480, 10.1016/j.bbagrm.2010.01.009 · DOI
- Neumann, 2009, A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation, Mol. Cell, 36, 153, 10.1016/j.molcel.2009.07.027 · DOI · Paper page
- Horn, 2001, The bromodomain: a regulator of ATP-dependent chromatin remodeling?, Front. Biosci., 6, D1019, 10.2741/Horn · DOI
- Owen, 2000, The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p, EMBO J., 19, 6141, 10.1093/emboj/19.22.6141 · DOI · Paper page
- Haynes, 1992, The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins, Nucleic Acids Res., 20, 2603, 10.1093/nar/20.10.2603 · DOI · Paper page
- Tamkun, 1992, Brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2, Cell, 68, 561, 10.1016/0092-8674(92)90191-E · DOI · Paper page
- Jeanmougin, 1997, The bromodomain revisited, Trends Biochem. Sci., 22, 151, 10.1016/S0968-0004(97)01042-6 · DOI · Paper page
- Dürr, 2006, Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures, Nucleic Acids Res., 34, 4160, 10.1093/nar/gkl540 · DOI
- Roberts, 1997, Essential functional interactions of SAGA, a Saccharomyces cerevisiae Complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes, Genetics, 147, 465, 10.1093/genetics/147.2.451 · DOI · Paper page
- Pollard, 1997, Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression, Mol. Cell. Biol., 17, 6212, 10.1128/MCB.17.11.6212 · DOI
- Pollard, 1998, Chromatin remodeling: a marriage between two families?, Bioessays, 20, 771, 10.1002/(SICI)1521-1878(199809)20:9<771::AID-BIES10>3.0.CO;2-V · DOI
- Cosma, 1999, Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter, Cell, 97, 299, 10.1016/S0092-8674(00)80740-0 · DOI · Paper page
- Natarajan, 1999, Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator, Mol. Cell, 4, 657, 10.1016/S1097-2765(00)80217-8 · DOI
- De Serna, 2005, MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex, Mol. Cell. Biol., 10, 3997, 10.1128/MCB.25.10.3997-4009.2005 · DOI · Paper page
- Salma, 2004, Temporal recruitment of transcription factors and SWI/SNF chromatin-remodeling enzymes during adipogenic induction of the peroxisome proliferator-activated receptor γ nuclear hormone receptor, Mol. Cell. Biol., 11, 4651, 10.1128/MCB.24.11.4651-4663.2004 · DOI · Paper page
- Agalioti, 2002, Deciphering the transcriptional histone acetylation code for a human gene, Cell, 111, 381, 10.1016/S0092-8674(02)01077-2 · DOI · Paper page
- Lee, 2010, A cooperative activation loop among SWI/SNF, gamma-H2AX and H3 acetylation for DNA double-strand break repair, EMBO J., 29, 1434, 10.1038/emboj.2010.27 · DOI · Paper page
- Syntichaki, 2000, The Gcn5 bromodomain co-ordinates nucleosome remodelling, Nature, 404, 414, 10.1038/35006136 · DOI
- Hassan, 2001, Histone acetyltransferase complexes stabilize SWI/SNF binding to promoter nucleosomes, Cell, 104, 817, 10.1016/S0092-8674(01)00279-3 · DOI · Paper page
- Chandy, 2006, SWI/SNF displaces SAGA-acetylated nucleosomes, Eukaryot. Cell, 5, 1738, 10.1128/EC.00165-06 · DOI
- Hassan, 2002, Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes, Cell, 111, 369, 10.1016/S0092-8674(02)01005-X · DOI · Paper page
- Prochasson, 2003, Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains, Mol. Cell, 12, 983, 10.1016/S1097-2765(03)00366-6 · DOI
- Ferreira, 2009, Activator-binding domains of the SWI/SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo, FEBS J., 276, 2557, 10.1111/j.1742-4658.2009.06979.x · DOI
- Kasten, 2004, Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14, EMBO J., 23, 1348, 10.1038/sj.emboj.7600143 · DOI
- Chatterjee, 2011, Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms, Nucleic Acids Res., 39, 8378, 10.1093/nar/gkr535 · DOI
- VanDemark, 2007, Autoregulation of the Rsc4 tandem bromodomain by Gcn5 acetylation, Mol. Cell, 27, 817, 10.1016/j.molcel.2007.08.018 · DOI
- Charlop-Powers, 2010, Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2, Cell Res., 20, 529, 10.1038/cr.2010.43 · DOI
- Nicolas, 1996, Molecular cloning of polybromo, a nuclear protein containing multiple domains including five bromodomains, a truncated HMG-box, and two repeats of a novel domain, Gene, 175, 233, 10.1016/0378-1119(96)82845-9 · DOI
- Middeljans, 2012, SS18 together with animal-specific factors defines human BAF-type SWI/SNF complexes, PLoS One, 7, e33834, 10.1371/journal.pone.0033834 · DOI
- Cairns, 1999, Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains, Mol. Cell, 4, 715, 10.1016/S1097-2765(00)80382-2 · DOI
- Altaf, 2010, NuA4-dependent acetylation of nucleosomal histones H4 and H2A directly stimulates incorporation of H2A.Z by the SWR1 complex, J. Biol. Chem., 285, 15966, 10.1074/jbc.M110.117069 · DOI
- Krogan, 2003, A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1, Mol. Cell, 12, 1565, 10.1016/S1097-2765(03)00497-0 · DOI · Paper page
- Mizuguchi, 2004, ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex, Science, 303, 343, 10.1126/science.1090701 · DOI · Paper page
- Kobor, 2004, A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin, PLoS Biol., 2, E131, 10.1371/journal.pbio.0020131 · DOI · Paper page
- Keogh, 2006, The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4, Genes Dev., 20, 660, 10.1101/gad.1388106 · DOI
- Ranjan, 2013, Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement, Cell, 154, 1232, 10.1016/j.cell.2013.08.005 · DOI
- Sims, 2006, Histone H3 Lys 4 methylation: caught in a bind?, Genes Dev., 20, 2779, 10.1101/gad.1468206 · DOI
- Petty, 2013, Balancing chromatin remodeling and histone modifications in transcription, Trends Genet., 29, 621, 10.1016/j.tig.2013.06.006 · DOI
- Li, 2007, Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger, Mol. Cell, 28, 677, 10.1016/j.molcel.2007.10.023 · DOI
- Bonasio, 2010, MBT domain proteins in development and disease, Semin. Cell Dev. Biol., 21, 221, 10.1016/j.semcdb.2009.09.010 · DOI
- Trojer, 2007, L3MBTL1, a histone-methylation-dependent chromatin lock, Cell, 129, 915, 10.1016/j.cell.2007.03.048 · DOI · Paper page
- Paro, 1991, The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila, Proc. Natl. Acad. Sci. U. S. A., 88, 263, 10.1073/pnas.88.1.263 · DOI · Paper page
- Fischle, 2003, Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains, Genes Dev., 17, 1870, 10.1101/gad.1110503 · DOI · Paper page
- Min, 2003, Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27, Genes Dev., 17, 1823, 10.1101/gad.269603 · DOI · Paper page
- Pascual, 2000, Structure of the PHD zinc finger from human Williams–Beuren syndrome transcription factor, J. Mol. Biol., 304, 723, 10.1006/jmbi.2000.4308 · DOI
- Brehm, 2004, The many colours of chromodomains, Bioessays, 26, 133, 10.1002/bies.10392 · DOI
- Qiu, 2010, Activity of a C-terminal plant homeodomain (PHD) of Msc1 is essential for function, J. Biol. Chem., 285, 36828, 10.1074/jbc.M110.157792 · DOI
- Marfella, 2007, The Chd family of chromatin remodelers, Mutat. Res., 618, 30, 10.1016/j.mrfmmm.2006.07.012 · DOI · Paper page
- Boyer, 2004, The SANT domain: a unique histone-tail-binding module?, Nat. Rev. Mol. Cell Biol., 5, 158, 10.1038/nrm1314 · DOI · Paper page
- Morettini, 2011, The chromodomains of CHD1 are critical for enzymatic activity but less important for chromatin localization, Nucleic Acids Res., 39, 3103, 10.1093/nar/gkq1298 · DOI
- Kelley, 1999, CHD1 interacts with SSRP1 and depends on both its chromodomain and its ATPase/helicase-like domain for proper association with chromatin, Chromosoma, 108, 10, 10.1007/s004120050347 · DOI
- Bouazoune, 2002, The dMi-2 chromodomains are DNA binding modules important for ATP-dependent nucleosome mobilization, EMBO J., 21, 2430, 10.1093/emboj/21.10.2430 · DOI
- Allen, 2013, The NuRD architecture, Cell. Mol. Life Sci., 70, 3513, 10.1007/s00018-012-1256-2 · DOI · Paper page
- Kehle, 1998, dMi-2, a Hunchback-Interacting Protein That Functions in Polycomb Repression, Science, 282, 1897, 10.1126/science.282.5395.1897 · DOI · Paper page
- Kaji, 2006, The NuRD component Mbd3 is required for pluripotency of embryonic stem cells, Nat. Cell Biol., 8, 285, 10.1038/ncb1372 · DOI · Paper page
- Yildirim, 2011, Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, 147, 1498, 10.1016/j.cell.2011.11.054 · DOI · Paper page
- Musselman, 2009, Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications, Biochem. J., 423, 179, 10.1042/BJ20090870 · DOI
- Pray-Grant, 2005, Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation, Nature, 433, 434, 10.1038/nature03242 · DOI · Paper page
- Flanagan, 2005, Double chromodomains cooperate to recognize the methylated histone H3 tail, Nature, 438, 1181, 10.1038/nature04290 · DOI · Paper page
- Sims, 2005, Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains, J. Biol. Chem., 280, 41789, 10.1074/jbc.C500395200 · DOI · Paper page
- Lin, 2011, Mediator coordinates PIC assembly with recruitment of CHD1, Genes Dev., 25, 2198, 10.1101/gad.17554711 · DOI
- Simic, 2003, Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes, EMBO J., 22, 1846, 10.1093/emboj/cdg179 · DOI · Paper page
- Wysocka, 2006, A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling, Nature, 442, 86, 10.1038/nature04815 · DOI · Paper page
- Li, 2006, Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF, Nature, 442, 91, 10.1038/nature04802 · DOI · Paper page
- Ruthenburg, 2011, Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions, Cell, 145, 692, 10.1016/j.cell.2011.03.053 · DOI · Paper page
- Ruthenburg, 2007, Multivalent engagement of chromatin modifications by linked binding modules, Nat. Rev. Mol. Cell Biol., 8, 983, 10.1038/nrm2298 · DOI · Paper page
- Badenhorst, 2002, Biological functions of the ISWI chromatin remodeling complex NURF, Genes Dev., 16, 3186, 10.1101/gad.1032202 · DOI
- Song, 2009, The ISWI-containing NURF complex regulates the output of the canonical Wingless pathway, EMBO Rep., 10, 1140, 10.1038/embor.2009.157 · DOI
- Landry, 2008, Essential role of chromatin remodeling protein BPTF in early mouse embryos and embryonic stem cells, PLoS Genet., 4, e1000241, 10.1371/journal.pgen.1000241 · DOI
- Kamine, 1996, Identification of a cellular protein that specifically interacts with the essential cysteine region of the HIV-1 Tat transactivator, Virology, 216, 357, 10.1006/viro.1996.0071 · DOI · Paper page
- Fazzio, 2008, An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity, Cell, 134, 162, 10.1016/j.cell.2008.05.031 · DOI · Paper page
- Brady, 1999, Tip60 is a nuclear hormone receptor coactivator, J. Biol. Chem., 274, 17599, 10.1074/jbc.274.25.17599 · DOI · Paper page
- Smith, 1998, ESA1 is a histone acetyltransferase that is essential for growth in yeast, Proc. Natl. Acad. Sci. U. S. A., 95, 3561, 10.1073/pnas.95.7.3561 · DOI · Paper page
- Ikura, 2000, Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis, Cell, 102, 463, 10.1016/S0092-8674(00)00051-9 · DOI · Paper page
- Kusch, 2004, Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions, Science, 306, 2084, 10.1126/science.1103455 · DOI · Paper page
- Auger, 2008, Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants, Mol. Cell. Biol., 28, 2257, 10.1128/MCB.01755-07 · DOI
- Xue, 1998, NURD, a novel complex with both and histone deacetylase activities, Mol. Cell, 2, 851, 10.1016/S1097-2765(00)80299-3 · DOI · Paper page
- Wade, 1999, Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation, Nat. Genet., 23, 62, 10.1038/12664 · DOI · Paper page
- Helbling Chadwick, 2009, The Mi-2/NuRD complex associates with pericentromeric heterochromatin during S phase in rapidly proliferating lymphoid cells, Chromosoma, 118, 445, 10.1007/s00412-009-0207-7 · DOI
- Sims, 2011, Mi-2/NuRD complex function is required for normal S phase progression and assembly of pericentric heterochromatin, Mol. Biol. Cell, 22, 3094, 10.1091/mbc.E11-03-0258 · DOI
- Pegoraro, 2009, Ageing-related chromatin defects through loss of the NURD complex, Nat. Cell Biol., 11, 1261, 10.1038/ncb1971 · DOI · Paper page
- Mermoud, 2011, Keeping chromatin quiet: how nucleosome remodeling restores heterochromatin after replication, Cell Cycle, 10, 4017, 10.4161/cc.10.23.18558 · DOI
- Rowbotham, 2011, Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1, Mol. Cell, 42, 285, 10.1016/j.molcel.2011.02.036 · DOI
- Costelloe, 2012, The yeast Fun30 and human SMARCAD1 chromatin remodellers promote DNA end resection, Nature, 489, 581, 10.1038/nature11353 · DOI · Paper page
- Chen, 2012, The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends, Nature, 489, 576, 10.1038/nature11355 · DOI
- Briggs, 2002, Gene silencing: trans-histone regulatory pathway in chromatin, Nature, 418, 498, 10.1038/nature00970 · DOI · Paper page
- Zediak, 2008, Hit and run: transient deubiquitylase activity in a chromatin-remodeling complex, Mol. Cell, 31, 773, 10.1016/j.molcel.2008.09.005 · doi:10.1016/j.molcel.2008.09.005
- Yao, 2008, Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex, Mol. Cell, 31, 909, 10.1016/j.molcel.2008.08.027 · DOI
- Logie, 1999, The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes, Biochemistry, 38, 2514, 10.1021/bi982109d · DOI
- Corona, 2002, Modulation of ISWI function by site-specific histone acetylation, EMBO Rep., 3, 242, 10.1093/embo-reports/kvf056 · DOI
- Clapier, 2012, Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes, Nature, 492, 280, 10.1038/nature11625 · DOI
- Manning, 2013, Releasing the brakes on a chromatin-remodeling enzyme, Nat. Struct. Mol. Biol., 20, 5, 10.1038/nsmb.2482 · doi:10.1038/nsmb.2482
- Mueller-Planitz, 2013, The ATPase domain of ISWI is an autonomous nucleosome remodeling machine, Nat. Struct. Mol. Biol., 20, 82, 10.1038/nsmb.2457 · DOI
- Hauk, 2010, The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor, Mol. Cell, 39, 711, 10.1016/j.molcel.2010.08.012 · DOI · Paper page
- Peterson, 2007, Genome integrity: a HAT needs a chaperone, Curr. Biol., 17, R324, 10.1016/j.cub.2007.03.011 · DOI
- Ozdemir, 2006, Histone H3 lysine 56 acetylation: a new twist in the chromosome cycle, Cell Cycle, 5, 2602, 10.4161/cc.5.22.3473 · doi:10.4161/cc.5.22.3473
- Kaplan, 2008, Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast, PLoS Genet., 4, e1000270, 10.1371/journal.pgen.1000270 · DOI
- Chen, 2008, Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair, Cell, 134, 231, 10.1016/j.cell.2008.06.035 · DOI · Paper page
- Das, 2009, CBP/p300-mediated acetylation of histone H3 on lysine 56, Nature, 459, 113, 10.1038/nature07861 · DOI · Paper page
- Tan, 2013, Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency, Proc. Natl. Acad. Sci. U. S. A., 110, 11493, 10.1073/pnas.1309914110 · DOI
- Watanabe, 2013, A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme, Science, 340, 195, 10.1126/science.1229758 · DOI
- Watanabe, 2013, Chromatin dynamics: flipping the switch on a chromatin remodeling machine, Cell Cycle, 12, 2337, 10.4161/cc.25704 · doi:10.4161/cc.25704
- Bennett, 2013, DNA repair choice defines a common pathway for recruitment of chromatin regulators, Nat. Commun., 4, 2084, 10.1038/ncomms3084 · DOI
- Rogakou, 1999, Megabase chromatin domains involved in DNA double-strand breaks in vivo, J. Cell Biol., 146, 905, 10.1083/jcb.146.5.905 · DOI · Paper page
- Shroff, 2004, Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break, Curr. Biol., 14, 1703, 10.1016/j.cub.2004.09.047 · DOI · Paper page
- Park, 2006, Mammalian SWI/SNF complexes facilitate DNA double-strand break repair by promoting gamma-H2AX induction, EMBO J., 25, 3986, 10.1038/sj.emboj.7601291 · DOI · Paper page
- Nakamura, 2011, Regulation of homologous recombination by RNF20-dependent H2B ubiquitination, Mol. Cell, 41, 515, 10.1016/j.molcel.2011.02.002 · DOI · Paper page
- Williams, 2007, Transcriptional regulation by chromatin disassembly and reassembly, Curr. Opin. Genet. Dev., 17, 88, 10.1016/j.gde.2007.02.001 · DOI
- Kizer, 2005, A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation, Mol. Cell. Biol., 25, 3305, 10.1128/MCB.25.8.3305-3316.2005 · DOI · Paper page
- Krogan, 2003, Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II, Mol. Cell. Biol., 23, 4207, 10.1128/MCB.23.12.4207-4218.2003 · DOI · Paper page
- Li, 2003, The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II, J. Biol. Chem., 278, 8897, 10.1074/jbc.M212134200 · DOI · Paper page
- Verreault, 2000, De novo nucleosome assembly: new pieces in an old puzzle, Genes Dev., 14, 1430, 10.1101/gad.14.12.1430 · DOI
- Li, 2007, Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription, Genes Dev., 21, 1422, 10.1101/gad.1539307 · DOI
- Carrozza, 2005, Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription, Cell, 123, 581, 10.1016/j.cell.2005.10.023 · DOI · Paper page
- Li, 2007, Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin, Science, 316, 1050, 10.1126/science.1139004 · DOI · Paper page
- Smolle, 2012, Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange, Nat. Struct. Mol. Biol., 19, 884, 10.1038/nsmb.2312 · DOI · Paper page
- Maltby, 2012, Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin, Mol. Cell. Biol., 32, 3479, 10.1128/MCB.00389-12 · DOI
- Lee, 2013, Chromatin remodelers fine-tune H3K36me-directed deacetylation of neighbor nucleosomes by Rpd3S, Mol. Cell, 52, 255, 10.1016/j.molcel.2013.08.024 · DOI
- Huh, 2012, Multivalent di-nucleosome recognition enables the Rpd3S histone deacetylase complex to tolerate decreased H3K36 methylation levels, EMBO J., 31, 3564, 10.1038/emboj.2012.221 · DOI
- Lee, 2012, Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1, Genes Dev., 26, 914, 10.1101/gad.186841.112 · DOI
- Côté, 1994, Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex, Science, 265, 53, 10.1126/science.8016655 · DOI · Paper page
- Kwon, 1994, Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex, Nature, 370, 477, 10.1038/370477a0 · DOI · Paper page
- Imbalzano, 1994, Facilitated binding of TATA-binding protein to nucleosomal DNA, Nature, 370, 481, 10.1038/370481a0 · DOI · Paper page
- Brownell, 1996, Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation, Cell, 84, 843, 10.1016/S0092-8674(00)81063-6 · DOI · Paper page
Cited by
Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies
Kciuk, M., Marciniak, B., Mojzych, M., & Kontek, R. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21197264 · Cited by 168
Chromatin and oxygen sensing in the context of JmjC histone demethylases
Shmakova, A., Batie, M., Druker, J., & Rocha, S. (2014) · Biochemical Journal · doi:10.1042/bj20140754 · Cited by 99
ATP-dependent chromatin remodelers in ageing and age-related disorders
Swer, P. B., & Sharma, R. (2021) · Biogerontology · doi:10.1007/s10522-020-09899-3 · Cited by 25
Structure and flexibility of the yeast NuA4 histone acetyltransferase complex
Zukin, S. A., Marunde, M. R., Popova, I. K., Soczek, K. M., Nogales, E., & Patel, A. B. (2022) · eLife · doi:10.7554/elife.81400 · Cited by 22
Metadata
- Authors
- Swygert, S. G., & Peterson, C. L.
- Venue
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Publisher
- Elsevier BV
- Published
- 2014-08
- Volume
- 1839
- Issue
- 8
- Pages
- 728-736
- ISSN
- 1874-9399 (ISSN-L)
- OpenAlex
- W2061434854
- Cited by
- 256
- References
- 10
- FWCI
- 11.07
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Chromatin dynamics: Interplay between remodeling enzymes and histone modifications. https://app.cochat.ai/papers/10.1016/j.bbagrm.2014.02.013
- The paper
- Swygert, S. G., & Peterson, C. L. (2014). Chromatin dynamics: Interplay between remodeling enzymes and histone modifications. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. https://doi.org/10.1016/j.bbagrm.2014.02.013
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.