The DOI matches its Crossref record; 72 of the 73 references it cites were found in a registry or an index.
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation
Open accessAbstract
Master regulatory genes require stable silencing by the polycomb group (PcG) to prevent misexpression during differentiation and development. Some PcG proteins covalently modify histones, which contributes to heritable repression. The role for other effects on chromatin structure is less understood. We characterized the organization of PcG target genes in ESCs and neural progenitors using 5C and super-resolution microscopy. The genomic loci of repressed PcG targets formed discrete, small (20-140 Kb) domains of tight interaction that corresponded to locations bound by canonical polycomb repressive complex 1 (PRC1). These domains changed during differentiation as PRC1 binding changed. Their formation depended upon the Polyhomeotic component of canonical PRC1 and occurred independently of PRC1-catalyzed ubiquitylation. PRC1 domains differ from topologically associating domains in size and boundary characteristics. These domains have the potential to play a key role in transmitting epigenetic silencing of PcG targets by linking PRC1 to formation of a repressive higher-order structure.
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“The spatial organization of chromatin, including a variety of long-range DNA interactions, plays a key role in controlling gene expression and maintaining cellular identity (Gorkin et al., 2014; Kundu et al., 2017; Narendra et al., 2015; Schoenfelder et al., 2015; Zirkel et al., 2018).”
From Loss of epigenetic information as a cause of mammalian aging (2023) · cites this paper as Kundu et al., 2017
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Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · cited 2×
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MethodTrapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
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 · cited 4×
“…Boundaries of all four marks correlate well with boundaries of PRC1-associated (D) Model to describe interpretation of presented data; see Discussion for a descr resolution Hi-C dataset generated in GM12878 cells by Rao et al. (2014), and Di range interaction and change during differentiation.”
BackgroundMethodInfluentialTopological 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 · cited 9×
“Data represented as mean ± SD. (E and F) HoxA and HoxD compaction domains are lost upon loss of canonical comprising HoxA (E) and HoxD (F) clusters in WT (left) and Phc1 KO (middle) ESCs Phc1 KO while Hi-C TADs are preserved.”
BackgroundInfluentialA bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361 · cited 2×
“The entire HoxA cluster is occupied by PRC1 and PRC2, and Hoxa genes are repressed in ESCs (Bernstein et al., 2006; Mazzoni et al., 2013; Narendra et al., 2015) (also Figure 3A).”
BackgroundRole of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing
Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R. S., & Zhang, Y. (2002) · Science · doi:10.1126/science.1076997 · Cited by 3,775 · cited 1×
“Disruption of H3K27 methylation is believed to be a key defect in human cancers such as glioblastoma (Cao et al., 2002; Czermin et al., 2002; Kuzmichev et al., 2002; Lewis et al., 2013; M€uller et al., 2002; Pengelly et al., 432 Molecular Cell 65, 432–446, February 2, 2017 ª 2017 Elsevier Inc 2013;…”
BackgroundDifferential analysis of gene regulation at transcript resolution with RNA-seq
Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology · doi:10.1038/nbt.2450 · Cited by 3,492 · cited 2×
“…et al., 2008 http://compbio.med.harvard.edu/Supplements/ChIP-seq/ TopHat Trapnell et al., 2009 https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ CuffDiff Trapnell et al., 2013 http://cole-trapnell-lab.github.io/cufflinks/”
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
Schwartzentruber, J., Korshunov, A., Liu, X.-Y., Jones, D. T. W., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A. M., Quang, D.-A. K., Tönjes, M., et al. (2012) · Nature · doi:10.1038/nature10833 · Cited by 2,631 · cited 1×
“…(Cao et al., 2002; Czermin et al., 2002; Kuzmichev et al., 2002; Lewis et al., 2013; M€uller et al., 2002; Pengelly et al., 432 Molecular Cell 65, 432–446, February 2, 2017 ª 2017 Elsevier Inc 2013; Schwartzentruber et al., 2012; Simon and Kingston, 2013; Voigt and Reinberg, 2013; Wu et al., 2012).”
BackgroundA long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 2,005 · cited 2×
“…G yr at io n HoxA HoxB HoxD Control *** *** ns *** *** ns *** *** ns 0.06 ns ns *** P 0.005 Phc1-KO ESC NPC WT ESC E (legend on next page) Molecular Cell 65, 432–446, February 2, 2017 437 activation, between the anterior HoxA cluster and the adjacent TAD increased (green arrow) (Wang et al., 2011).”
BackgroundInfluentialSelf-citation
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1 of the 73 references couldn’t be matched to a known paper.
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Genome Regulation by Polycomb and Trithorax: 70 Years and Counting
Schuettengruber, B., Bourbon, H.-M., Di Croce, L., & Cavalli, G. (2017) · Cell · doi:10.1016/j.cell.2017.08.002 · Cited by 1,094
“In particular, oligomerization mediated by the SAM domain of the Ph/PHC1 subunit of cPRC1 (Figures 5D and 5E) is crucial for the condensation of individual Polycomb domains (Kundu et al., 2017) as well as for mediating long-range Polycomb domain interactions (Isono et al., 2013; Wani et al., 2016).”
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
Organization of Chromatin by Intrinsic and Regulated Phase Separation
Gibson, B. A., Doolittle, L. K., Schneider, M. W. G., Jensen, L. E., Gamarra, N. I., Henry, L., Gerlich, D. W., Redding, S., & Rosen, M. K. (2019) · Cell · doi:10.1016/j.cell.2019.08.037 · Cited by 1,080
“Polycomb Group Regions: Polycomb group regions were defined as H3K27me3 ChIP-seq peaks from E14tga2 mouse ES cells (Consortium, 2012) that overlap with H3K27me3, H2Aub, EZH2, and Ring1b ChIP-seq peaks from mouse ES cells (Kundu et al., 2017).”
BackgroundThe role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 742
Loss of epigenetic information as a cause of mammalian aging
Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.027 · Cited by 643
Metadata
- Authors
- Kundu, S., Ji, F., Sunwoo, H., Jain, G., Lee, J. T., Sadreyev, R. I., Dekker, J., & Kingston, R. E.
- Affiliations
- Harvard University (US)
- University of Massachusetts Chan Medical School (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Kingston, Robert E.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 65
- Issue
- 3
- Pages
- 432-446.e5
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC5421375
- OpenAlex
- W2585920126
- Cited by
- 333
- References
- 73
- Citations by year
- 2026: 19 · 2025: 23 · 2024: 27 · 2023: 23 · 2022: 45 · 2021: 55 · 2020: 41 · 2019: 48 · 2018: 35 · 2017: 17
- FWCI
- 15.74
- Type
- journal article
- Language
- en
- Update notices
- erratum (2018-07-05)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship@UMassChan (submittedVersion)
- Funders
- National Institutes of Health (5R01GM043901-24, DK107980, HG003143, P30 DK40561, R01-GM090278)
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- 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
- Keywords
- PRC1, Polycomb group proteins, chromatin condensation, polyhomeotic, epigenetic silencing, chromatin looping, topologically associating domains, neural progenitor cells, embryonic stem cells, cell differentiation, chromatin organization, higher-order chromatin structure
- MeSH terms
- Protein Domains, Animals, Cell Differentiation, Cells, Cultured, Chromatin, DNA, Histones, Humans, Homeodomain Proteins, Gene Expression Regulation, Developmental, Epigenesis, Genetic, Mice, Embryonic Stem Cells, Ubiquitination, Neural Stem Cells, Polycomb Repressive Complex 1
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