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Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts
Open accessAbstract
Background: Polycomb group proteins form multicomponent complexes that are important for establishing lineage-specific patterns of gene expression. Mammalian cells encode multiple permutations of the prototypic Polycomb repressive complex 1 (PRC1) with little evidence for functional specialization. An aim of this study is to determine whether the multiple orthologs that are co-expressed in human fibroblasts act on different target genes and whether their genomic location changes during cellular senescence. Results: Deep sequencing of chromatin immunoprecipitated with antibodies against CBX6, CBX7, CBX8, RING1 and RING2 reveals that the orthologs co-localize at multiple sites. PCR-based validation at representative loci suggests that a further six PRC1 proteins have similar binding patterns. Importantly, sequential chromatin immunoprecipitation with antibodies against different orthologs implies that multiple variants of PRC1 associate with the same DNA. At many loci, the binding profiles have a distinctive architecture that is preserved in two different types of fibroblast. Conversely, there are several hundred loci at which PRC1 binding is cell type-specific and, contrary to expectations, the presence of PRC1 does not necessarily equate with transcriptional silencing. Interestingly, the PRC1 binding profiles are preserved in senescent cells despite changes in gene expression. Conclusions: The multiple permutations of PRC1 in human fibroblasts congregate at common rather than specific sites in the genome and with overlapping but distinctive binding profiles in different fibroblasts. The data imply that the effects of PRC1 complexes on gene expression are more subtle than simply repressing the loci at which they bind.
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Comparison of SILAC data with published CBX7 ChIP-seq in human fibroblasts found 20 proteins whose genes are potential targets for CBX proteins, including CDKN2A.
“We found 20 proteins whose genes are potential targets for CBX proteins, including CDKN2A”
From Integrin Beta 3 Regulates Cellular Senescence by Activating the TGF-β Pathway (2017) · cites this paper as Pemberton et al., 2014
ITGB3 has been previously identified as a Polycomb target by ChIP sequencing in mouse embryonic stem cells and human primary fibroblasts.
“ITGB3 has been previously identified as a Polycomb target by ChIP sequencing in other biological contexts, such as mouse embryonic stem cells (ESCs) (Morey et al., 2013) and human primary fibroblasts (Pemberton et al., 2014)”
From Integrin Beta 3 Regulates Cellular Senescence by Activating the TGF-β Pathway (2017) · cites this paper as Pemberton et al., 2014
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Citations
Cites
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Cellular senescence: when bad things happen to good cells
Campisi, J., & d'Adda di Fagagna, F. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2233 · Cited by 4,441
Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence
Narita, M., Nuñez, S., Heard, E., Narita, M., Lin, A. W., Hearn, S. A., Spector, D. L., Hannon, G. J., & Lowe, S. W. (2003) · Cell · doi:10.1016/s0092-8674(03)00401-x · Cited by 2,278
Cellular senescence in cancer and aging.
Collado, M., Blasco, M. A., & Serrano, M. (2007) · Cell · doi:10.1016/j.cell.2007.07.003 · Cited by 1,708
Jacobs, J. J. L., Kieboom, K., Marino, S., DePinho, R. A., & van Lohuizen, M. (1999) · Nature · doi:10.1038/16476 · Cited by 1,580
Mechanisms of Polycomb gene silencing: knowns and unknowns
Simon, J. A., & Kingston, R. E. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2763 · Cited by 1,360
Diversity, topographic differentiation, and positional memory in human fibroblasts
Chang, H. Y., Chi, J., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., & Brown, P. O. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162488599 · Cited by 1,151
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains
Ku, M., Koche, R. P., Rheinbay, E., Mendenhall, E. M., Endoh, M., Mikkelsen, T. S., Aiden, A. P., Nusbaum, C., Xie, X. S., Chi, A. S., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000242 · Cited by 1,053
PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes
Gao, Z., Zhang, J., Bonasio, R., Strino, F., Sawai, A., Parisi, F., Kluger, Y., & Reinberg, D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.01.002 · Cited by 852
Bracken, A. P., Kleine-Kohlbrecher, D., Dietrich, N., Pasini, D., Gargiulo, G., Beekman, C., Theilgaard-Mönch, K., Minucci, S., Porse, B. T., Marine, J.-C., et al. (2007) · Genes & Development · doi:10.1101/gad.415507 · Cited by 850
Regulation of the INK4b–ARF–INK4a tumour suppressor locus: all for one or one for all
Gil, J., & Peters, G. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1987 · Cited by 843
Self-citationStabilization of Chromatin Structure by PRC1, a Polycomb Complex
Shao, Z., Raible, F., Mollaaghababa, R., Guyon, J. R., Wu, C.-T., Bender, W. W., & Kingston, R. E. (1999) · Cell · doi:10.1016/s0092-8674(00)80604-2 · Cited by 821
Simon, J. A., & Kingston, R. E. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.013 · Cited by 754
Stock, J. K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A. G., & Pombo, A. (2007) · Nature Cell Biology · doi:10.1038/ncb1663 · Cited by 650
Self-citationThe Polycomb Protein Pc2 Is a SUMO E3
Kagey, M. H., Melhuish, T. A., & Wotton, D. (2003) · Cell · doi:10.1016/s0092-8674(03)00159-4 · Cited by 596
Tavares, L., Dimitrova, E., Oxley, D., Webster, J. A., Poot, R. A., Demmers, J., Bezstarosti, K., Taylor, S., Ura, H., Koide, H., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.029 · Cited by 583
Eskeland, R., Leeb, M., Grimes, G. R., Kress, C., Boyle, S., Sproul, D., Gilbert, N., Fan, Y., Skoultchi, A. I., Wutz, A., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.032 · Cited by 571
Bernstein, E., Duncan, E. M., Masui, O., Gil, J., Heard, É., & Allis, C. D. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.26.7.2560-2569.2006 · Cited by 531
Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Rinn, J. L., Bondre, C., Gladstone, H. B., Brown, P. O., & Chang, H. Y. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020119 · Cited by 505
Control of the replicative life span of human fibroblasts by p16 and the polycomb protein Bmi-1
Itahana, K., Zou, Y., Itahana, Y., Martinez, J.-L., Beausejour, C., Jacobs, J. J. L., van Lohuizen, M., Band, V., Campisi, J., & Dimri, G. P. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.1.389-401.2003 · Cited by 438
Molecular dissection of formation of senescence-associated heterochromatin foci
Zhang, R., Chen, W., & Adams, P. D. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.02019-06 · Cited by 415
A Drosophila Polycomb group complex includes Zeste and dTAFII proteins
Saurin, A. J., Shao, Z., Erdjument‐Bromage, H., Tempst, P., & Kingston, R. E. (2001) · Nature · doi:10.1038/35088096 · Cited by 403
Polycomb group protein-mediated repression of transcription
Morey, L., & Helin, K. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.02.009 · Cited by 395
Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS
Barradas, M., Anderton, E., Acosta, J. C., Li, S., Banito, A., Rodriguez-Niedenführ, M., Maertens, G., Banck, M., Zhou, M.-M., Walsh, M. J., et al. (2009) · Genes & Development · doi:10.1101/gad.511109 · Cited by 352
Self-citationNonoverlapping Functions of the Polycomb Group Cbx Family of Proteins in Embryonic Stem Cells
Morey, L., Pascual, G., Cozzuto, L., Roma, G., Wutz, A., Benitah, S. A., & Croce, L. D. (2012) · Cell stem cell · doi:10.1016/j.stem.2011.12.006 · Cited by 343
Polycomb CBX7 has a unifying role in cellular lifespan.
Gil, J., Bernard, D., Martínez, D., & Beach, D. (2004) · Nature Cell Biology · doi:10.1038/ncb1077 · Cited by 341
Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.057 · Cited by 331
Recognition and Specificity Determinants of the Human Cbx Chromodomains
Kaustov, L., Ouyang, H., Amaya, M. F., Lemak, A. S., Nady, N., Duan, S., Wasney, G. A., Li, Z., Vedadi, M., Schapira, M., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.191411 · Cited by 309
Chandra, T., Kirschner, K., Thuret, J.-Y., Pope, B. D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S. A., Salama, R., Carroll, T., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.010 · Cited by 308
Saurin, A. J., Shiels, C., Williamson, J. A., Satijn, D. P. E., Otte, A. P., Sheer, D., & Freemont, P. S. (1998) · The Journal of Cell Biology · doi:10.1083/jcb.142.4.887 · Cited by 291
Biochemical mechanisms of gene regulation by polycomb group protein complexes
Müller, J., & Verrijzer, C. P. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.03.001 · Cited by 262
Alkema, M. J., Bronk, M., Verhoeven, E., Otte, A. P., Veer, L. V. ‘., Berns, A. J. M., & van Lohuizen, M. (1997) · Genes & Development · doi:10.1101/gad.11.2.226 · Cited by 245
Garcı́a, E., Marcos‐Gutiérrez, C., Lorente, M., Moreno, J. C., & Vidal, M. (1999) · The EMBO Journal · doi:10.1093/emboj/18.12.3404 · Cited by 228
Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster.Preprint
Messmer, S., Franke, A., & Paro, R. (1992) · Genes & Development · doi:10.1101/gad.6.7.1241 · Cited by 227
Sánchez, C., Sánchez, I., Demmers, J., Rodriguez, P., Strouboulis, J., & Vidal, M. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600275-mcp200 · Cited by 223
MicroRNA Regulation of Cbx7 Mediates a Switch of Polycomb Orthologs during ESC Differentiation
O’Loghlen, A., Muñoz-Cabello, A. M., Gaspar‐Maia, A., Wu, H., Banito, A., Kunowska, N., Racek, T., Pemberton, H. N., Beolchi, P., Lavial, F., et al. (2012) · Cell stem cell · doi:10.1016/j.stem.2011.12.004 · Cited by 213
Self-citationMorey, L., Aloia, L., Cozzuto, L., Benitah, S. A., & Di Croce, L. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.11.026 · Cited by 201
Buchenau, P., Hodgson, J. W., Strutt, H. L., & Arndt‐Jovin, D. J. (1998) · The Journal of Cell Biology · doi:10.1083/jcb.141.2.469 · Cited by 198
Polycomb Group proteins: an evolutionary perspective
Whitcomb, S. J., Basu, A., Allis, C. D., & Bernstein, E. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.08.006 · Cited by 191
Dietrich, N., Bracken, A. P., Trinh, E., Schjerling, C. K., Koseki, H., Rappsilber, J., Helin, K., & Hansen, K. H. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601632 · Cited by 187
A view of nuclear Polycomb bodies
Pirrotta, V., & Li, H. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.11.004 · Cited by 184
Hernández‐Muñoz, I., Taghavi, P., Kuijl, C. P., Neefjes, J., & van Lohuizen, M. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.24.11047-11058.2005 · Cited by 170
Voncken, J. W., Schweizer, D., Aagaard, L., Sattler, L., Jantsch, M. F., & van Lohuizen, M. (1999) · Journal of Cell Science · doi:10.1242/jcs.112.24.4627 · Cited by 157
Vandamme, J., Völkel, P., Rosnoblet, C., Faou, P. L., & Angrand, P. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002642 · Cited by 152
The role of the histone H2A ubiquitinase Sce in Polycomb repression
Gutiérrez, L., Oktaba, K., Scheuermann, J. C., Gambetta, M. C., Ly‐Hartig, N., & Müller, J. (2011) · Development · doi:10.1242/dev.074450 · Cited by 119
Satijn, D. P. E., Olson, D. J., van der Vlag, J., Hamer, K. M., Lambrechts, C., Masselink, H., Gunster, M. J., Sewalt, R. G. A. B., DRIEL, R. V., & Otte, A. P. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.10.6076 · Cited by 114
Several Distinct Polycomb Complexes Regulate and Co-Localize on the INK4a Tumor Suppressor Locus
Maertens, G. N., Messaoudi, S. E., Racek, T., Stock, J. K., Nicholls, J., Rodríguez‐Niedenführ, M., Gil, J., & Peters, G. G. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006380 · Cited by 109
Self-citationPolycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain
Wang, R., Taylor, A. B., Leal, B. Z., Chadwell, L. V., Ilangovan, U., Robinson, A. K., Schirf, V. R., Hart, P. J., Lafer, E. M., Demeler, B., et al. (2010) · Structure · doi:10.1016/j.str.2010.04.013 · Cited by 107
Contribution of p16INK4a to replicative senescence of human fibroblasts
Brookes, S., Rowe, J., del Arroyo, A. G., BOND, J. A., & Peters, G. G. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.04.035 · Cited by 85
Self-citationCmarko, D., Verschure, P. J., Otte, A. P., et al. (2002) · Journal of Cell Science · doi:10.1242/jcs.00225 · Cited by 71
Production of Monoclonal Antibodies Against Mammalian Ring1B Proteins
Atsuta, T., Fujimura, S., Moriya, H., Vidal, M., Akasaka, T., & Koseki, H. (2001) · Hybridoma · doi:10.1089/027245701300060427 · Cited by 58
Gagrica, S., Brookes, S., Anderton, E., Rowe, J., & Peters, G. G. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-2552 · Cited by 26
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- Gene Expression Ominbus (GEO). [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40740]
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Integrin Beta 3 Regulates Cellular Senescence by Activating the TGF-β Pathway
Rapisarda, V., Borghesan, M., Miguela, V., Encheva, V., Snijders, A. P., Lujambio, A., & O’Loghlen, A. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.02.012 · Cited by 190
Metadata
- Authors
- Pemberton, H., Anderton, E., Patel, H., Brookes, S., Chandler, H., Palermo, R., Stock, J., Rodriguez-Niedenführ, M., Racek, T., de Breed, L., Stewart, A., Matthews, N., & Peters, G.
- Affiliations
- Cancer Research UK (GB)
- Corresponding author
- Peters, Gordon
- Venue
- Genome Biology
- Published
- 2014-02-03
- Volume
- 15
- Issue
- 2
- Pages
- R23-R23
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4053772
- OpenAlex
- W2139096612
- Cited by
- 50
- References
- 53
- Citations by year
- 2025: 2 · 2023: 2 · 2022: 3 · 2021: 3 · 2020: 3 · 2019: 4 · 2018: 3 · 2017: 9 · 2016: 5 · 2015: 10 · 2014: 6
- FWCI
- 4.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Leukaemia and Lymphoma Research
- 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, CBX6, CBX7, CBX8, RING1, gene expression regulation, cellular senescence, human fibroblasts, cell type-specific binding, transcriptional silencing, chromatin immunoprecipitation
- MeSH terms
- Fibroblasts, Humans, Protein Binding, Genome, Human, Cellular Senescence, Gene Expression Regulation, Developmental, Cell Lineage, Polycomb-Group Proteins, Polycomb Repressive Complex 1
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