The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Chromatin structure dynamics during the mitosis-to-G1 phase transition
Open accessAbstract
Features of higher-order chromatin organization-such as A/B compartments, topologically associating domains and chromatin loops-are temporarily disrupted during mitosis 1,2. Because these structures are thought to influence gene regulation, it is important to understand how they are re-established after mitosis. Here we examine the dynamics of chromosome reorganization by Hi-C after mitosis in highly purified, synchronous mouse erythroid cell populations. We observed rapid establishment of A/B compartments, followed by their gradual intensification and expansion. Contact domains form from the 'bottom up'-smaller subTADs are formed initially, followed by convergence into multi-domain TAD structures. CTCF is partially retained on mitotic chromosomes and immediately resumes full binding in ana/telophase. By contrast, cohesin is completely evicted from mitotic chromosomes and regains focal binding at a slower rate. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contact patterns-anchored by CTCF-grow in length, which is consistent with a loop-extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, with rates exceeding those of CTCF/cohesin-anchored contacts. Notably, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering chromatin loops. We also describe the relationship between transcription reactivation and architectural features. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin reconfiguration.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The cited source says what the claim attributes to it.
In the citing paper
“Cis-regulatory contacts were also shown to emerge prior to the formation of TADs in murine cells exiting mitosis [455].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [455]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
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
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730
Two independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Weintraub, A. S., Li, C. H., Zamudio, A. V., Sigova, A. A., Hannett, N. M., Day, D. S., Abraham, B. J., Cohen, M. A., Nabet, B., Buckley, D. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.008 · Cited by 992
Organization of the mitotic chromosome
Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013) · Science · doi:10.1126/science.1236083 · Cited by 976
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317788111 · Cited by 779
A pathway for mitotic chromosome formation
Gibcus, J. H., Samejima, K., Goloborodko, A. A., Samejima, I., Naumova, N., Nuebler, J., Kanemaki, M. T., Xie, L., Paulson, J. R., Earnshaw, W. C., et al. (2018) · Science · doi:10.1126/science.aao6135 · Cited by 744
The Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
Rowley, M. J., Nichols, M. H., Lyu, X., Ando‐Kuri, M., Rivera, S., Hermetz, K. E., Wang, P., Ruan, Y., & Corces, V. G. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.022 · Cited by 560
CTCF Tethers an Insulator to Subnuclear Sites, Suggesting Shared Insulator Mechanisms across Species
Yusufzai, T. M., Tagami, H., Nakatani, Y., & Felsenfeld, G. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00029-2 · Cited by 479
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461
Weiss, M. J., Yu, C., & Orkin, S. H. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.3.1642 · Cited by 349
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
Beagan, J. A., Duong, M. T., Titus, K. R., Zhou, L., Cao, Z., Ma, J., Lachanski, C. V., Gillis, D. R., & Phillips-Cremins, J. E. (2017) · Genome Research · doi:10.1101/gr.215160.116 · Cited by 299
Self-citationA Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
Li, B., Qing, T., Zhu, J., Wen, Z., Yu, Y., Fukumura, R., Zheng, Y., Gondo, Y., & Shi, L. (2017) · Scientific Reports · doi:10.1038/s41598-017-04520-z · Cited by 184
Dileep, V., Ay, F., Sima, J., Vera, D. L., Noble, W. S., & Gilbert, D. M. (2015) · Genome Research · doi:10.1101/gr.183699.114 · Cited by 177
Detecting hierarchical genome folding with network modularity
Norton, H. K., Emerson, D. J., Huang, H., Kim, J., Titus, K. R., Gu, S., Bassett, D. S., & Phillips-Cremins, J. E. (2018) · Nature Methods · doi:10.1038/nmeth.4560 · Cited by 146
Self-citationThe BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries
Hsu, S. C., Gilgenast, T. G., Bartman, C., Edwards, C. R., Stonestrom, A. J., Huang, P., Emerson, D. J., Evans, P., Werner, M. T., Keller, C. A., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.02.027 · Cited by 143
Self-citationCTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioningPreprint
Oomen, M. E., Hansen, A. S., Liu, Y., Darzacq, X., & Dekker, J. (2019) · Genome Research · doi:10.1101/gr.241547.118 · Cited by 137
Experimental and computational framework for a dynamic protein atlas of human cell division
Cai, Y., Hossain, M. J., Hériché, J.-K., Politi, A. Z., Walther, N., Koch, B., Wachsmuth, M., Nijmeijer, B., Kueblbeck, M., Martinic-Kavur, M., et al. (2018) · Nature · doi:10.1038/s41586-018-0518-z · Cited by 121
Dogan, N., Wu, W., Morrissey, C. S., Chen, K.-B., Stonestrom, A., Long, M., Keller, C. A., Cheng, Y., Jain, D., Visel, A., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0009-5 · Cited by 114
Self-citationA hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transitionPreprint
Hsiung, C. C. ‐., Bartman, C., Huang, P., Ginart, P., Stonestrom, A. J., Keller, C. A., Face, C. J., Jahn, K. S., Evans, P., Sankaranarayanan, L., et al. (2016) · Genes & Development · doi:10.1101/gad.280859.116 · Cited by 105
Self-citationWu, W.-S., Morrissey, C. S., Keller, C. A., Mishra, T., Pimkin, M., Blobel, G. A., Weiss, M. J., & Hardison, R. C. (2014) · Genome Research · doi:10.1101/gr.164830.113 · Cited by 84
Self-citationCTCF confers local nucleosome resiliency after DNA replication and during mitosis
Owens, N. D. L., Papadopoulou, T., Festuccia, N., Tachtsidi, A., González, I., Dubois, A., Vandormael‐Pournin, S., Nora, E. P., Bruneau, B. G., Cohen‐Tannoudji, M., et al. (2019) · eLife · doi:10.7554/elife.47898 · Cited by 81
Yu, W.-B., He, B., & Tan, K. (2017) · Nature Communications · doi:10.1038/s41467-017-00478-8 · Cited by 78
Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription
Behera, V., Stonestrom, A. J., Hamagami, N., Hsiung, C. C. ‐., Keller, C. A., Giardine, B. M., Sidoli, S., Yuan, Z., Bhanu, N. V., Werner, M. T., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.057 · Cited by 70
Self-citation
Cited by
Sorted by citations
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Darzacq, X., & Tjian, R. (2022) · Nature Genetics · doi:10.1038/s41588-022-01223-8 · Cited by 406
The relationship between genome structure and function
Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304
DNA methylation atlas of the mouse brain at single-cell resolution
Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2021) · Nature · doi:10.1038/s41586-020-03182-8 · Cited by 289
Characterizing cis-regulatory elements using single-cell epigenomics
Preissl, S., Gaulton, K. J., & Ren, B. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-022-00509-1 · Cited by 251
Transcription shapes 3D chromatin organization by interacting with loop extrusion
Banigan, E. J., Tang, W., van den Berg, A. A., Stocsits, R. R., Wutz, G., Brandão, H. B., Busslinger, G. A., Peters, J., & Mirny, L. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2210480120 · Cited by 238
Metadata
- Authors
- Zhang, H., Emerson, D. J., Gilgenast, T. G., Titus, K. R., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C. A., Giardine, B., Hardison, R. C., Phillips-Cremins, J. E., & Blobel, G. A.
- Affiliations
- Children's Hospital of Philadelphia (US)
- University of Pennsylvania (US)
- Pennsylvania State University (US)
- Corresponding author
- Blobel, Gerd A.
- ORCID
- Venue
- Nature
- Published
- 2019-11-27
- Volume
- 576
- Issue
- 7785
- Pages
- 158-162
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6895436
- OpenAlex
- W2990380375
- Cited by
- 271
- References
- 27
- Citations by year
- 2026: 31 · 2025: 57 · 2024: 28 · 2023: 45 · 2022: 31 · 2021: 48 · 2020: 29 · 2019: 2
- FWCI
- 9.68
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (U01HL129998)
- National Institute of Mental Health (DP2MH110247)
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK058044, R01DK058044, R24DK106766)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- chromatin reorganization, A/B compartments, topologically associating domains, CTCF, cohesin, chromatin looping, loop extrusion, erythroid cells
- MeSH terms
- Cohesins, Animals, Chromatin, Chromosomal Proteins, Non-Histone, Mitosis, G1 Phase, Cell Cycle Proteins, Mice
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
