Chromatin Higher-order Structure and Dynamics

Woodcock, C. L.; Ghosh, R. P.

doi:10.1101/cshperspect.a000596

Cited by 384Genomics and Chromatin DynamicsNuclear Structure and FunctionChromatin Remodeling and Cancer

Chromatin Higher-order Structure and Dynamics

Open access

Woodcock, C. L., Ghosh, R. P.·2010·Cold Spring Harbor Perspectives in Biology

DOI 10.1101/cshperspect.a000596PMC PMC2857170

Open this paper in CoChat — free account

Abstract

The primary role of the nucleus as an information storage, retrieval, and replication site requires the physical organization and compaction of meters of DNA. Although it has been clear for many years that nucleosomes constitute the first level of chromatin compaction, this contributes a relatively small fraction of the condensation needed to fit the typical genome into an interphase nucleus or set of metaphase chromosomes, indicating that there are additional "higher order" levels of chromatin condensation. Identifying these levels, their interrelationships, and the principles that govern their occurrence has been a challenging and much discussed problem. In this article, we focus on recent experimental advances and the emerging evidence indicating that structural plasticity and chromatin dynamics play dominant roles in genome organization. We also discuss novel approaches likely to yield important insights in the near future, and suggest research areas that merit further study.

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

Crossref · 10.1101/cshperspect.a000596

Cites

137 of 137 references verified0 citation errors · 0 not checkable

Statistics

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.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Chromosomal contacts follow the law of constrained Brownian motion, with contact probabilities showing a strong power-law dependence on linear genomic distance.
“Chromosomal contacts follow the law of constrained Brownian motion (reviewed in [465]), with the contact probabilities showing a strong power–law dependence on the “linear” genomic distance [272, 466].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [465]
Chromatin condensation status and existing chromatin dynamics influence both UV damage occurrence and repair capacity.
“One of the critical factors that influence both damage occurrence and repair capacity is certainly the chromatin condensation status and existing chromatin dynamics.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [31]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883 · see citing works
Translating the Histone Code
Jenuwein, T., & Allis, C. D. (2001) · Science · doi:10.1126/science.1063127 · Cited by 9,756 · 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
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works
Lanthanum Chloride Inhibits LPS Mediated Expressions of Pro-Inflammatory Cytokines and Adhesion Molecules in HUVECs: Involvement of NF-κB-Jmjd3 Signaling
Chen, X., Xiu, M., Xing, J., Yu, S., Min, D., & Guo, F. (2017) · Cellular Physiology and Biochemistry · doi:10.1159/000479439 · Cited by 5,759 · see citing works
The biology of chromatin remodeling complexes.
Clapier, C. R., & Cairns, B. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062706.153223 · Cited by 2,384 · see citing works
Long noncoding RNAs: functional surprises from the RNA worldPreprint
Wilusz, J. E., Sunwoo, H., & Spector, D. L. (2009) · Genes & Development · doi:10.1101/gad.1800909 · Cited by 2,298 · see citing works
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions
Shogren‐Knaak, M. A., Ishii, H., Sun, J.-M., Pazin, M. J., Davie, J., & Peterson, C. L. (2006) · Science · doi:10.1126/science.1124000 · Cited by 1,876 · see citing works
Super-resolution fluorescence microscopy
Huang, B., Bates, M., & Zhuang, X. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.061906.092014 · Cited by 1,657 · see citing works
The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media
Minton, A. P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.r100005200 · Cited by 1,474 · see citing works
RNAi-Mediated Targeting of Heterochromatin by the RITS Complex
Verdel, A., Jia, S., Gerber, S. A., Sugiyama, T., Gygi, S. P., Grewal, S. I. S., & Moazed, D. (2004) · Science · doi:10.1126/science.1093686 · Cited by 1,221 · see citing works
High mobility of proteins in the mammalian cell nucleus
Phair, R. D., & Misteli, T. (2000) · Nature · doi:10.1038/35007077 · Cited by 1,212 · see citing works
Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy
Schermelleh, L., Carlton, P. M., Haase, S., Shao, L., Winoto, L., Kner, P., Burke, B. E., Cardoso, M. C., Agard, D. A., Gustafsson, M. G. L., et al. (2008) · Science · doi:10.1126/science.1156947 · Cited by 1,126 · 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
Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomainsPreprint
Fischle, W., Wang, Y., Jacobs, S. A., Kim, Y., Allis, C. D., & Khorasanizadeh, S. (2003) · Genes & Development · doi:10.1101/gad.1110503 · Cited by 993 · see citing works
X-ray structure of a tetranucleosome and its implications for the chromatin fibre
Schalch, T., Duda, S., Sargent, D. F., & Richmond, T. J. (2005) · Nature · doi:10.1038/nature03686 · Cited by 839 · see citing works
Structure of HP1 Chromodomain Bound to a Lysine 9-Methylated Histone H3 Tail
Jacobs, S. A., & Khorasanizadeh, S. (2002) · Science · doi:10.1126/science.1069473 · Cited by 834 · see citing works
Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin.
Brown, K., Guest, S. S., Smale, S., Hahm, K., Merkenschlager, M., & Fisher, A. (1997) · Cell · doi:10.1016/s0092-8674(00)80472-9 · Cited by 824 · see citing works
Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution
Solovei, I. V., Kreysing, M., Lanctôt, C., Kösem, S., Peichl, L., Cremer, T. J., Guck, J. R., & Joffe, B. I. (2009) · Cell · doi:10.1016/j.cell.2009.01.052 · Cited by 785 · see citing works
The Organization of Replication and Transcription
Cook, P. R. (1999) · Science · doi:10.1126/science.284.5421.1790 · Cited by 752 · see citing works
Subnuclear Compartmentalization of Immunoglobulin Loci During Lymphocyte Development
Kosak, S. T., Skok, J. A., Medina, K. L., Riblet, R. J., Beau, M. M. L., Fisher, A. G., & Singh, H. (2002) · Science · doi:10.1126/science.1068768 · Cited by 722 · see citing works
Interphase chromosomes undergo constrained diffusional motion in living cells
Marshall, W. F., Straight, A. F., Marko, J. F., Swedlow, J. R., Dernburg, A. F., Belmont, A. S., Murray, A. W., Agard, D. A., & Sedat, J. W. (1997) · Current Biology · doi:10.1016/s0960-9822(06)00412-x · Cited by 673 · see citing works
Formation in Vitro of Sperm Pronuclei and Mitotic Chromosomes Induced by Amphibian Ooplasmic Components
Lohka, M. J., & Masui, Y. (1983) · Science · doi:10.1126/science.6601299 · Cited by 634 · see citing works
Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcriptionPreprint
Chambeyron, S., & Bickmore, W. A. (2004) · Genes & Development · doi:10.1101/gad.292104 · Cited by 618 · see citing works
Genomic views of distant-acting enhancers
Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610 · see citing works
Facultative Heterochromatin: Is There a Distinctive Molecular Signature?
Trojer, P., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.011 · Cited by 609 · see citing works
Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin
Bednář, J., Horowitz, R. A., Grigoryev, S. A., Carruthers, L. M., Hansen, J. C., Koster, A. J., & Woodcock, C. L. F. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.24.14173 · Cited by 593 · see citing works
Self-citation
Chromatin Motion Is Constrained by Association with Nuclear Compartments in Human Cells
Chubb, J. R., Boyle, S., Perry, P., & Bickmore, W. A. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00695-4 · Cited by 580 · see citing works
At the heart of the chromosome: SMC proteins in action
Hirano, T. (2006) · Nature reviews. Molecular cell biology · doi:10.1038/nrm1909 · Cited by 569 · see citing works
Nucleosome Arrays Reveal the Two-Start Organization of the Chromatin Fiber
Dorigo, B., Schalch, T., Kulangara, A., Duda, S., Schroeder, R. R., & Richmond, T. J. (2004) · Science · doi:10.1126/science.1103124 · Cited by 562 · see citing works
Long-Range Directional Movement of an Interphase Chromosome Site
Chuang, C.-H., Carpenter, A. E., Fuchsová, B., Johnson, T., de Lanerolle, P., & Belmont, A. S. (2006) · Current Biology · doi:10.1016/j.cub.2006.03.059 · Cited by 556 · see citing works
Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy
Marko, M., Hsieh, C., Schalek, R. L., et al. (2007) · Nature Methods · doi:10.1038/nmeth1014 · Cited by 545 · see citing works
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
Luger, K., Suto, R. K., Clarkson, M. J., & Tremethick, D. J. (2000) · Nature Structural Biology · doi:10.1038/81971 · Cited by 541 · see citing works
Metaphase chromosome structure
Gasser, S. M., Laroche, T., Falquet, J., et al. (1986) · Journal of Molecular Biology · doi:10.1016/s0022-2836(86)80010-9 · Cited by 541 · see citing works
The concept of self-organization in cellular architecture
Misteli, T. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200108110 · Cited by 522 · see citing works
EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure
Robinson, P. J. J., Fairall, L., Huynh, V. A. T., & Rhodes, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601212103 · Cited by 517 · see citing works
Chd1 regulates open chromatin and pluripotency of embryonic stem cells
Gaspar‐Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M. J., Heidersbach, A. J., Ramalho‐Santos, J., McManus, M. T., Plath, K., Meshorer, E., et al. (2009) · Nature · doi:10.1038/nature08212 · Cited by 509 · see citing works
Supercoils in human dna
Cook, P. R., & Brazell, I. A. (1975) · Journal of Cell Science · doi:10.1242/jcs.19.2.261 · Cited by 488 · see citing works
Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
Cui, Y., & Bustamante, C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.1.127 · Cited by 488 · see citing works
Chromosome Dynamics in the Yeast Interphase Nucleus
Heun, P., Laroche, T., Shimada, K., et al. (2001) · Science · doi:10.1126/science.1065366 · Cited by 486 · see citing works
Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length
Woodcock, C. L. F., Skoultchi, A. I., & Fan, Y. (2006) · Chromosome Research · doi:10.1007/s10577-005-1024-3 · Cited by 467 · see citing works
Self-citation
Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: A model system for study of higher order structure
Simpson, R. T., Thoma, F., & Brubaker, J. M. (1985) · Cell · doi:10.1016/0092-8674(85)90276-4 · Cited by 466 · see citing works
Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei
Volpi, E. V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J. A., Beck, S., Campbell, R. D., Goldsworthy, M. E., Powis, S. H., Ragoussis, J., et al. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.9.1565 · Cited by 441 · see citing works
Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin
Bancaud, A., Huet, S., Daigle, N., Mozziconacci, J., Beaudouin, J., & Ellenberg, J. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.340 · Cited by 438 · see citing works
Histone H3 variants and their potential role in indexing mammalian genomes: The “H3 barcode hypothesis”
Hake, S. B., & Allis, C. D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600803103 · Cited by 435 · see citing works
Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division.
Brown, K., Baxter, J., Graf, D., Merkenschlager, M., & Fisher, A. G. (1999) · Molecules and Cells · doi:10.1016/s1097-2765(00)80311-1 · Cited by 426 · see citing works
Spatial proximity of translocation-prone gene loci in human lymphomas
Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A., & Misteli, T. (2003) · Nature Genetics · doi:10.1038/ng1177 · Cited by 414 · see citing works
Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ
Eltsov, M., MacLellan‐Gibson, K., Maeshima, K., Frangakis, A. S., & Dubochet, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810057105 · Cited by 404 · see citing works
A means to a DNA end: the many roles of Ku
Downs, J. A., & Jackson, S. P. (2004) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1367 · Cited by 393 · see citing works
Induced Chromosomal Proximity and Gene Fusions in Prostate Cancer
Mani, R. S., Tomlins, S. A., Callahan, K., Ghosh, A., Nyati, M. K., Varambally, S., Palanisamy, N., & Chinnaiyan, A. M. (2009) · Science · doi:10.1126/science.1178124 · Cited by 391 · see citing works
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure
Routh, A. L., Sandin, S., & Rhodes, D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802336105 · Cited by 372 · see citing works
Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain
Tumbar, T., Sudlow, G., & Belmont, A. S. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.145.7.1341 · Cited by 351 · see citing works
Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure.
Belmont, A. S., & Bruce, K. (1994) · The Journal of Cell Biology · doi:10.1083/jcb.127.2.287 · Cited by 344 · see citing works
Higher-Order Structures of Chromatin: The Elusive 30 nm Fiber
Tremethick, D. J. (2007) · Cell · doi:10.1016/j.cell.2007.02.008 · Cited by 344 · see citing works
Visualizing Chromatin Dynamics in Interphase Nuclei
Gasser, S. M. (2002) · Science · doi:10.1126/science.1067703 · Cited by 334 · see citing works
H1 Linker Histones Are Essential for Mouse Development and Affect Nucleosome Spacing In Vivo
Fan, Y., Tv, N., Morin‐Kensicki, E., Zhao, J., Magnuson, T., Woodcock, C. L. F., & Skoultchi, A. I. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.13.4559-4572.2003 · Cited by 325 · see citing works
Self-citation
Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locusPreprint
Schübeler, D., Francastel, C., Cimbora, D. M., Reik, A., Martin, D. I. K., & Groudine, M. T. (2000) · Genes & Development · doi:10.1101/gad.14.8.940 · Cited by 308 · see citing works
H2A.Z Alters the Nucleosome Surface to Promote HP1α-Mediated Chromatin Fiber Folding
Fan, J. Y., Rangasamy, D., Luger, K., & Tremethick, D. J. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.10.023 · Cited by 305 · see citing works
Architecture of metaphase chromosomes and chromosome scaffolds
Earnshaw, W. C., & Laemmli, U. K. (1983) · Journal of Cell Biology · doi:10.1083/jcb.96.1.84 · Cited by 305 · see citing works
Higher-order structure of chromatin and chromosomes
Woodcock, C. L. F., & Dimitrov, S. I. (2001) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00169-6 · Cited by 300 · see citing works
Self-citation
Half a Century of “The Nuclear Matrix”
Pederson, T. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.3.799 · Cited by 298 · see citing works
Molecular crowding effects on structure and stability of DNA
Miyoshi, D., & Sugimoto, N. (2008) · Biochimie · doi:10.1016/j.biochi.2008.02.009 · Cited by 290 · see citing works
Rabl's model of the interphase chromosome arrangement tested in Chinise hamster cells by premature chromosome condensation and laser-UV-microbeam experiments
Cremer, T. J., Cremer, C. G., Baumann, H., Luedtke, E. K., Sperling, K., Teuber, V., & Zorn, C. (1982) · Human Genetics · doi:10.1007/bf00281263 · Cited by 288 · see citing works
Electrostatic mechanism of chromatin folding
Clark, D. J., & Kimura, T. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90081-v · Cited by 267 · see citing works
Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
Kruithof, M., Chien, F.-T., Routh, A. L., Logie, C., Rhodes, D., & van Noort, J. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1590 · Cited by 265 · see citing works
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions
Grigoryev, S. A., Arya, G., Correll, S., Woodcock, C. L. F., & Tamar Schlick, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903280106 · Cited by 263 · see citing works
Self-citation
Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus
Vazquez, J., Belmont, A. S., & Sedat, J. W. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00390-6 · Cited by 261 · see citing works
Cation–chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes
Strick, R., Strissel, P. L., Gavrilov, K. L., et al. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200105026 · Cited by 248 · see citing works
The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon.
Horowitz, R. A., Agard, D. A., Sedat, J. W., et al. (1994) · The Journal of Cell Biology · doi:10.1083/jcb.125.1.1 · Cited by 245 · see citing works
Nucleosome Positioning: Occurrence, Mechanisms, and Functional Consequences
Simpson, R. T. (1991) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60841-7 · Cited by 244 · see citing works
Chromatin Dynamics in Interphase Cells Revealed by Tracking in a Two-Photon Excitation Microscope
Levi, V., Ruan, Q., Plutz, M. J., Belmont, A. S., & Gratton, E. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.066670 · Cited by 240 · see citing works
Chromatin loops in gene regulation
Kadauke, S., & Blobel, G. A. (2008) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2008.07.002 · Cited by 237 · see citing works
Replication fork movement sets chromatin loop size and origin choice in mammalian cells
Courbet, S., Gay, S., Arnoult, N., Wronka, G., Anglana, M., Brison, O., & Debatisse, M. (2008) · Nature · doi:10.1038/nature07233 · Cited by 237 · see citing works
Topoisomerase II does not play a scaffolding role in the organization of mitotic chromosomes assembled in Xenopus egg extracts.
Hirano, T., & Mitchison, T. J. (1993) · The Journal of Cell Biology · doi:10.1083/jcb.120.3.601 · Cited by 233 · see citing works
Condensin and cohesin: more than chromosome compactor and glue
Hagstrom, K., & Meyer, B. J. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1110 · Cited by 228 · see citing works
Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex
Rando, O. J., Zhao, K., Janmey, P. A., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032662899 · Cited by 228 · see citing works
Nucleosome and chromatin fiber dynamics
Luger, K., & Hansen, J. C. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.03.006 · Cited by 227 · see citing works
Condensin and Repo-Man–PP1 co-operate in the regulation of chromosome architecture during mitosis
Vagnarelli, P., Hudson, D. F., Ribeiro, S. A., et al. (2006) · Nature Cell Biology · doi:10.1038/ncb1475 · Cited by 227 · see citing works
Visualization of early chromosome condensation
Kireeva, N., Lakonishok, M., Kireev, I. I., Hirano, T., & Belmont, A. S. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200406049 · Cited by 209 · see citing works
Dynamic elastic behavior of alpha-satellite DNA domains visualized in situ in living human cells.
Shelby, R. D., Hahn, K. M., & Sullivan, K. F. (1996) · The Journal of Cell Biology · doi:10.1083/jcb.135.3.545 · Cited by 207 · see citing works
Nuclear re-organisation of the Hoxb complex during mouse embryonic development
Chambeyron, S., Silva, N. D., Lawson, K. A., & Bickmore, W. A. (2005) · Development · doi:10.1242/dev.01813 · Cited by 202 · see citing works
Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins
Chen, D., Dundr, M., Wang, C., Leung, A. K. L., Lamond, A. I., Misteli, T., & Huang, S. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200407182 · Cited by 200 · see citing works
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
Arya, G., & Schlick, T. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604817103 · Cited by 200 · see citing works
Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro
Belmont, A. S., Braunfeld, M. B., Sedat, J. W., et al. (1989) · Chromosoma · doi:10.1007/bf00291049 · Cited by 198 · see citing works
Transcription factors mediate long-range enhancer–promoter interactions
Nolis, I. K., McKay, D. J., Mantouvalou, E., Lomvardas, S., Merika, M., & Thanos, D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902454106 · Cited by 191 · see citing works
Mitotic chromosome structure and condensation
Belmont, A. S. (2006) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2006.09.007 · Cited by 189 · see citing works
Sir-Mediated Repression Can Occur Independently of Chromosomal and Subnuclear Contexts
Gartenberg, M. R., Neumann, F. R., Laroche, T., et al. (2004) · Cell · doi:10.1016/j.cell.2004.11.008 · Cited by 188 · see citing works
Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter
Müller, W. G., Walker, D. A., Hager, G. L., & McNally, J. G. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200011069 · Cited by 186 · see citing works
Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold
Poirier, M. G., & Marko, J. F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.232442599 · Cited by 182 · see citing works
Elasticity and Structure of Eukaryote Chromosomes Studied by Micromanipulation and Micropipette Aspiration
Houchmandzadeh, B., Marko, J. F., Chatenay, D., et al. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.139.1.1 · Cited by 171 · see citing works
Chromatin Dynamics
Hübner, M. R., & Spector, D. L. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131348 · Cited by 171 · see citing works
Chromatin Higher Order Structure: Chasing a Mirage?
Holde, K. V., & Zlatanova, J. S. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.15.8373 · Cited by 171 · see citing works
A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus
Hancock, R. (2004) · Journal of Structural Biology · doi:10.1016/j.jsb.2003.12.008 · Cited by 167 · see citing works
The Nuclear Matrix
Penman, S., Blencowe, B. J., & Nickerson, J. A. (1997) · Elsevier eBooks · doi:10.1016/b978-012100160-5/50002-6 · Cited by 165 · 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
Chromosome crosstalk in three dimensions
Göndör, A., & OHLSSON, R. I. (2009) · Nature · doi:10.1038/nature08453 · Cited by 151 · see citing works
Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence
Shopland, L. S., Lynch, C. R., Peterson, K. A., Thornton, K. R., Kepper, N., Hase, J. V., Stein, S., Vincent, S., Molloy, K. R., Kreth, G., et al. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200603083 · Cited by 149 · see citing works
Dynamics and function of compact nucleosome arrays
Poirier, M. G., Oh, E., Tims, H. S., & Widom, J. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1650 · Cited by 142 · see citing works
Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template
Hu, Y., Kireev, I. I., Plutz, M., et al. (2009) · The Journal of Cell Biology · doi:10.1083/jcb.200809196 · Cited by 139 · see citing works
Macromolecular crowding and its potential impact on nuclear function
Richter, K., Neßling, M., & Lichter, P. (2008) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2008.07.017 · Cited by 133 · see citing works
Chromatin architecture
Woodcock, C. L. F. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.02.005 · Cited by 131 · see citing works
Self-citation
Chromosome Alignment and Transvection Are Antagonized by Condensin II
Hartl, T. A., Smith, H. F., & Bosco, G. (2008) · Science · doi:10.1126/science.1164216 · Cited by 128 · see citing works
Order and Disorder in the Nucleus
Marshall, W. F. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00724-8 · Cited by 127 · see citing works
Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules
Verschure, P. J., van der Kraan, I., Manders, E. M. M., Hoogstraten, D., Houtsmuller, A. B., & DRIEL, R. V. (2003) · EMBO Reports · doi:10.1038/sj.embor.embor922 · Cited by 126 · see citing works
Micromechanical studies of mitotic chromosomes
Marko, J. F. (2008) · Chromosome Research · doi:10.1007/s10577-008-1233-7 · Cited by 124 · see citing works
The 3D Positioning of ANT2 and ANT3 Genes within Female X Chromosome Territories Correlates with Gene Activity
Dietzel, S. (1999) · Experimental Cell Research · doi:10.1006/excr.1999.4635 · Cited by 117 · see citing works
Chromosome structure and the C-value paradox.
Gall, J. G. (1981) · The Journal of Cell Biology · doi:10.1083/jcb.91.3.3s · Cited by 110 · see citing works
Physical Constraints in the Condensation of Eukaryotic Chromosomes. Local Concentration of DNA versus Linear Packing Ratio in Higher Order Chromatin Structures
Daban, J. (2000) · Biochemistry · doi:10.1021/bi992628w · Cited by 109 · see citing works
Mobility and immobility of chromatin in transcription and genome stability
Soutoglou, E., & Misteli, T. (2007) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2007.08.004 · Cited by 106 · see citing works
Chromatin organization re-viewed
Woodcock, C. L. F., & Horowitz, R. A. (1995) · Trends in Cell Biology · doi:10.1016/s0962-8924(00)89038-8 · Cited by 103 · see citing works
Self-citation
Linker histone H1 is essential for Drosophila development, the establishment of pericentric heterochromatin, and a normal polytene chromosome structurePreprint
Lu, X., Wontakal, S. N., Emelyanov, A. V., Morcillo, P., Konev, A. Y., Fyodorov, D. V., & Skoultchi, A. I. (2009) · Genes & Development · doi:10.1101/gad.1749309 · Cited by 101 · see citing works
Chromatin fiber structure: Where is the problem now?
van Holde, K., & Zlatanova, J. S. (2007) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2007.08.005 · Cited by 97 · see citing works
Nuclear actin and actin-related proteins in chromatin dynamics
Chen, M., & Shen, X. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.009 · Cited by 91 · see citing works
Internal organisation of the nucleus: assembly of compartments by macromolecular crowding and the nuclear matrix model
Hancock, R. (2004) · Biology of the Cell · doi:10.1016/j.biolcel.2004.05.003 · Cited by 90 · see citing works
Curvilinear, Three-Dimensional Motion of Chromatin Domains and Nucleoli in Neuronal Interphase Nuclei
Boni, U. D., & Mintz, A. H. (1986) · Science · doi:10.1126/science.3775367 · Cited by 78 · see citing works
Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae
Buchberger, J. R., Onishi, M., Li, G., et al. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01210-08 · Cited by 71 · see citing works
High concentration of DNA in condensed chromatin.
Daban, J. (2003) · Biochemistry and cell biology = Biochimie et biologie cellulaire · doi:10.1139/o03-037 · Cited by 68 · see citing works
Micromechanical Studies of Mitotic Chromosomes
Poirier, M. G., & Marko, J. F. (2003) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/s0070-2153(03)01002-0 · Cited by 65 · see citing works
Chapter 13: Visualization of Large-Scale Chromatin Structure and Dynamics Using the lac Operator/lac Repressor Reporter System
Belmont, A. S., Li, G., Sudlow, G., et al. (1998) · Methods in cell biology · doi:10.1016/s0091-679x(08)61957-3 · Cited by 64 · see citing works
Epigenetic reprogramming in mammalian reproduction: Contribution from histone variants
Santenard, A., & Torres‐Padilla, M. (2009) · Epigenetics · doi:10.4161/epi.4.2.7838 · Cited by 59 · see citing works
Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes
Müller, W. G., Rieder, D., Kreth, G., et al. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.21.9359-9370.2004 · Cited by 53 · see citing works
Spatio-Temporal Dynamics of Chromatin Containing DNA Breaks
Kruhlak, M. J., Celeste, A., & Nussenzweig, A. (2006) · Cell Cycle · doi:10.4161/cc.5.17.3169 · Cited by 52 · see citing works
The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography
König, P., Braunfeld, M. B., Sedat, J. W., & Agard, D. A. (2007) · Chromosoma · doi:10.1007/s00412-007-0101-0 · Cited by 47 · see citing works
Pictures in cell biology
Yi, W., & Allis, C. D. (1998) · Trends in Cell Biology · doi:10.1016/s0962-8924(98)01287-2 · Cited by 46 · see citing works
In vivo immunogold labeling confirms large-scale chromatin folding motifs
Kireev, I. I., Lakonishok, M., Liu, W., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1196 · Cited by 44 · see citing works
Studies on the Mechanism of RNAi-dependent Heterochromatin AssemblyPreprint
Moazed, D., Bühler, M., Buker, S. M., Colmenares, S. U., Gerace, E. L., Gerber, S. A., Hong, E., MOTAMEDI, M. R., Verdel, A., Villén, J., et al. (2006) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2006.71.044 · Cited by 42 · see citing works
Mitotic chromosome structure: reproducibility of folding and symmetry between sister chromatids.
Strukov, Y., & Belmont, A. S. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.10.051 · Cited by 40 · see citing works
An Alpha Motif at Tas3 C Terminus Mediates RITS cis Spreading and Promotes Heterochromatic Gene Silencing
Li, H., Motamedi, M. R., Yip, C. K., Wang, Z., Walz, T., Patel, D. J., & Moazed, D. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.032 · Cited by 36 · see citing works
Sir3 C-Terminal Domain Involvement in the Initiation and Spreading of Heterochromatin
Liaw, H., & Lustig, A. J. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01082-06 · Cited by 28 · see citing works
The Long and the Short of it: Linker Histone H1 is Required for Metaphase Chromosome Compaction
Maresca, T. J., & Heald, R. (2006) · Cell Cycle · doi:10.4161/cc.5.6.2581 · Cited by 24 · see citing works
Domains of Heterochromatin Protein 1 Required forDrosophila melanogasterHeterochromatin Spreading
Hines, K. A., Cryderman, D. E., Flannery, K. M., Yang, H., Vitalini, M. W., Hazelrigg, T. I., Mizzen, C. A., & Wallrath, L. L. (2009) · Genetics · doi:10.1534/genetics.109.105338 · Cited by 22 · see citing works
H1 Linker Histones Are Essential for Mouse Development and Affect Nucleosome Spacing In Vivo
Fan, Y., Morin-Kensicki, E. M., Magnuson, T. R., et al. (2020) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/dvn9-ny73 · Cited by 13 · see citing works
When ChIA PETs meet Hi-C
Rusk, N. (2009) · Nature Methods · doi:10.1038/nmeth1209-863 · Cited by 8 · see citing works
Unusual chromosome architecture and behaviour at an HSR
Sullivan, B. A., & Bickmore, W. A. (2000) · Chromosoma · doi:10.1007/s004120050426 · Cited by 3 · see citing works
FIB Milling of Frozen-hydrated Cells and Tissue for TEM Cryo-Tomography
Marko, M., Hsieh, C., Salmon, N. J., et al. (2008) · Microscopy and Microanalysis · doi:10.1017/s1431927608088673 · Cited by 3 · see citing works
Pictures in cell biology
Gall, J. G., & Murphy, C. (1998) · Trends in Cell Biology · doi:10.1016/s0962-8924(98)01260-4 · Cited by 2 · see citing works
Micromechanical studies of mitotic chromosomes
Poirier, M. G., & Marko, J. F. (2003) · Springer eBooks · doi:10.1007/978-94-010-0147-2_4 · Cited by 2 · see citing works

Flagged first, then by citations

Research works printed but not linked: 5

Heitz E 1928. Das Heterochromatin der Moose, 1, Jahrb Wiss Bot 69:762–818 [Google Scholar]
Hines KA, Cryderman DE, Flannery KM, Yang H, Vitalini MW, Hazelrigg T, Mizzen CA, Wallrath L 2009. Domains of HP1 Required for Drosophila melanogaster heterochromatin spreading. Genetics 182:967–77 [DOI] [PMC free article] [PubMed] [Google Scholar]
Shelby RD, Hahn KM, Sullivan KF 1996. Dynamic elastic behavior of alpha satellite domains visualized in living cells. J Cell Biol 135:545–557 [DOI] [PMC free article] [PubMed] [Google Scholar]
van Holde K 1989. Chromatin. Springer Verlag, New York [Google Scholar]
van Holde K, Zlatanova J 1995. Chromatin structure: Chasing a mirage? J Biol Chem 270:8373–8376 [DOI] [PubMed] [Google Scholar]

Sorted by citations

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
Chromatin higher-order structures and gene regulation
Li, G., & Reinberg, D. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.01.022 · Cited by 454 · see citing works
Histones: At the Crossroads of Peptide and Protein Chemistry
Müller, M. M., & Muir, T. W. (2015) · Chemical Reviews · doi:10.1021/cr5003529 · Cited by 247 · see citing works
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 · see citing works
Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Autoimmunity and SLE: factual and semantic evidence-based critical analyses of definitions, etiology, and pathogenesis
Rekvig, O. P. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.569234 · Cited by 42 · see citing works
Role of histone acetyltransferases MOF and Tip60 in genome stability
Mir, U. S., Bhat, A., Mushtaq, A., Pandita, S., Altaf, M., & Pandita, T. K. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103205 · Cited by 32 · see citing works

Effect of addition of polyethylene on properties of polypropylene/ethylene-propylene rubber blends
Petrov, Z., Bud�nski-Simend�, J., Divjakovi, V., & krbi, E. (1996) · Journal of Applied Polymer Science · doi:10.1002/(sici)1097-4628(19960110)59:2 · Cited by 39 · see citing works
Minimum Halloysite Length for Efficient Load Transfer Through the Interphase of Polymer Nanocomposites in Biomedical Applications
Zare, Y., & Rhee, K. Y. (2022) · JOM · doi:10.1007/s11837-022-05570-z · Cited by 5 · see citing works
Weight-change analysis of the interphase in hygrothermally aged FRP: Consideration of debonding
Morii, T., Ikuta, N., Kiyosumi, K., et al. (1997) · Composites Science and Technology · doi:10.1016/s0266-3538(97)00051-1 · Cited by 34 · see citing works
Computer Simulation of the Interphase Boundary Evolution in Ni75AlxV25-x Alloy
YongshengLI, ZhengChen, YanliLU, et al. (2005) · Acta Scientiarum Naturalium Universitatis Sunyatseni · Cited by 1 · see citing works
Modeling of Nanocomposite Structures to Evaluate the Effect of Nanoplatelet Interphase Region on Electric Field Intensity
Sharip, M. R. M., Lau, K. Y., & Zaidel, D. N. A. (2016) · Journal of Telecommunication Electronic and Computer Engineering (JTEC)

Authors: Woodcock, C. L., & Ghosh, R. P.
Affiliations: University of Massachusetts Amherst (US)
ORCID: Ghosh, R. P.
Venue: Cold Spring Harbor Perspectives in Biology
Publisher: Cold Spring Harbor Laboratory
Published: 2010-04-07
Volume: 2
Issue: 5
Pages: a000596-a000596
ISSN: 1943-0264 (ISSN-L)
DOI: 10.1101/cshperspect.a000596
PMC: PMC2857170
OpenAlex: W2019129277
Cited by: 384
References: 137
Citations by year: 2026: 4 · 2025: 15 · 2024: 25 · 2023: 15 · 2022: 14 · 2021: 32 · 2020: 24 · 2019: 26 · 2018: 20 · 2017: 19 · 2016: 36 · 2015: 27 · 2014: 29 · 2013: 30 · 2012: 28
Type: posted content
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Cold Spring Harbor Perspectives in Biology (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords: higher-order chromatin structure, chromatin condensation, chromatin dynamics, structural plasticity, genome organization, nucleosome, interphase nuclei, metaphase chromosomes, DNA condensation
MeSH terms: Cell Nucleus, Chromatin, Computer Simulation, Nucleic Acid Conformation, Protein Conformation

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

Chromatin Higher-order Structure and Dynamics

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks