Genomes and Genes
chromatin assembly and disassembly
Summary: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.
- Lee R, Stewart C, Carter S, Ambrogio L, Cibulskis K, Sougnez C, et al. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J Clin Invest. 2012;122:2983-8 pubmed publisher..Our results demonstrate that high mutation rates are dispensable for the genesis of cancers driven by mutation of a chromatin remodeling complex. Consequently, cancer can be a remarkably genetically simple disease...
- Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, et al. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell. 2012;151:1608-16 pubmed publisher..Thus, both epigenetic and genetic regulators cooperate to control nucleosome dynamics during ES cell fate decisions. ..
- Morra R, Lee B, Shaw H, Tuma R, Mancini E. Concerted action of the PHD, chromo and motor domains regulates the human chromatin remodelling ATPase CHD4. FEBS Lett. 2012;586:2513-21 pubmed publisher..Our results demonstrate functional interdependency between domains within a chromatin remodeller. ..
- Yen K, Vinayachandran V, Batta K, Koerber R, Pugh B. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 2012;149:1461-73 pubmed publisher..Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays. ..
- Zhu J, Adli M, Zou J, Verstappen G, Coyne M, Zhang X, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013;152:642-54 pubmed publisher..We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming. ..
- Chandler R, Brennan J, Schisler J, Serber D, Patterson C, Magnuson T. ARID1a-DNA interactions are required for promoter occupancy by SWI/SNF. Mol Cell Biol. 2013;33:265-80 pubmed publisher..These findings support the model wherein cooperative interactions among intrinsic subunit-chromatin interaction domains and sequence-specific transcription factors drive SWI/SNF recruitment. ..
- Kapoor P, Chen M, Winkler D, Luger K, Shen X. Evidence for monomeric actin function in INO80 chromatin remodeling. Nat Struct Mol Biol. 2013;20:426-32 pubmed publisher..Our results establish an evolutionarily conserved function of nuclear actin in its monomeric form and suggest that nuclear actin can utilize a fundamentally distinct mechanism from that of cytoplasmic actin. ..
- Burgess R, Zhang Z. Histone chaperones in nucleosome assembly and human disease. Nat Struct Mol Biol. 2013;20:14-22 pubmed publisher..Alterations or mutations in factors involved in nucleosome assembly have also been implicated in cancer and other human diseases. This review highlights the recent progress and outlines future challenges in the field. ..
- Arvey A, Agius P, Noble W, Leslie C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 2012;22:1723-34 pubmed publisher..Our results suggest that using a single motif for each TF and filtering for chromatin accessible loci is not always sufficient to accurately account for cell-type-specific binding profiles. ..
- Swarnalatha M, Singh A, Kumar V. The epigenetic control of E-box and Myc-dependent chromatin modifications regulate the licensing of lamin B2 origin during cell cycle. Nucleic Acids Res. 2012;40:9021-35 pubmed publisher..Intriguingly, the genome-wide 43% occurrence of E-box among the human origins could support our hypothesis that epigenetic control of E-box could be a molecular switch for the licensing of early replicating origins. ..
- Koike N, Yoo S, Huang H, Kumar V, Lee C, Kim T, et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science. 2012;338:349-54 pubmed publisher..We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling. ..
- Hughes A, Jin Y, Rando O, Struhl K. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell. 2012;48:5-15 pubmed publisher..We suggest a three-step model in which nucleosome remodelers, general transcription factors, and the transcriptional elongation machinery are primarily involved in generating the nucleosome positioning pattern in vivo. ..
- Dykhuizen E, Hargreaves D, Miller E, Cui K, Korshunov A, Kool M, et al. BAF complexes facilitate decatenation of DNA by topoisomerase II?. Nature. 2013;497:624-7 pubmed publisher..These studies indicate that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumour suppressors. ..
- Buscaino A, Lejeune E, Audergon P, Hamilton G, Pidoux A, Allshire R. Distinct roles for Sir2 and RNAi in centromeric heterochromatin nucleation, spreading and maintenance. EMBO J. 2013;32:1250-64 pubmed publisher..These analyses reveal that Sir2, together with RNAi, are sufficient to ensure heterochromatin integrity and provide evidence for sequential establishment, spreading and maintenance steps in the assembly of centromeric heterochromatin. ..
- Deindl S, Hwang W, Hota S, Blosser T, Prasad P, Bartholomew B, et al. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell. 2013;152:442-52 pubmed publisher..Our results suggest a remodeling mechanism with well-defined coordination at different nucleosomal sites featuring DNA translocation toward the exit side in 1 bp steps preceding multi-bp steps of DNA movement on the entry side. ..
- Williamson I, Eskeland R, Lettice L, Hill A, Boyle S, Grimes G, et al. Anterior-posterior differences in HoxD chromatin topology in limb development. Development. 2012;139:3157-67 pubmed publisher..This is the first example of A-P differences in chromatin compaction and chromatin looping in the development of the mammalian secondary body axis (limb)...
- Struhl K, Segal E. Determinants of nucleosome positioning. Nat Struct Mol Biol. 2013;20:267-73 pubmed publisher..These determinants influence each other such that the resulting nucleosome positioning patterns are likely to differ among genes and among cells in a population, with consequent effects on gene expression. ..
- Kowalski A, Pałyga J. Linker histone subtypes and their allelic variants. Cell Biol Int. 2012;36:981-96 pubmed publisher..This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance. ..
- Hota S, Bhardwaj S, Deindl S, Lin Y, Zhuang X, Bartholomew B. Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat Struct Mol Biol. 2013;20:222-9 pubmed publisher..Not only is extranucleosomal DNA required to help recruit ISW2, but also the interactions of the SLIDE domain with extranucleosomal DNA are functionally required to move nucleosomes. ..
- Florescu A, Schiessel H, Blossey R. Kinetic control of nucleosome displacement by ISWI/ACF chromatin remodelers. Phys Rev Lett. 2012;109:118103 pubmed..ATP-dependent remodeling by bidirectional motors is shown to reinforce positioning as compared to statistical positioning. ..
- Barbieri M, Chotalia M, Fraser J, Lavitas L, Dostie J, Pombo A, et al. Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci U S A. 2012;109:16173-8 pubmed publisher..Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations. ..
- Smeenk G, Wiegant W, Marteijn J, Luijsterburg M, Sroczynski N, Costelloe T, et al. Poly(ADP-ribosyl)ation links the chromatin remodeler SMARCA5/SNF2H to RNF168-dependent DNA damage signaling. J Cell Sci. 2013;126:889-903 pubmed publisher..Our study unveils a functional link between DNA damage-induced poly(ADP-ribosyl)ation, SMARCA5-mediated chromatin remodeling and RNF168-dependent signaling and repair of DSBs. ..
- Zhang Y, Liu Z, Medrzycki M, Cao K, Fan Y. Reduction of Hox gene expression by histone H1 depletion. PLoS ONE. 2012;7:e38829 pubmed publisher..We suggest possible mechanisms for such an unexpected role of histone H1 in Hox gene regulation. ..
- Durand Dubief M, Will W, Petrini E, Theodorou D, Harris R, Crawford M, et al. SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae. PLoS Genet. 2012;8:e1002974 pubmed publisher..As centromeres in budding yeast are not embedded in heterochromatin, our findings indicate a direct role of Fun30 in centromere chromatin by promoting correct chromatin architecture. ..
- Kundaje A, Kyriazopoulou Panagiotopoulou S, Libbrecht M, Smith C, Raha D, Winters E, et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012;22:1735-47 pubmed publisher..Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins. ..
- Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, et al. The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends. Nature. 2012;489:576-80 pubmed publisher..Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection. ..
- Mueller Planitz F, Klinker H, Ludwigsen J, Becker P. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat Struct Mol Biol. 2013;20:82-9 pubmed publisher..Nucleosome-remodeling enzymes may thus have evolved directly from ancestral helicase-type motors, and peripheral domains have furnished regulatory capabilities that bias the remodeling reaction toward different structural outcomes. ..
- Bouazoune K, Kingston R. Chromatin remodeling by the CHD7 protein is impaired by mutations that cause human developmental disorders. Proc Natl Acad Sci U S A. 2012;109:19238-43 pubmed publisher..We propose that nucleosome remodeling is a key function for CHD7 during developmental processes and provide a molecular basis for predicting the impact of disease mutations on that function. ..
- Zhu Y, Rowley M, Böhmdorfer G, Wierzbicki A. A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell. 2013;49:298-309 pubmed publisher..We further propose that guiding ATP-dependent chromatin-remodeling complexes may be a more general function of lncRNAs. ..
- Hennig B, Bendrin K, Zhou Y, Fischer T. Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep. 2012;13:997-1003 pubmed publisher..These data indicate several mechanisms in the repression of cryptic promoter activity in eukaryotic cells. ..
- Costelloe T, Louge R, Tomimatsu N, Mukherjee B, Martini E, Khadaroo B, et al. The yeast Fun30 and human SMARCAD1 chromatin remodellers promote DNA end resection. Nature. 2012;489:581-4 pubmed publisher..These findings unveil an evolutionarily conserved role for the Fun30 and SMARCAD1 chromatin remodellers in controlling end resection, homologous recombination and genome stability in the context of chromatin. ..
- Bieberstein N, Carrillo Oesterreich F, Straube K, Neugebauer K. First exon length controls active chromatin signatures and transcription. Cell Rep. 2012;2:62-8 pubmed publisher..Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures. ..
- Tollervey J, Lunyak V. Epigenetics: judge, jury and executioner of stem cell fate. Epigenetics. 2012;7:823-40 pubmed publisher..Further investigation into stem cell epigenetics promises to provide novel advances in the diagnosis and treatment of a wide array of human diseases. ..
- Banerjee C, Archin N, Michaels D, Belkina A, Denis G, Bradner J, et al. BET bromodomain inhibition as a novel strategy for reactivation of HIV-1. J Leukoc Biol. 2012;92:1147-54 pubmed publisher..Thus, JQ1 may be useful in studies of potentially novel mechanisms for transcriptional control as well as in translational efforts to identify therapeutic molecules to achieve viral eradication. ..
- Lo S, Follmer N, Lengsfeld B, Madamba E, Seong S, Grau D, et al. A bridging model for persistence of a polycomb group protein complex through DNA replication in vitro. Mol Cell. 2012;46:784-96 pubmed publisher..This mechanism may allow inheritance of chromatin proteins including PRC1 through DNA replication to maintain chromatin states. ..
- Dawson M, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150:12-27 pubmed publisher..This information, along with the promising clinical and preclinical results seen with epigenetic drugs against chromatin regulators, signifies that it is time to embrace the central role of epigenetics in cancer. ..
- Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza J, Innocenti C, et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 2012;22:2399-408 pubmed publisher..Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. ..
- Sanz A, Garcia R, Rodriguez Peña J, Diez Muñiz S, Nombela C, Peterson C, et al. Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway. Mol Biol Cell. 2012;23:2805-17 pubmed publisher..Taken together, our results identify the SWI/SNF complex as a key element of the CWI MAPK pathway that mediates the chromatin remodeling necessary for adequate transcriptional response to cell wall stress. ..
- Schubert H, Wittmeyer J, Kasten M, Hinata K, Rawling D, Heroux A, et al. Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A. 2013;110:3345-50 pubmed publisher..Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity. ..
- Chen D, Fang F, Yang Y, Chen J, Xu G, Xu Y, et al. Brahma-related gene 1 (Brg1) epigenetically regulates CAM activation during hypoxic pulmonary hypertension. Cardiovasc Res. 2013;100:363-73 pubmed publisher..As such, targeting Brg1 in endothelial cells may yield promising strategies in the intervention and/or prevention of HPH. ..
- Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biol. 2015;5: pubmed publisher..These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells. ..
- Scarpa A, Chang D, Nones K, Corbo V, Patch A, Bailey P, et al. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature. 2017;543:65-71 pubmed publisher..In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling. ..
- Simard O, Niavarani S, Gaudreault V, Boissonneault G. Torsional stress promotes trinucleotidic expansion in spermatids. Mutat Res. 2017;800-802:1-7 pubmed publisher..The transient increase in torsional stress during spermiogenesis may therefore provide an ideal context for the generation of such secondary DNA structures leading to the paternal anticipation of trinucleotidic diseases. ..
- Gong F, Clouaire T, Aguirrebengoa M, Legube G, Miller K. Histone demethylase KDM5A regulates the ZMYND8-NuRD chromatin remodeler to promote DNA repair. J Cell Biol. 2017;216:1959-1974 pubmed publisher..Thus, this study identifies a crucial function for KDM5A in demethylating H3K4 to allow ZMYND8-NuRD to operate within damaged chromatin to repair DSBs. ..