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Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM. Wutz G, et al. Among authors: varnai c. EMBO J. 2017 Dec 15;36(24):3573-3599. doi: 10.15252/embj.201798004. Epub 2017 Dec 7. EMBO J. 2017. PMID: 29217591 Free PMC article.
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL.
Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM. Wutz G, et al. Among authors: varnai c. Elife. 2020 Feb 17;9:e52091. doi: 10.7554/eLife.52091. Elife. 2020. PMID: 32065581 Free PMC article.
Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.
Groves IJ, Drane ELA, Michalski M, Monahan JM, Scarpini CG, Smith SP, Bussotti G, Várnai C, Schoenfelder S, Fraser P, Enright AJ, Coleman N. Groves IJ, et al. Among authors: varnai c. PLoS Pathog. 2021 Aug 25;17(8):e1009875. doi: 10.1371/journal.ppat.1009875. eCollection 2021 Aug. PLoS Pathog. 2021. PMID: 34432858 Free PMC article.
3D genome architecture from populations to single cells.
Furlan-Magaril M, Várnai C, Nagano T, Fraser P. Furlan-Magaril M, et al. Among authors: varnai c. Curr Opin Genet Dev. 2015 Apr;31:36-41. doi: 10.1016/j.gde.2015.04.004. Epub 2015 May 16. Curr Opin Genet Dev. 2015. PMID: 25966907 Review.
Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.
Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD. Koohy H, et al. Among authors: varnai c. Genome Biol. 2018 Sep 5;19(1):126. doi: 10.1186/s13059-018-1489-y. Genome Biol. 2018. PMID: 30180872 Free PMC article.
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. Cairns J, et al. Among authors: varnai c. Genome Biol. 2016 Jun 15;17(1):127. doi: 10.1186/s13059-016-0992-2. Genome Biol. 2016. PMID: 27306882 Free PMC article.
34 results