Understanding nucleosome dynamics and their links to gene expression and DNA replication

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Crystal structure of the nucleosome core particle at 2.8 Å resolution

Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. (1997) · Nature · doi:10.1038/38444 · Cited by 9,466 · see citing works

The language of covalent histone modifications

Strahl, B. D., & Allis, C. D. (2000) · Nature · doi:10.1038/47412 · Cited by 8,679 · see citing works

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works

Chromatin Structure: A Repeating Unit of Histones and DNA

Kornberg, R. D. (1974) · Science · doi:10.1126/science.184.4139.868 · Cited by 2,662 · see citing works

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033 · see citing works

A general method for the covalent labeling of fusion proteins with small molecules in vivo

Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H. M., Vogel, H., & Johnsson, K. (2002) · Nature Biotechnology · doi:10.1038/nbt765 · Cited by 1,964 · see citing works

Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome

Kornberg, R. D., & Lorch, Y. (1999) · Cell · doi:10.1016/s0092-8674(00)81958-3 · Cited by 1,833 · see citing works

A genomic code for nucleosome positioning

Segal, E., Fondufe‐Mittendorf, Y. N., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J.-P. Z., & Widom, J. (2006) · Nature · doi:10.1038/nature04979 · Cited by 1,492 · see citing works

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Pokholok, D., Harbison, C. T., Levine, S. S., Cole, M. F., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, A., Herbolsheimer, E., et al. (2005) · Cell · doi:10.1016/j.cell.2005.06.026 · Cited by 1,433 · see citing works

The DNA-encoded nucleosome organization of a eukaryotic genome

Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A., Tillo, D., Field, Y., Leproust, E., Hughes, T., Lieb, J., Widom, J., et al. (2008) · Nature · doi:10.1038/nature07667 · Cited by 1,296 · see citing works

The structure of DNA in the nucleosome core

Richmond, T. J., & Davey, C. A. (2003) · Nature · doi:10.1038/nature01595 · Cited by 1,287 · see citing works

Role of the polycomb protein EED in the propagation of repressive histone marks

Margueron, R., Justin, N., Ohno, K., Sharpe, M. L., Son, J., Drury, W. J., Voigt, P., Martin, S. R., Taylor, W. R., Marco, V. D., et al. (2009) · Nature · doi:10.1038/nature08398 · Cited by 1,203 · see citing works

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174 · see citing works

Nucleosome positioning and gene regulation: advances through genomics

Jiang, C., & Pugh, B. F. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2522 · Cited by 1,059 · see citing works

Histone core modifications regulating nucleosome structure and dynamics

Tessarz, P., & Kouzarides, T. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3890 · Cited by 1,018 · see citing works

Histone exchange, chromatin structure and the regulation of transcription

Venkatesh, S., & Workman, J. L. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3941 · Cited by 940 · see citing works

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 · see citing works

Getting up to speed with transcription elongation by RNA polymerase II

Jonkers, I., & Lis, J. T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3953 · Cited by 876 · see citing works

FACT Facilitates Transcription-Dependent Nucleosome Alteration

Belotserkovskaya, R., Oh, S., Bondarenko, V. A., Orphanides, G., Studitsky, V. M., & Reinberg, D. (2003) · Science · doi:10.1126/science.1085703 · Cited by 869 · see citing works

Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics

Kadoch, C., & Crabtree, G. R. (2015) · Science Advances · doi:10.1126/sciadv.1500447 · Cited by 843 · see citing works

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Hsieh, T.-H. S., Weiner, A., Lajoie, B., Dekker, J., Friedman, N., & Rando, O. J. (2015) · Cell · doi:10.1016/j.cell.2015.05.048 · Cited by 788 · see citing works

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome

Albert, I. U., Mavrich, T. N., Tomsho, L. P., Qi, J., Zanton, S. J., Schuster, S. C., & Pugh, B. F. (2007) · Nature · doi:10.1038/nature05632 · Cited by 694 · see citing works

Determinants of nucleosome positioning

Struhl, K., & Segal, E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2506 · Cited by 685 · see citing works

RSC, an Essential, Abundant Chromatin-Remodeling Complex

Cairns, B. R., Lorch, Y., Li, Y., Zhang, M., Lacomis, L., Erdjument‐Bromage, H., Tempst, P., Du, J., Laurent, B. C., & Kornberg, R. D. (1996) · Cell · doi:10.1016/s0092-8674(00)81820-6 · Cited by 667 · see citing works

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

Narlikar, G. J., Sundaramoorthy, R., & Owen‐Hughes, T. (2013) · Cell · doi:10.1016/j.cell.2013.07.011 · Cited by 659 · see citing works

The SWI/SNF complex — chromatin and cancer

Roberts, C. W. M., & Orkin, S. H. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1273 · Cited by 603 · see citing works

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

Dion, M. F., Kaplan, T., Kim, M., Buratowski, S., Friedman, N., & Rando, O. J. (2007) · Science · doi:10.1126/science.1134053 · Cited by 556 · see citing works

Genome-wide structure and organization of eukaryotic pre-initiation complexes

Rhee, H. S., & Pugh, B. F. (2012) · Nature · doi:10.1038/nature10799 · Cited by 496 · see citing works

Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones

Deal, R., Henikoff, J., & Henikoff, S. (2010) · Science · doi:10.1126/science.1186777 · Cited by 493 · see citing works

Chromatin remodelling at promoters suppresses antisense transcription

Whitehouse, I., Rando, O. J., Delrow, J., & Tsukiyama, T. (2007) · Nature · doi:10.1038/nature06391 · Cited by 456 · see citing works

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

Kelly, T. K., Liu, Y., Lay, F. D., Liang, G., Berman, B. P., & Jones, P. A. (2012) · Genome Research · doi:10.1101/gr.143008.112 · Cited by 455 · see citing works

A map of nucleosome positions in yeast at base-pair resolution

Brogaard, K., Xi, L., Wang, J.-P., & Widom, J. (2012) · Nature · doi:10.1038/nature11142 · Cited by 452 · see citing works

Cell Cycle Regulation of DNA Replication

Sclafani, R. A., & Holzen, T. M. (2007) · Annual Review of Genetics · doi:10.1146/annurev.genet.41.110306.130308 · Cited by 448 · see citing works

Nucleosome destabilization in the epigenetic regulation of gene expression

Henikoff, S. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2206 · Cited by 439 · see citing works

Chromatin accessibility: a window into the genome

Tsompana, M., & Buck, M. J. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-33 · Cited by 437 · see citing works

The Chd family of chromatin remodelers

Marfella, C. G. A., & Imbalzano, A. N. (2007) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2006.07.012 · Cited by 432 · see citing works

Mechanisms that Specify Promoter Nucleosome Location and Identity

Hartley, P. D., & Madhani, H. D. (2009) · Cell · doi:10.1016/j.cell.2009.02.043 · Cited by 406 · see citing works

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S. J. M., Hirst, M., & Iyer, V. R. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060065 · Cited by 401 · see citing works

H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State

Brickner, D. G., Cajigas, I., Fondufe‐Mittendorf, Y. N., Ahmed, S. A. A., Lee, P., Widom, J., & Brickner, J. H. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050081 · Cited by 390 · see citing works

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

Ray-Gallet, D., Woolfe, A., Vassias, I., Pellentz-Lemattre, C., Lacoste, N., Puri, A., Schultz, D., Pchelintsev, N. A., Adams, P. D., Jansen, L. E. T., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.12.006 · Cited by 387 · see citing works

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

Weber, C. M., Ramachandran, S., & Henikoff, S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.014 · Cited by 386 · see citing works

The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo

Deuring, R., Fanti, L., Armstrong, J. A., Sarte, M., Papoulas, O., Prestel, M., Daubresse, G., Verardo, M., Moseley, S. L., Berloco, M. F., et al. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80430-x · Cited by 385 · see citing works

Conserved nucleosome positioning defines replication originsPreprint

Eaton, M. L., Galani, K., Kang, S., Bell, S. P., & MacAlpine, D. M. (2010) · Genes & Development · doi:10.1101/gad.1913210 · Cited by 384 · see citing works

Histone chaperones in nucleosome assembly and human disease

Burgess, R. J., & Zhang, Z. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2461 · Cited by 383 · see citing works

Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers

de la Serna, I. L., Ohkawa, Y., & Imbalzano, A. N. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1882 · Cited by 376 · see citing works

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

Schep, A. N., Buenrostro, J. D., Denny, S. K., Schwartz, K., Sherlock, G., & Greenleaf, W. J. (2015) · Genome Research · doi:10.1101/gr.192294.115 · Cited by 375 · see citing works

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G. M., Snyder, M. P., Kadonaga, J. T., Liu, X. S., & Struhl, K. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1636 · Cited by 365 · see citing works

Epigenetic Centromere Propagation and the Nature of CENP-A Nucleosomes

Black, B. E., & Cleveland, D. W. (2011) · Cell · doi:10.1016/j.cell.2011.02.002 · Cited by 355 · see citing works

Chromosome Duplication in Saccharomyces cerevisiae

Bell, S. P., & Labib, K. P. M. (2016) · Genetics · doi:10.1534/genetics.115.186452 · Cited by 352 · see citing works

Partitioning of Histone H3-H4 Tetramers During DNA Replication–Dependent Chromatin Assembly

Xu, M., Long, C., Chen, X., Huang, C., Chen, S., & Zhu, B. (2010) · Science · doi:10.1126/science.1178994 · Cited by 351 · see citing works

Histone variants on the move: substrates for chromatin dynamics

Talbert, P. B., & Henikoff, S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.148 · Cited by 347 · see citing works

Variants of core histones and their roles in cell fate decisions, development and cancer

Buschbeck, M., & Hake, S. B. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.166 · Cited by 343 · see citing works

Histones H2a, H2b, H3, and H4 form a tetrameric complex in solutions of high salt

Weintraub, H., Palter, K. B., & Lente, F. V. (1975) · Cell · doi:10.1016/0092-8674(75)90077-x · Cited by 337 · see citing works

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

Meyer, C. A., & Liu, X. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3788 · Cited by 329 · see citing works

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

Yen, K., Vinayachandran, V., Batta, K., Koerber, R. T., & Pugh, B. F. (2012) · Cell · doi:10.1016/j.cell.2012.04.036 · Cited by 327 · see citing works

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

Zhang, Z., Wippo, C. J., Wal, M., Ward, E., Korber, P., & Pugh, B. F. (2011) · Science · doi:10.1126/science.1200508 · Cited by 318 · see citing works

Nucleosome positions predicted through comparative genomics

Ioshikhes, I. P., Albert, I. U., Zanton, S. J., & Pugh, B. F. (2006) · Nature Genetics · doi:10.1038/ng1878 · Cited by 317 · see citing works

Histone Chaperones: Assisting Histone Traffic and Nucleosome Dynamics

Gurard‐Levin, Z. A., Quivy, J., & Almouzni, G. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035536 · Cited by 310 · see citing works

NoRC—a novel member of mammalian ISWI‐containing chromatin remodeling machines

Strohner, R., Németh, A., Jansa, P., Hofmann‐Rohrer, U., Santoro, R., Längst, G., & Grummt, I. (2001) · The EMBO Journal · doi:10.1093/emboj/20.17.4892 · Cited by 308 · see citing works

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

Adams, C. C., & Workman, J. L. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.3.1405 · Cited by 307 · see citing works

Nucleosome positioning: How is it established, and why does it matter?

Radman‐Livaja, M., & Rando, O. J. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.06.012 · Cited by 304 · see citing works

Nucleosome displacement in transcription: Figure 1.Preprint

Workman, J. L. (2006) · Genes & Development · doi:10.1101/gad.1435706 · Cited by 303 · see citing works

The Isw2 Chromatin Remodeling Complex Represses Early Meiotic Genes upon Recruitment by Ume6p

Goldmark, J. P., Fazzio, T. G., Estep, P. W., Church, G. M., & Tsukiyama, T. (2000) · Cell · doi:10.1016/s0092-8674(00)00134-3 · Cited by 300 · see citing works

Histone variants: dynamic punctuation in transcriptionPreprint

Weber, C. M., & Henikoff, S. (2014) · Genes & Development · doi:10.1101/gad.238873.114 · Cited by 297 · see citing works

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites 1 1Edited by T. Richmond

Anderson, J. D., & Widom, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3531 · Cited by 294 · see citing works

A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M. M., Workman, J. L., Barton, G. J., & Owen‐Hughes, T. (2011) · Science · doi:10.1126/science.1206097 · Cited by 288 · see citing works

Nucleosomes Positioned by ORC Facilitate the Initiation of DNA Replication

Lipford, J. R., & Bell, S. P. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00151-4 · Cited by 288 · see citing works

Genomic Nucleosome Organization Reconstituted with Pure Proteins

Krietenstein, N., Wal, M., Watanabe, S., Park, B., Peterson, C. L., Pugh, B. F., & Korber, P. (2016) · Cell · doi:10.1016/j.cell.2016.09.045 · Cited by 274 · see citing works

From DNA sequence to transcriptional behaviour: a quantitative approach

Segal, E., & Widom, J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2591 · Cited by 262 · see citing works

Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome

Zofall, M., Persinger, J., Kassabov, S. R., & Bartholomew, B. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1071 · Cited by 258 · see citing works

Chromatin remodeling and cancer, part II: ATP-dependent chromatin remodeling

Wang, G. G., Allis, C. D., & Chi, P. (2007) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2007.07.004 · Cited by 254 · see citing works

A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites

Polach, K. J., & Widom, J. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0288 · Cited by 249 · see citing works

ChIP-seq: welcome to the new frontier

Mardis, E. R. (2007) · Nature Methods · doi:10.1038/nmeth0807-613 · Cited by 244 · see citing works

A model for chromatin based upon two symmetrically paired half-nucleosomes

Weintraub, H. M., Worcel, A., & Alberts, B. (1976) · Cell · doi:10.1016/0092-8674(76)90085-4 · Cited by 243 · see citing works

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

Rhee, H. S., Bataille, A. R., Zhang, L., & Pugh, B. F. (2014) · Cell · doi:10.1016/j.cell.2014.10.054 · Cited by 243 · see citing works

A unique binding mode enables MCM2 to chaperone histones H3–H4 at replication forks

Huang, H., Strømme, C. B., Saredi, G., Hödl, M., Strandsby, A., González‐Aguilera, C., Chen, S., Groth, A., & Patel, D. J. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3055 · Cited by 240 · see citing works

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promotersPreprint

Fenouil, R., Cauchy, P., Koch, F., Descostes, N., Cabeza, J. Z., Innocenti, C., Ferrier, P., Spicuglia, S., Gut, M., Gut, I. G., et al. (2012) · Genome Research · doi:10.1101/gr.138776.112 · Cited by 238 · see citing works

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Mieczkowski, J., Cook, A., Bowman, S., Mueller, B., Alver, B. H., Kundu, S., Deaton, A. M., Urban, J. A., Larschan, E., Park, P. J., et al. (2016) · Nature Communications · doi:10.1038/ncomms11485 · Cited by 235 · see citing works

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns, B. R. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1333 · Cited by 233 · see citing works

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes

Wade, J. T., Hall, D. B., & Struhl, K. (2004) · Nature · doi:10.1038/nature03175 · Cited by 232 · see citing works

The octamer is the major form of CENP-A nucleosomes at human centromeres

Hasson, D., Panchenko, T., Salimian, K. J., Salman, M. U., Sekulić, N., Alonso, A., Warburton, P. E., & Black, B. E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2562 · Cited by 230 · see citing works

Structure and Subunit Topology of the INO80 Chromatin Remodeler and Its Nucleosome Complex

Tosi, A., Haas, C., Herzog, F., Gilmozzi, A., Berninghausen, O., Ungewickell, C., Gerhold, C., Lakomek, K., Aebersold, R. H., Beckmann, R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.016 · Cited by 229 · see citing works

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genomes

Jiang, C., & Pugh, B. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-10-r109 · Cited by 227 · see citing works

Multiple roles for ISWI in transcription, chromosome organization and DNA replication.

Corona, D., & Tamkun, J. (2004) · Biochimica et Biophysica Acta · doi:10.1016/j.bbaexp.2003.09.018 · Cited by 218 · see citing works

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

de Dieuleveult, M., Yen, K., Hmitou, I., Depaux, A., Boussouar, F., Dargham, D. B., Jounier, S., Humbertclaude, H., Ribiérre, F., Baulard, C., et al. (2016) · Nature · doi:10.1038/nature16505 · Cited by 215 · see citing works

Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA

Sirbu, B. M., Couch, F. B., & Cortez, D. (2012) · Nature Protocols · doi:10.1038/nprot.2012.010 · Cited by 209 · see citing works

When repair meets chromatin

Green, C., & Almouzni, G. (2002) · EMBO Reports · doi:10.1093/embo-reports/kvf005 · Cited by 207 · see citing works

Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors

Längst, G., & Becker, P. B. (2001) · Journal of Cell Science · doi:10.1242/jcs.114.14.2561 · Cited by 201 · see citing works

Asymmetric Division of Drosophila Male Germline Stem Cell Shows Asymmetric Histone Distribution

Tran, V., Lim, C., Xie, J., & Chen, X. (2012) · Science · doi:10.1126/science.1226028 · Cited by 197 · see citing works

A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme

Watanabe, S., Radman‐Livaja, M., Rando, O. J., & Peterson, C. L. (2013) · Science · doi:10.1126/science.1229758 · Cited by 196 · see citing works

ChIP‐exo Method for Identifying Genomic Location of DNA‐Binding Proteins with Near‐Single‐Nucleotide Accuracy

Rhee, H. S., & Pugh, B. F. (2012) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2124s100 · Cited by 195 · see citing works

SWR-C and INO80 Chromatin Remodelers Recognize Nucleosome-free Regions Near +1 Nucleosomes

Yen, K., Vinayachandran, V., & Pugh, B. F. (2013) · Cell · doi:10.1016/j.cell.2013.08.043 · Cited by 194 · see citing works

Chromatin and DNA ReplicationPreprint

MacAlpine, D. M., & Almouzni, G. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a010207 · Cited by 194 · see citing works

Analysis of Nucleosome Repositioning by Yeast ISWI and Chd1 Chromatin Remodeling Complexes

Stockdale, C., Flaus, A., Ferreira, H. C., & Owen‐Hughes, T. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m600682200 · Cited by 193 · see citing works

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters

Tolstorukov, M. Y., Sansam, C. G., Lu, P., Koellhoffer, E. C., Helming, K. C., Alver, B. H., Tillman, E. J., Evans, J. A., Wilson, B. G., Park, P. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302209110 · Cited by 190 · see citing works

The Nucleosome Family: Dynamic and Growing

Zlatanova, J. S., Bishop, T. C., Victor, J., Jackson, V. E., & van Holde, K. E. (2009) · Structure · doi:10.1016/j.str.2008.12.016 · Cited by 185 · see citing works

RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes

Parnell, T. J., Huff, J. T., & Cairns, B. R. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601946 · Cited by 183 · see citing works

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

Kubik, S., Bruzzone, M. J., Jacquet, P., Falcone, J.-L., Rougemont, J., & Shore, D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.002 · Cited by 182 · see citing works

Structural basis of histone H2A–H2B recognition by the essential chaperone FACT

Hondele, M., Stuwe, T., Hassler, M., Halbach, F., Bowman, A. J., Zhang, E., Nijmeijer, B., Kotthoff, C., Rybin, V., Amlacher, S., et al. (2013) · Nature · doi:10.1038/nature12242 · Cited by 181 · see citing works

Chromatin remodeling complexes: strength in diversity, precision through specialization

Cairns, B. R. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.01.003 · Cited by 174 · see citing works

Split Decision: What Happens to Nucleosomes during DNA Replication?

Annunziato, A. T. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.r400039200 · Cited by 172 · see citing works

Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex

Dumesic, P. A., Homer, C. M., Moresco, J. J., Pack, L. R., Shanle, E. K., Coyle, S. M., Strahl, B. D., Fujimori, D. G., Yates, J. R., & Madhani, H. D. (2014) · Cell · doi:10.1016/j.cell.2014.11.039 · Cited by 165 · see citing works

Chromatin signatures of the Drosophila replication programPreprint

Eaton, M. L., Prinz, J. A., MacAlpine, H. K., Tretyakov, G., Kharchenko, P. V., & MacAlpine, D. M. (2010) · Genome Research · doi:10.1101/gr.116038.110 · Cited by 164 · see citing works

H2A.Z contributes to the unique 3D structure of the centromere

Greaves, I. K., Rangasamy, D., Ridgway, P., & Tremethick, D. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607870104 · Cited by 163 · see citing works

Transcriptional Regulators Compete with Nucleosomes Post-replication

Ramachandran, S., & Henikoff, S. (2016) · Cell · doi:10.1016/j.cell.2016.02.062 · Cited by 162 · see citing works

Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications

O’Geen, H., Echipare, L., & Farnham, P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-316-5_20 · Cited by 161 · see citing works

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

Zhou, C. Y., Johnson, S. L., Gamarra, N. I., & Narlikar, G. J. (2016) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-051013-022819 · Cited by 158 · see citing works

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

Kraushaar, D. C., Jin, W., Maunakea, A. K., Abraham, B. J., Ha, M., & Zhao, K. (2013) · Genome biology · doi:10.1186/gb-2013-14-10-r121 · Cited by 151 · see citing works

Histone variants in pluripotency and disease

Skene, P. J., & Henikoff, S. (2013) · Development · doi:10.1242/dev.091439 · Cited by 149 · see citing works

Mammalian SWI-SNF Complexes Contribute to Activation of the hsp70 Gene

de la Serna, I. L., Carlson, K. A., Hill, D. A., Guidi, C. J., Stephenson, R. O., Sif, S., Kingston, R. E., & Imbalzano, A. N. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.8.2839-2851.2000 · Cited by 147 · see citing works

Mechanism of transcription through a nucleosome by RNA polymerase II

Kulaeva, O. I., Hsieh, F., Chang, H.-W., Luse, D. S., & Studitsky, V. M. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.08.015 · Cited by 144 · see citing works

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activationPreprint

Xi, Y., Yao, J., Chen, R., Li, W., & He, X. (2011) · Genome Research · doi:10.1101/gr.117101.110 · Cited by 143 · see citing works

Structure, dynamics, and evolution of centromeric nucleosomes

Dalal, Y., Furuyama, T., Vermaak, D., & Henikoff, S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707648104 · Cited by 135 · see citing works

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

Chereji, R. V., Ocampo, J., & Clark, D. J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.009 · Cited by 134 · see citing works

Molecular mechanisms of ribosomal protein gene coregulationPreprint

Reja, R., Vinayachandran, V., Ghosh, S., & Pugh, B. F. (2015) · Genes & Development · doi:10.1101/gad.268896.115 · Cited by 132 · see citing works

Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor CPreprint

Franco, A. A., Lam, W. M., Burgers, P., & Kaufman, P. D. (2005) · Genes & Development · doi:10.1101/gad.1305005 · Cited by 131 · see citing works

A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern

Hughes, A. L., Jin, Y., Rando, O. J., & Struhl, K. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.07.003 · Cited by 128 · see citing works

Nucleosome Positioning in Saccharomyces cerevisiae

Jansen, A., & Verstrepen, K. J. (2011) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00046-10 · Cited by 125 · see citing works

ISWI chromatin remodeling complexes in the DNA damage response

Aydın, Ö. Z., Vermeulen, W., & Lans, H. (2014) · Cell Cycle · doi:10.4161/15384101.2014.956551 · Cited by 125 · see citing works

Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

Koerber, R. T., Rhee, H. S., Jiang, C., & Pugh, B. F. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.09.011 · Cited by 123 · see citing works

Mechanisms Underlying Nucleosome Positioning In Vivo

Hughes, A. L., & Rando, O. J. (2014) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-051013-023114 · Cited by 122 · see citing works

Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regionsPreprint

Lorch, Y., Maier-Davis, B., & Kornberg, R. D. (2014) · Genes & Development · doi:10.1101/gad.250704.114 · Cited by 118 · see citing works

Structural Analysis of the Hexasome, Lacking One Histone H2A/H2B Dimer from the Conventional Nucleosome

Arimura, Y., Tachiwana, H., Oda, T., Sato, M., & Kurumizaka, H. (2012) · Biochemistry · doi:10.1021/bi300129b · Cited by 118 · see citing works

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcriptionPreprint

Knight, B., Kubik, S., Ghosh, B., Bruzzone, M. J., Geertz, M., Martín, V. S., Dénervaud, N., Jacquet, P., Özkan, B., Rougemont, J., et al. (2014) · Genes & Development · doi:10.1101/gad.244434.114 · Cited by 115 · see citing works

Domain Architecture of the Catalytic Subunit in the ISW2-Nucleosome Complex

Dang, W., & Bartholomew, B. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01351-07 · Cited by 114 · see citing works

The Histone Chaperone FACT Contributes to DNA Replication-Coupled Nucleosome Assembly

Yang, J., Zhang, X., Feng, J., Leng, H., Li, S., Xiao, J., Liu, S., Xu, Z., Xu, J., Li, D., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.096 · Cited by 114 · see citing works

Rules and regulation in the primary structure of chromatin

Rando, O. J., & Ahmad, K. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.006 · Cited by 113 · see citing works

Dynamic regulation of transcription factors by nucleosome remodeling

Li, M., Hada, A., Sen, P., Olufemi, L., Hall, M. A., Smith, B. Y., Forth, S. T., McKnight, J. N., Patel, A. K., Bowman, G. D., et al. (2015) · eLife · doi:10.7554/elife.06249 · Cited by 112 · see citing works

Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics

Nekrasov, M., Amrichová, J., Parker, B. J., Soboleva, T., Jack, C., Williams, R. B. H., Huttley, G. A., & Tremethick, D. J. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2424 · Cited by 111 · see citing works

Loss of CHD1 causes DNA repair defects and enhances prostate cancer therapeutic responsiveness

Kari, V., Mansour, W. Y., Raul, S. K., Baumgart, S. J., Mund, A., Grade, M., Sirma, H., Simon, R., Will, H., Dobbelstein, M., et al. (2016) · EMBO Reports · doi:10.15252/embr.201642352 · Cited by 111 · see citing works

ISWI complexes in Saccharomyces cerevisiae

Mellor, J., & Morillon, A. (2003) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2003.10.014 · Cited by 107 · see citing works

Nucleosome sequence preferences influence in vivo nucleosome organization

Kaplan, N., Moore, I. K., Fondufe‐Mittendorf, Y. N., Gossett, A. J., Tillo, D., Field, Y., Hughes, T. R., Lieb, J. D., Widom, J., & Segal, E. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0810-918 · Cited by 104 · see citing works

Tripartite organization of centromeric chromatin in budding yeast

Krassovsky, K., Henikoff, J. G., & Henikoff, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118898109 · Cited by 104 · see citing works

Asymmetric nucleosomes flank promoters in the budding yeast genomePreprint

Ramachandran, S., Zentner, G. E., & Henikoff, S. (2014) · Genome Research · doi:10.1101/gr.182618.114 · Cited by 96 · see citing works

Enhancer regions show high histone H3.3 turnover that changes during differentiation

Deaton, A. M., Rodríguez, M. G., Mieczkowski, J., Tolstorukov, M. Y., Kundu, S., Sadreyev, R. I., Jansen, L. E. T., & Kingston, R. E. (2016) · eLife · doi:10.7554/elife.15316 · Cited by 96 · see citing works

Dynamics of Nucleosome Positioning Maturation following Genomic Replication

Vasseur, P., Tonazzini, S., Ziane, R., Camasses, A., Rando, O. J., & Radman‐Livaja, M. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.07.083 · Cited by 93 · see citing works

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T. D., Codomo, C. A., Brogaard, K., Widom, J., Wang, J.-P., & Henikoff, J. G. (2014) · eLife · doi:10.7554/elife.01861 · Cited by 88 · see citing works

MPE-seq, a new method for the genome-wide analysis of chromatin structure

Ishii, H., Kadonaga, J. T., & Ren, B. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1424804112 · Cited by 85 · see citing works

Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code

Clark, D. J. (2010) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/073911010010524945 · Cited by 84 · see citing works

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex

Tramantano, M., Sun, L., Au, C., Labuz, D., Liu, Z., Chou, M., Shen, C., & Luk, E. (2016) · eLife · doi:10.7554/elife.14243 · Cited by 84 · see citing works

SWI-SNF Complex Participation in Transcriptional Activation at a Step Subsequent to Activator Binding

Ryan, M. P., Jones, R., & Morse, R. H. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.4.1774 · Cited by 82 · see citing works

The dynamics of eukaryotic replication initiation: Origin specificity, licensing, and firing at the single-molecule level

Duzdevich, D., Warner, M. D., Ticau, S., Ivica, N. A., Bell, S. P., & Greene, E. C. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.03.017 · Cited by 81 · see citing works

A Positioned Nucleosome on the Human U6 Promoter Allows Recruitment of SNAPc by the Oct-1 POU Domain

Zhao, X., Pendergrast, P. S., & Hernandez, N. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00201-5 · Cited by 80 · see citing works

Stable and dynamic nucleosome states during a meiotic developmental processPreprint

Zhang, L., Mā, H., & Pugh, B. F. (2011) · Genome Research · doi:10.1101/gr.117465.110 · Cited by 80 · see citing works

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

Aguilar‐Gurrieri, C., Larabi, A., Vinayachandran, V., Patel, N. A., Yen, K., Reja, R., Ebong, I.-O., Schoehn, G., Robinson, C. V., Pugh, B. F., et al. (2016) · The EMBO Journal · doi:10.15252/embj.201694105 · Cited by 80 · see citing works

Stepwise nucleosome translocation by RSC remodeling complexes

Harada, B. T., Hwang, W. L., Deindl, S., Chatterjee, N., Bartholomew, B., & Zhuang, X. (2016) · eLife · doi:10.7554/elife.10051 · Cited by 79 · see citing works

A Nucleosome Positioned in the Distal Promoter Region Activates Transcription of the Human U6 Gene

Stünkel, W., Kober, I., & Seifart, K. H. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.8.4397 · Cited by 78 · see citing works

Splitting of H3–H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange

Katan‐Khaykovich, Y., & Struhl, K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018308108 · Cited by 75 · see citing works

The prenucleosome, a stable conformational isomer of the nucleosomePreprint

Fei, J., Torigoe, S. E., Brown, C. R., Khuong, M. T., Kassavetis, G. A., Boeger, H., & Kadonaga, J. T. (2015) · Genes & Development · doi:10.1101/gad.272633.115 · Cited by 73 · see citing works

Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1Preprint

Lee, J., Garrett, A. S., Yen, K., Takahashi, Y.-H., Hu, D., Jackson, J., Seidel, C. W., Pugh, B. F., & Shilatifard, A. (2012) · Genes & Development · doi:10.1101/gad.186841.112 · Cited by 72 · see citing works

Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains

Hota, S. K., Bhardwaj, S. K., Deindl, S., Lin, Y.-C., Zhuang, X., & Bartholomew, B. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2486 · Cited by 72 · see citing works

Chromatin dynamics during DNA replicationPreprint

Bar‐Ziv, R., Voichek, Y., & Barkai, N. (2016) · Genome Research · doi:10.1101/gr.201244.115 · Cited by 67 · see citing works

Swi2/Snf2 remodelers: hybrid views on hybrid molecular machines

Hopfner, K., Gerhold, C., Lakomek, K., & Wollmann, P. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.02.007 · Cited by 66 · see citing works

Genome-Wide Mapping of Nucleosome Positions in Yeast Using High-Resolution MNase ChIP-Seq

Wal, M., & Pugh, B. F. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-391938-0.00010-0 · Cited by 66 · see citing works

Variety of genomic DNA patterns for nucleosome positioningPreprint

Ioshikhes, I. P., Hosid, S., & Pugh, B. F. (2011) · Genome Research · doi:10.1101/gr.116228.110 · Cited by 61 · see citing works

SWI/SNF Binding to the HO Promoter Requires Histone Acetylation and Stimulates TATA-Binding Protein Recruitment

Mitra, D., Parnell, E. J., Landon, J. W., Yu, Y., & Stillman, D. J. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01849-05 · Cited by 61 · see citing works

The Fork in the Road: Histone Partitioning During DNA Replication

Annunziato, A. T. (2015) · Genes · doi:10.3390/genes6020353 · Cited by 60 · see citing works

Evidence against a genomic code for nucleosome positioning Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization”

Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G. M., Snyder, M. P., Kadonaga, J. T., Liu, X. S., & Struhl, K. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0810-920 · Cited by 52 · see citing works

Nucleosome Dynamics as Modular Systems that Integrate DNA Damage and RepairPreprint

Peterson, C. L., & Almouzni, G. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012658 · Cited by 51 · see citing works

The mammalian INO80 chromatin remodeling complex is required for replication stress recovery

Vassileva, I., Yanakieva, I., Peycheva, M., Gospodinov, A. G., & Anachkova, B. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku605 · Cited by 51 · see citing works

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatinPreprint

Svensson, J. P., Shukla, M. S., Menéndez-Benito, V., Axelsson, U., Audergon, P. N. C. B., Sinha, I., Tanny, J. C., Allshire, R. C., & Ekwall, K. (2015) · Genome Research · doi:10.1101/gr.188870.114 · Cited by 51 · see citing works

ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling

Torigoe, S. E., Patel, A. K., Khuong, M. T., Bowman, G. D., & Kadonaga, J. T. (2013) · eLife · doi:10.7554/elife.00863 · Cited by 46 · see citing works

Reconstitution of hemisomes on budding yeast centromeric DNA

Furuyama, T., Codomo, C. A., & Henikoff, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt314 · Cited by 46 · see citing works

Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions

Dutta, A., Gogol, M., Kim, J.-H., Smolle, M., Venkatesh, S., Gilmore, J., Florens, L., Washburn, M. P., & Workman, J. L. (2014) · Genes & Development · doi:10.1101/gad.243584.114 · Cited by 45 · see citing works

Comment on “A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme”

Wang, F., Ranjan, A., Wei, D., & Wu, C. (2016) · Science · doi:10.1126/science.aad5921 · Cited by 43 · see citing works

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

Rizzo, J. M., Bard, J., & Buck, M. (2012) · BMC Molecular Biology · doi:10.1186/1471-2199-13-15 · Cited by 40 · see citing works

Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing

Cui, F., Cole, H. A., Clark, D. J., & Zhurkin, V. B. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks870 · Cited by 40 · see citing works

Nucleosome architecture throughout the cell cycle

Deniz, Ö., Flores, O., Aldea, M., Soler‐López, M., & Orozco, M. (2016) · Scientific Reports · doi:10.1038/srep19729 · Cited by 39 · see citing works

A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution

Zhou, X., Blocker, A. W., Airoldi, E. M., & O’Shea, E. K. (2016) · eLife · doi:10.7554/elife.16970 · Cited by 32 · see citing works

The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome

Nodelman, I. M., Horvath, K. C., Levendosky, R. F., Winger, J., Ren, R., Patel, A. K., Li, M., Wang, M. D., Roberts, E., & Bowman, G. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw406 · Cited by 31 · see citing works

Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns

Park, D., Shivram, H., & Iyer, V. R. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-32 · Cited by 30 · see citing works

Nucleosome dynamics during chromatin remodelingin vivo

Ramachandran, S., & Henikoff, S. (2016) · Nucleus · doi:10.1080/19491034.2016.1149666 · Cited by 28 · see citing works

Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodelerPreprint

McKnight, J. N., Tsukiyama, T., & Bowman, G. D. (2016) · Genome Research · doi:10.1101/gr.199919.115 · Cited by 28 · see citing works

A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters

Yıldırım, Ö., Hung, J., Cedeno, R. J., Weng, Z., Lengner, C. J., & Rando, O. J. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004515 · Cited by 27 · see citing works

Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile

de Boer, C. G., & Hughes, T. R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110479 · Cited by 21 · see citing works

Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure

Studitsky, V. M., & Nizovtseva, E. V. (2016) · Biochemistry & Molecular Biology Journal · doi:10.21767/2471-8084.100017 · Cited by 18 · see citing works

Independent RNA polymerase II preinitiation complex dynamics and nucleosome turnover at promoter sites in vivoPreprint

Grimaldi, Y., Ferrari, P., & Strubin, M. (2013) · Genome Research · doi:10.1101/gr.157792.113 · Cited by 17 · see citing works

Histone post-translational modifications - cause and consequence of genome function

Millán-Zambrano, G., Burton, A., Bannister, A. J., & Schneider, R. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00468-7 · Cited by 1,116 · see citing works

Ultrastructural Details of Mammalian Chromosome Architecture

Krietenstein, N., Abraham, S., Venev, S. V., Abdennur, N., Gibcus, J., Hsieh, T.-H. S., Parsi, K. M., Yang, L., Maehr, R., Mirny, L. A., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.003 · Cited by 622 · see citing works

Transcription regulation by the Mediator complex

Soutourina, J. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.115 · Cited by 591 · see citing works

Chromatin accessibility profiling by ATAC-seq

Grandi, F. C., Modi, H., Kampman, L., & Corces, M. R. (2022) · Nature Protocols · doi:10.1038/s41596-022-00692-9 · Cited by 557 · see citing works

Born to run: control of transcription elongation by RNA polymerase II

Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447 · see citing works

Epigenetic Regulation in Neurodegenerative Diseases

Berson, A., Nativio, R., Berger, S. L., & Bonini, N. M. (2018) · Trends in Neurosciences · doi:10.1016/j.tins.2018.05.005 · Cited by 386 · see citing works

Epigenetics in hepatocellular carcinoma

Nagaraju, G. P., Dariya, B., Kasa, P., Peela, S., & El‐Rayes, B. F. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.07.017 · Cited by 346 · see citing works

The epigenetic basis of cellular heterogeneity

Carter, B. C., & Zhao, K. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00300-0 · Cited by 314 · see citing works

The DNA methylation landscape in cancer

Skvortsova, K., Stirzaker, C., & Taberlay, P. C. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190037 · Cited by 312 · see citing works

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression

Fursova, N. A., Blackledge, N. P., Nakayama, M., Ito, S., Koseki, Y., Farcas, A. M., King, H. W., Koseki, H., & Klose, R. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.024 · Cited by 267 · see citing works

Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health

Xavier, M. J., Roman, S. D., Aitken, R. J., & Nixon, B. (2019) · Human Reproduction Update · doi:10.1093/humupd/dmz017 · Cited by 258 · see citing works

Causes and consequences of RNA polymerase II stalling during transcript elongation

González, M. N., Blears, D., & Svejstrup, J. Q. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00308-8 · Cited by 238 · see citing works

FACT caught in the act of manipulating the nucleosome

Liu, Y., Zhou, K., Zhang, N., Wei, H. A., Tan, Y. Z., Zhang, Z., Carragher, B. O., Potter, C. S., D’Arcy, S., & Luger, K. (2019) · Nature · doi:10.1038/s41586-019-1820-0 · Cited by 214 · see citing works

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Lee, I., Razaghi, R., Gilpatrick, T., Molnar, M. M., Gershman, A., Sadowski, N., Sedlazeck, F. J., Hansen, K. D., Simpson, J. T., & Timp, W. (2020) · Nature Methods · doi:10.1038/s41592-020-01000-7 · Cited by 212 · see citing works

Chromatin accessibility profiling methods

Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206 · see citing works

Structural basis of the nucleosome transition during RNA polymerase II passage

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., & Kurumizaka, H. (2018) · Science · doi:10.1126/science.aau9904 · Cited by 202 · see citing works

In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras -Mutant Lung Adenocarcinoma

Li, F., Huang, Q., Luster, T. A., Hu, H., Zhang, H., Ng, W., Khodadadi‐Jamayran, A., Wang, W., Chen, T., Deng, J., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0780 · Cited by 201 · see citing works

Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancerPreprint

Bracken, A. P., Brien, G. L., & Verrijzer, C. P. (2019) · Genes & Development · doi:10.1101/gad.326066.119 · Cited by 192 · see citing works

Epigenetic regulation of abiotic stress memory: maintaining the good things while they last

Oberkofler, V., Pratx, L., & Bäurle, I. (2021) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2021.102007 · Cited by 172 · see citing works

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

Aoi, Y., Smith, E. R., Shah, A. P., Rendleman, E. J., Marshall, S. A., Woodfin, A. R., Chen, F., Shiekhattar, R., & Shilatifard, A. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.02.014 · Cited by 164 · see citing works

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variantsPreprint

Pampari, A., Shcherbina, A., Kvon, E. Z., Kosicki, M., Nair, S., Kundu, S., Kathiria, A. S., Risca, V. I., Kuningas, K., Alasoo, K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.25.630221 · Cited by 161 · see citing works

Phase separation directs ubiquitination of gene-body nucleosomes

Gallego, L. D., Schneider, M., Mittal, C., Romanauska, A., Carrillo, R. M. G., Schubert, T., Pugh, B. F., & Köhler, A. (2020) · Nature · doi:10.1038/s41586-020-2097-z · Cited by 152 · see citing works

Energy-driven genome regulation by ATP-dependent chromatin remodellers

Eustermann, S., Patel, A. B., Hopfner, K., He, Y., & Korber, P. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00683-y · Cited by 139 · see citing works

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation

Hughes, A. L., Kelley, J. R., & Klose, R. J. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194567 · Cited by 139 · see citing works

Epigenetic regulation of thermomorphogenesis and heat stress tolerance

Perrella, G., Bäurle, I., & van Zanten, M. (2022) · New Phytologist · doi:10.1111/nph.17970 · Cited by 138 · see citing works

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

Brahma, S., & Henikoff, S. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.046 · Cited by 137 · see citing works

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription

Kubik, S., O’Duibhir, E., de Jonge, W. J., Mattarocci, S., Albert, B., Falcone, J.-L., Bruzzone, M. J., Holstege, F. C. P., & Shore, D. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.030 · Cited by 133 · see citing works

Precision (Personalized) Nutrition: Understanding Metabolic Heterogeneity

Zeisel, S. H. (2020) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-032519-051736 · Cited by 130 · see citing works

Structural basis of nucleosome transcription mediated by Chd1 and FACT

Farnung, L., Ochmann, M., Engeholm, M., & Cramer, P. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00578-6 · Cited by 129 · see citing works

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Kubik, S., Bruzzone, M. J., Challal, D., Dreos, R., Mattarocci, S., Bucher, P., Libri, D., & Shore, D. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0273-3 · Cited by 126 · see citing works

Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg

Fernández-Barrena, M. G., Arechederra, M., Colyn, L., Berasain, C., & Avila, M. A. (2020) · JHEP Reports · doi:10.1016/j.jhepr.2020.100167 · Cited by 126 · see citing works

Super-enhancers: critical roles and therapeutic targets in hematologic malignancies

Jia, Y., Chng, W. J., & Zhou, J. (2019) · Journal of Hematology & Oncology · doi:10.1186/s13045-019-0757-y · Cited by 112 · see citing works

Beads on a string—nucleosome array arrangements and folding of the chromatin fiber

Baldi, S., Korber, P., & Becker, P. B. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0368-x · Cited by 112 · see citing works

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization

Beh, L. Y., Debelouchina, G. T., Clay, D. M., Thompson, R. E., Lindblad, K. A., Hutton, E. R., Bracht, J. R., Sebra, R., Muir, T. W., & Landweber, L. F. (2019) · Cell · doi:10.1016/j.cell.2019.04.028 · Cited by 109 · see citing works

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

Jerónimo, C., Poitras, C., & Robert, F. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.06.097 · Cited by 107 · see citing works

Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment

Le, J., Dian, Y., Zhao, D., Guo, Z., Luo, Z., Chen, X., Zeng, F., & Deng, G. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02426-3 · Cited by 109 · see citing works

The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin

Francette, A. M., Tripplehorn, S. A., & Arndt, K. M. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166979 · Cited by 104 · see citing works

Structure of transcribing RNA polymerase II-nucleosome complex

Farnung, L., Vos, S. M., & Cramer, P. (2018) · Nature Communications · doi:10.1038/s41467-018-07870-y · Cited by 100 · see citing works

Dietary Modulation of the Epigenome

Ideraabdullah, F., & Zeisel, S. H. (2018) · Physiological Reviews · doi:10.1152/physrev.00010.2017 · Cited by 98 · see citing works

Multiscale modeling of genome organization with maximum entropy optimization

Lin, X., Qi, Y., Latham, A. P., & Zhang, B. (2021) · The Journal of Chemical Physics · doi:10.1063/5.0044150 · Cited by 96 · see citing works

Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity

Hu, Y., Shen, F., Yang, X., Han, T., Long, Z., Wen, J., Huang, J., Shen, J., & Guo, Q. (2023) · Clinical Epigenetics · doi:10.1186/s13148-023-01574-x · Cited by 97 · see citing works

Transcription through the nucleosome

Kujirai, T., & Kurumizaka, H. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.10.007 · Cited by 94 · see citing works

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory

Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., & Cramer, P. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00768-w · Cited by 93 · see citing works

The Histone H3 Lysine 4 Presenter WDR5 as an Oncogenic Protein and Novel Epigenetic Target in Cancer

Lu, K., Tao, H., Si, X., & Chen, Q. (2018) · Frontiers in Oncology · doi:10.3389/fonc.2018.00502 · Cited by 88 · see citing works

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

Oldfield, A., Henriques, T., Kumar, D., Burkholder, A., Cinghu, S., Paulet, D., Bennett, B. D., Yang, P., Scruggs, B. S., Lavender, C. A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10905-7 · Cited by 88 · see citing works

Design, Synthesis, and Evaluation of WD-Repeat-Containing Protein 5 (WDR5) Degraders

Dölle, A., Adhikari, B., Krämer, A., Weckesser, J., Berner, N., Berger, L. M., Diebold, M., Szewczyk, M. M., Baršytė-Lovejoy, D., Arrowsmith, C. H., et al. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c00146 · Cited by 86 · see citing works

The nucleosome core particle remembers its position through DNA replication and RNA transcription

Schlissel, G., & Rine, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1911943116 · Cited by 81 · see citing works

Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Oberbeckmann, E., Niebauer, V., Watanabe, S., Farnung, L., Moldt, M., Schmid, A., Cramer, P., Peterson, C. L., Eustermann, S., Hopfner, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23015-0 · Cited by 80 · see citing works

Multiscale footprints reveal the organization of cis-regulatory elements

Yan, H., Horlbeck, M. A., Zhang, R., Ma, S., Shrestha, R., Kartha, V. K., Duarte, F. M., Hock, C., Savage, R. E., Labade, A. S., et al. (2025) · Nature · doi:10.1038/s41586-024-08443-4 · Cited by 80 · see citing works

Mechanosensing dysregulation in the fibroblast: A hallmark of the aging heart

Angelini, A., Trial, J., Ortiz-Urbina, J., & Cieslik, K. A. (2020) · Ageing Research Reviews · doi:10.1016/j.arr.2020.101150 · Cited by 79 · see citing works

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network

Hammond, C. M., Bao, H., Hendriks, I. A., Carraro, M., García-Nieto, A., Liu, Y., Reverón-Gómez, N., Spanos, C., Chen, L., Rappsilber, J., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.041 · Cited by 79 · see citing works

Fragmentomic analysis of circulating tumor DNA-targeted cancer panels

Helzer, K. T., Sharifi, M. N., Sperger, J. M., Shi, Y., Annala, M., Bootsma, M. L., Reese, S. R., Taylor, A. K., Kaufmann, K. R., Krause, H., et al. (2023) · Annals of Oncology · doi:10.1016/j.annonc.2023.06.001 · Cited by 79 · see citing works

Structures of +1 nucleosome–bound PIC-Mediator complex

Chen, X., Wang, X., Liu, W., Ren, Y., Qu, X., Li, J., Yin, X., & Xu, Y. (2022) · Science · doi:10.1126/science.abn8131 · Cited by 76 · see citing works

Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Ranjan, A., Nguyen, V. Q., Liu, S., Wiśniewski, J., Kim, J. M., Tang, X., Mizuguchi, G., Elalaoui, E., Nickels, T. J., Jou, V., et al. (2020) · eLife · doi:10.7554/elife.55667 · Cited by 75 · see citing works

Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes

Sarkar, N. D., Patton, R. D., Doebley, A.-L., Hanratty, B. P., Kreitzman, A. J., Sarthy, J. F., Ko, M., Adil, M., Brahma, S., Meers, M. P., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0692 · Cited by 75 · see citing works

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

Jerónimo, C., Angel, A., Nguyen, V. Q. C., Kim, J. M., Poitras, C., Lambert, É., Collin, P., Mellor, J., Wu, C., & Robert, F. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.010 · Cited by 73 · see citing works

Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function

Singh, R., Bassett, E. A., Chakravarti, A., & Parthun, M. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky768 · Cited by 69 · see citing works

Single-molecule long-read sequencing reveals the chromatin basis of gene expressionPreprint

Wang, Y., Wang, A., Liu, Z., Thurman, A. L., Powers, L. S., Zou, M., Zhao, Y., Hefel, A., Li, Y., Zabner, J., et al. (2019) · Genome Research · doi:10.1101/gr.251116.119 · Cited by 68 · see citing works

KDM5B demethylates H3K4 to recruit XRCC1 and promote chemoresistance

Xu, W., Zhou, B., Zhao, X., Zhu, L., Xu, J., Jiang, Z., Chen, D., Wei, Q., Han, M., Feng, L., et al. (2018) · International Journal of Biological Sciences · doi:10.7150/ijbs.25881 · Cited by 67 · see citing works

Targeting Chromatin Remodeling for Cancer Therapy

Kaur, J., Daoud, A., & Eblen, S. T. (2019) · Current Molecular Pharmacology · doi:10.2174/1874467212666190215112915 · Cited by 65 · see citing works

Sentinels of chromatin: chromodomain helicase DNA-binding proteins in development and diseasePreprint

Alendar, A., & Berns, A. J. M. (2021) · Genes & Development · doi:10.1101/gad.348897.121 · Cited by 65 · see citing works

Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

Kim, J. M., Visanpattanasin, P., Jou, V., Liu, S., Tang, X., Zheng, Q., Li, K. Y., Snedeker, J. C., Lavis, L. D., Lionnet, T., et al. (2021) · eLife · doi:10.7554/elife.69387 · Cited by 64 · see citing works

Shared genetic and epigenetic changes link aging and cancer

Zabransky, D. J., Jaffee, E. M., & Weeraratna, A. T. (2022) · Trends in Cell Biology · doi:10.1016/j.tcb.2022.01.004 · Cited by 64 · see citing works

Histone chaperone FACT complex mediates oxidative stress response to promote liver cancer progression

Shen, J., Chen, M., Lee, D., Law, C., Wei, L., Tsang, F. H., Chin, D. W., Cheng, C. L., Lee, J. M., Ng, I. O., et al. (2019) · Gut · doi:10.1136/gutjnl-2019-318668 · Cited by 64 · see citing works

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

(2023) · doi:10.1016/j.molcel.2023.02.009 · Cited by 62 · see citing works

Transcription-coupled repair of DNA–protein cross-links depends on CSA and CSB

Carnie, C. J., Acampora, A. C., Bader, A. S., Erdenebat, C., Zhao, S., Bitensky, E. M., van den Heuvel, D., Parnas, A., Gupta, V., D’Alessandro, G., et al. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01391-1 · Cited by 61 · see citing works

Structure of transcribing RNA polymerase II-nucleosome complex

Farnung, L., Vos, S. M., & Cramer, P. (2018) · Worldwide Protein Data Bank · doi:10.2210/pdb6i84/pdb · Cited by 61 · see citing works

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

Oberbeckmann, E., Krietenstein, N., Niebauer, V., Wang, Y., Schall, K., Moldt, M., Straub, T., Rohs, R., Hopfner, K., Korber, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23016-z · Cited by 60 · see citing works

Regulation of neuronal connectivity in the mammalian brain by chromatin remodeling

Goodman, J. V., & Bonni, A. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.04.010 · Cited by 60 · see citing works

General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation

Challal, D., Barucco, M., Kubik, S., Feuerbach, F., Candelli, T., Geoffroy, H., Benaksas, C., Shore, D., & Libri, D. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.11.037 · Cited by 60 · see citing works

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Clarkson, C. T., Deeks, E. A., Samarista, R., Mamayusupova, H., Zhurkin, V. B., & Teif, V. B. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz908 · Cited by 60 · see citing works

DNA mechanics and its biological impact

Basu, A., Bobrovnikov, D. G., & Ha, T. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166861 · Cited by 59 · see citing works

Structure of a backtracked hexasomal intermediate of nucleosome transcription

Farnung, L., Ochmann, M., Garg, G., Vos, S. M., & Cramer, P. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.027 · Cited by 59 · see citing works

Structural transition of the nucleosome during chromatin remodeling and transcription

Kobayashi, W., & Kurumizaka, H. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.07.011 · Cited by 58 · see citing works

Pharmacological targeting of the cancer epigenome

Mabe, N. W., Perry, J. A., Malone, C. F., & Stegmaier, K. (2024) · Nature Cancer · doi:10.1038/s43018-024-00777-2 · Cited by 58 · see citing works

Histone chaperone FACT FAcilitates Chromatin Transcription: mechanistic and structural insights

Zhou, K., Liu, Y., & Luger, K. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.05.019 · Cited by 58 · see citing works

Resetting the Yeast Epigenome with Human Nucleosomes

Truong, D. M., & Boeke, J. D. (2017) · Cell · doi:10.1016/j.cell.2017.10.043 · Cited by 57 · see citing works

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

Brandani, G. B., & Takada, S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006512 · Cited by 57 · see citing works

Structural visualization of key steps in nucleosome reorganization by human FACT

Mayanagi, K., Saikusa, K., Miyazaki, N., Akashi, S., Iwasaki, K., Nishimura, Y., Morikawa, K., & Tsunaka, Y. (2019) · Scientific Reports · doi:10.1038/s41598-019-46617-7 · Cited by 57 · see citing works

Unravelling the role of epigenetics in reproductive adaptations to early-life environment

Bar-Sadeh, B., Rudnizky, S., Pnueli, L., Bentley, G. R., Stöger, R. J., Kaplan, A., & Melamed, P. (2020) · Nature Reviews Endocrinology · doi:10.1038/s41574-020-0370-8 · Cited by 57 · see citing works

Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR

Kitevski-LeBlanc, J. L., Yuwen, T., Dyer, P. N., Rudolph, J., Luger, K., & Kay, L. E. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b00931 · Cited by 56 · see citing works

Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications

Arora, I., & Tollefsbol, T. O. (2020) · Methods · doi:10.1016/j.ymeth.2020.09.008 · Cited by 56 · see citing works

Current and Emerging Methods for the Synthesis of Single-Stranded DNA

Hao, M., Qiao, J., & Qi, H. (2020) · Genes · doi:10.3390/genes11020116 · Cited by 55 · see citing works

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome

Sharma, D., Falco, L. D., Padavattan, S., Rao, C., Shochat, S. G., Liu, C., & Davey, C. A. (2019) · Nature Communications · doi:10.1038/s41467-019-13641-0 · Cited by 55 · see citing works

The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain

Goodman, J. V., Yamada, T., Yang, Y., Kong, L., Wu, D. Y., Zhao, G.-Y., Gabel, H. W., & Bonni, A. (2020) · Nature Communications · doi:10.1038/s41467-020-17065-z · Cited by 55 · see citing works

Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication

Gruszka, D. T., Xie, S., Kimurâ, H., & Yardimci, H. (2020) · Science Advances · doi:10.1126/sciadv.abc0330 · Cited by 49 · see citing works

Structural basis of transcription reduction by a promoter-proximal +1 nucleosome

Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., & Cramer, P. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.011 · Cited by 48 · see citing works

The role of histone post-translational modifications in cancer and cancer immunity: functions, mechanisms and therapeutic implications

Duan, X., Xing, Z., Qiao, L., Qin, S., Zhao, X., Gong, Y., & Li, X. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1495221 · Cited by 48 · see citing works

Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response

Pai, A. A., & Luca, F. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1503 · Cited by 47 · see citing works

Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells

Cole, L. A., Kurscheid, S., Nekrasov, M., Domaschenz, R., Vera, D. L., Dennis, J. H., & Tremethick, D. J. (2021) · Nature Communications · doi:10.1038/s41467-021-22688-x · Cited by 47 · see citing works

Global transcriptional activity dynamics reveal functional enhancer RNAsPreprint

Kim, Y. J., Xie, P., Cao, L. F., Zhang, M. Q., & Kim, T. H. (2018) · Genome Research · doi:10.1101/gr.233486.117 · Cited by 47 · see citing works

Valuing the Diversity of Research Methods to Advance Nutrition Science

Mattes, R. D., Rowe, S. B., Ohlhorst, S. D., Brown, A. W., Hoffman, D. J., Liska, D. J., Feskens, E. J. M., Dhillon, J., Tucker, K. L., Epstein, L. H., et al. (2022) · Advances in Nutrition · doi:10.1093/advances/nmac043 · Cited by 46 · see citing works

The biogenesis and function of nucleosome arrays

Singh, A. K., Schauer, T., Pfaller, L., Straub, T., & Mueller‐Planitz, F. (2021) · Nature Communications · doi:10.1038/s41467-021-27285-6 · Cited by 45 · see citing works

Structural mechanism of extranucleosomal DNA readout by the INO80 complex

Kunert, F., Metzner, F. J., Jung, J., Höpfler, M., Woike, S., Schall, K., Kostrewa, D., Moldt, M., Chen, J., Bantele, S. C. S., et al. (2022) · Science Advances · doi:10.1126/sciadv.add3189 · Cited by 45 · see citing works

Entering the Next Dimension: Plant Genomes in 3D

Sotelo-Silveira, M., Montes, R. A. C., Sotelo-Silveira, J. R., Marsch‐Martínez, N., & de Folter, S. (2018) · Trends in Plant Science · doi:10.1016/j.tplants.2018.03.014 · Cited by 45 · see citing works

The epigenetic chromatin-based regulation of somatic heat stress memory in plants

Haider, S., Iqbal, J., Shaukat, M., Naseer, S., & Mahmood, T. (2021) · Plant Gene · doi:10.1016/j.plgene.2021.100318 · Cited by 44 · see citing works

The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

Torres, E., & Deal, R. B. (2019) · The Plant Journal · doi:10.1111/tpj.14281 · Cited by 44 · see citing works

Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX

de Nonneville, A. T., & Reddel, R. R. (2021) · Nature Communications · doi:10.1038/s41467-021-21794-0 · Cited by 44 · see citing works

Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis

Zhao, T., Lu, J., Zhang, H., Xue, M., Pan, J., Ma, L., Berger, F., & Jiang, D. (2022) · Nature Communications · doi:10.1038/s41467-022-35509-6 · Cited by 43 · see citing works

Distinct guard cell–specific remodeling of chromatin accessibility during abscisic acid– and CO 2 -dependent stomatal regulation

Seller, C. A., & Schroeder, J. I. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2310670120 · Cited by 42 · see citing works

Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes

de Fenffe, C. M. D., Govers, J., & Mattiroli, F. (2025) · Biochemistry · doi:10.1021/acs.biochem.5c00114 · Cited by 10 · see citing works

Nucleosome Structure and Function

Chodaparambil, J. V., Edayathumangalam, R. S., Bao, Y., Park, Y., & Luger, K. (2006) · Springer eBooks · doi:10.1007/3-540-37633-x_2 · Cited by 24 · see citing works

Rules and regulation in the primary structure of chromatin

Rando, O. J., & Ahmad, K. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.006 · Cited by 113 · see citing works

Mechanisms of Nucleosome Dynamics In VivoPreprint

Henikoff, S. (2016) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a026666 · Cited by 26 · see citing works

Dynamic nucleosomes

Luger, K. (2006) · Chromosome Research · doi:10.1007/s10577-005-1026-1 · Cited by 172 · see citing works