Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping
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Polycomb repressive complex 1 shapes 3D loops associated with transcription of key developmental genes.
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PRC1 mediates chromatin interactions between a subset of active developmental enhancers and promoters in Drosophila.
“Moreover, PRC1 was recently found to mediate chromatin interactions between a subset of active developmental enhancers and promoters in Drosophila [361].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [361]
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Cites
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works
Multiscale 3D Genome Rewiring during Mouse Neural Development
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338 · cited 14× · see citing works
“H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 ChIP-seq datasets from ESCs, RNA-seq, and Hi-C data from ESCs and NPCs were taken from (24) (table S10). k-Means clustering of RING1B peaks from NPCs RING1B PRC1 peak coordinates reported in (25) were lifted over to the mm10 version of the mouse genome, and the peaks that were c…”
BackgroundMethodInfluentialSelf-citationGenome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125 · see citing works
Jacobs, J., Atkins, M., Davie, K., Imrichova, H., Romanelli, L., Christiaens, V., Hulselmans, G., Potier, D., Wouters, J., Taskiran, I. I., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0140-x · Cited by 155 · see citing works
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Research works printed but not linked: 44
- [1]Schuettengruber B., Bourbon H. M., Di Croce L., Cavalli G., Genome regulation by polycomb and trithorax: 70 years and counting. Cell 171, 34– 57 (2017). 28938122
- [2]Loubiere V., Martinez A. M., Cavalli G., Cell fate and developmental regulation dynamics by polycomb proteins and 3D genome architecture. BioEssays 41, e1800222 (2019). 30793782
- [3]Loubiere V., Delest A., Thomas A., Bonev B., Schuettengruber B., Sati S., Martinez A.-M., Cavalli G., Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nat. Genet. 48, 1436– 1442 (2016). 27643538 PMC5407438
- [4]Pherson M., Misulovin Z., Gause M., Mihindukulasuriya K., Swain A., Dorsett D., Polycomb repressive complex 1 modifies transcription of active genes. Sci. Adv. 3, e1700944 (2017). 28782042 PMC5540264
- [5]Morey L., Santanach A., Blanco E., Aloia L., Nora E. P., Bruneau B. G., Croce L. D., Polycomb regulates mesoderm cell fate-specification in embryonic stem cells through activation and repression mechanisms. Cell Stem Cell 17, 300– 315 (2015). 26340528
- [6]Cohen I., Zhao D., Bar C., Valdes V. J., Dauber-Decker K. L., Nguyen M. B., Nakayama M., Rendl M., Bickmore W. A., Koseki H., Zheng D., Ezhkova E., PRC1 fine-tunes gene repression and activation to safeguard skin development and stem cell specification. Cell Stem Cell 22, 726– 739.e7 (2018). 29727681 PMC5944606
- [7]Eagen K. P., Aiden E. L., Kornberg R. D., Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Proc. Natl. Acad. Sci. U.S.A. 114, 8764– 8769 (2017). 28765367 PMC5565414
- [8]Ogiyama Y., Schuettengruber B., Papadopoulos G. L., Chang J.-M., Cavalli G., Polycomb-dependent chromatin looping contributes to gene silencing during Drosophila development. Mol. Cell 71, 73– 88 (2018). 30008320
- [9]Mortazavi A., Pepke S., Jansen C., Marinov G. K., Ernst J., Kellis M., Hardison R. C., Myers R. M., Wold B. J., Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Res. 23, 2136– 2148 (2013). 24170599 PMC3847782
- [10]Filion G. J., van Bemmel J. G., Braunschweig U., Talhout W., Kind J., Ward L. D., Brugman W., de Castro I. J., Kerkhoven R. M., Bussemaker H. J., van Steensel B., Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143, 212– 224 (2010). 20888037 PMC3119929
- [11]Lee H.-G., Kahn T. G., Simcox A., Schwartz Y. B., Pirrotta V., Genome-wide activities of Polycomb complexes control pervasive transcription. Genome Res. 25, 1170– 1181 (2015). 25986499 PMC4510001
- [13]Sexton T., Yaffe E., Kenigsberg E., Bantignies F., Leblanc B., Hoichman M., Parrinello H., Tanay A., Cavalli G., Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458– 472 (2012). 22265598
- [14]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., Sandstrom R., Bernstein B., Bender M. A., Groudine M., Gnirke A., Stamatoyannopoulos J., Mirny L. A., Lander E. S., Dekker J., Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289– 293 (2009). 19815776 PMC2858594
- [15]Davie K., Jacobs J., Atkins M., Potier D., Christiaens V., Halder G., Aerts S., Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLOS Genet. 11, e1004994 (2015). 25679813 PMC4334524
- [16]McKay D. J., Lieb J. D., A common set of DNA regulatory elements shapes Drosophila appendages. Dev. Cell 27, 306– 318 (2013). 24229644 PMC3866527
- [17]Yanez-Cuna J. O., Arnold C. D., Stampfel G., Boryń Ł. M., Gerlach D., Rath M., Stark A., Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res. 24, 1147– 1156 (2014). 24714811 PMC4079970
- [19]Erceg J., Pakozdi T., Marco-Ferreres R., Ghavi-Helm Y., Girardot C., Bracken A. P., Furlong E. E. M., Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes Dev. 31, 590– 602 (2017). 28381411 PMC5393054
- [21]Curtiss J., Burnett M., Mlodzik M., distal antenna and distal antenna-related function in the retinal determination network during eye development in Drosophila. Dev. Biol. 306, 685– 702 (2007). 17493605 PMC1986786
- [22]Davis T. L., Rebay I., Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev. Biol. 421, 93– 107 (2017). 27979656 PMC5496713
- [23]Kondo T., Isono K., Kondo K., Endo T. A., Itohara S., Vidal M., Koseki H., Polycomb potentiates meis2 activation in midbrain by mediating interaction of the promoter with a tissue-specific enhancer. Dev. Cell 28, 94– 101 (2014). 24374176
- [25]Kloet S. L., Makowski M. M., Baymaz H. I., van Voorthuijsen L., Karemaker I. D., Santanach A., Jansen P. W. T. C., Croce L. D., Vermeulen M., The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nat. Struct. Mol. Biol. 23, 682– 690 (2016). 27294783 PMC4939079
- [26]Stowers R. S., Schwarz T. L., A genetic method for generating Drosophila eyes composed exclusively of mitotic clones of a single genotype. Genetics 152, 1631– 1639 (1999). 10430588 PMC1460682
- [27]Loubiere V., Delest A., Schuettengruber B., Martinez A.-M., Cavalli G., Chromatin immunoprecipitation experiments from whole drosophila embryos or larval imaginal discs. Bio Protoc. 7, e2327 (2017). PMC8410254 34541088
- [28]Strutt H., Paro R., The polycomb group protein complex of Drosophila melanogaster has different compositions at different target genes. Mol. Cell. Biol. 17, 6773– 6783 (1997). 9372908 PMC232533
- [29]Bantignies F., Cavalli G., Topological organization of Drosophila Hox genes using DNA fluorescent in situ hybridization. Methods Mol. Biol. 1196, 103– 120 (2014). 25151160
- [30]Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S., Schmid B., Tinevez J.-Y., White D. J., Hartenstein V., Eliceiri K., Tomancak P., Cardona A., Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676– 682 (2012). 22743772 PMC3855844
- [31]Langmead B., Salzberg S. L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357– 359 (2012). 22388286 PMC3322381
- [32]Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R.; Genome Project Data Processing Subgroup, The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078– 2079 (2009). 19505943 PMC2723002
- [33]Zhang Y., Liu T., Meyer C. A., Eeckhoute J., Johnson D. S., Bernstein B. E., Nusbaum C., Myers R. M., Brown M., Li W., Liu X. S., Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008). 18798982 PMC2592715
- [34]Ramirez F., Ryan D. P., Grüning B., Bhardwaj V., Kilpert F., Richter A. S., Heyne S., Dündar F., Manke T., deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160– W165 (2016). 27079975 PMC4987876
- [35]Kent W. J., Zweig A. S., Barber G., Hinrichs A. S., Karolchik D., BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204– 2207 (2010). 20639541 PMC2922891
- [36]Robinson J. T., Thorvaldsdóttir H., Winckler W., Guttman M., Lander E. S., Getz G., Mesirov J. P., Integrative genomics viewer. Nat. Biotechnol. 29, 24– 26 (2011). 21221095 PMC3346182
- [37]Stempor P., Ahringer J., SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics. Wellcome Open Res. 1, 14 (2016). 27918597 PMC5133382
- [38]Pohl A., Beato M., bwtool: A tool for bigWig files. Bioinformatics 30, 1618– 1619 (2014). 24489365 PMC4029031
- [39]Kohonen T., Self-organizing neural projections. Neural Netw. 19, 723– 733 (2006). 16774731
- [40]R. Wehrens, L. M. C. Buydens, Self- and Super-organizing Maps in R: The kohonen Package. 2007 21, 19%J Journal of Statistical Software (2007).
- [41]Nagano T., Lubling Y., Várnai C., Dudley C., Leung W., Baran Y., Cohen N. M., Wingett S., Fraser P., Tanay A., Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547, 61– 67 (2017). 28682332 PMC5567812
- [42]N. M. Cohen, P. Olivares-Chauvet, Y. Lubling, Y. Baran, A. Lifshitz, M. Hoichman, A. Tanay, SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices. bioRxiv 187203; doi: 10.1101/187203 · DOI
- [43]Dobin A., Davis C. A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T. R., STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15– 21 (2013). 23104886 PMC3530905
- [44]Anders S., Pyl P. T., Huber W., HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166– 169 (2015). 25260700 PMC4287950
- [45]Love M. I., Huber W., Anders S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014). 25516281 PMC4302049
- [46]Huang D. W., Sherman B. T., Lempicki R. A., Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44– 57 (2009). 19131956
- [47]Yu G., Wang L.-G., Han Y., He Q.-Y., clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 16, 284– 287 (2012). 22455463 PMC3339379
- [48]Quinlan A. R., Hall I. M., BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841– 842 (2010). 20110278 PMC2832824
Cited by
Sorted by citations
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
Paldi, F., Szalay, M.-F., Dufau, S., Di Stefano, M., Reboul, H., Jost, D., Bantignies, F., & Cavalli, G. (2026) · Nature Genetics · doi:10.1038/s41588-025-02489-4 · Cited by 18 · see citing works
Self-citation
- Authors
- Loubiere, V., Papadopoulos, G. L., Szabo, Q., Martinez, A.-M., & Cavalli, G.
- Affiliations
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France.
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Martinez, A-M.
- Cavalli, G.
- Venue
- Science Advances
- Published
- 2020-01-10
- Volume
- 6
- Issue
- 2
- Pages
- eaax4001-eaax4001
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC6954061
- OpenAlex
- W2999808884
- Cited by
- 126
- References
- 4
- Citations by year
- 2026: 13 · 2025: 24 · 2024: 16 · 2023: 24 · 2022: 21 · 2021: 22 · 2020: 6
- FWCI
- 5.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Science Advances (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by-nc)
- Funders
- H2020 European Research Council (2017-AdG No 788972)
- European Research Council (ERC-2008-AdG No 232947)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- PRC1, chromatin looping, developmental gene expression, RING1B, 3D genome organization, neuronal differentiation, transcriptional regulation, chromatin interactions
- MeSH terms
- Animals, Cell Differentiation, Chromatin, Drosophila melanogaster, Enhancer Elements, Genetic, Promoter Regions, Genetic, Protein Binding, Gene Expression Regulation, Developmental, Response Elements, Genes, Developmental, Mice, Genetic Loci, Neural Stem Cells, Imaginal Discs, Polycomb Repressive Complex 1
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