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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
...protein complex contributes to transcriptional regulation in a CTCF-independent manner by colocalizing with master regulators at tissue-specific loci. The regulation of transcription involves the concerted action of multiple transcription factors (TFs) and cohesin’s role in this context of combinatorial...
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Research: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control
- Valentina Casa,
- Macarena Moronta Gines,
- Eduardo Gade Gusmao,
- Johan A. Slotman,
- Anne Zirkel,
- Natasa Josipovic,
- Edwin Oole,
- Wilfred F.J. van IJcken,
- Adriaan B. Houtsmuller,
- Argyris Papantonis,
- and Kerstin S. Wendt
Genome Res. April 2020 30: 515-527; Published in Advance April 6, 2020, doi:10.1101/gr.253211.119
..., signal at the TSS, pointing to a CTCF-independent binding here, as reported for particular promoters before (Schmidt et al. 2010). Genes down-regulated after STAG2 degradation have enriched cohesin and CTCF signal at both the TSS and TTS, suggesting that long-range interactions spanning their gene bodies...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
.... This supports the idea that different functions may be a result of the context of CTCF binding (Gaszner and Felsenfeld 2006), and it is possible that coordinate binding of cohesin may influence CTCF. Cohesin is involved in tissue-specific transcriptional control (Faure et al. 2012) and associated...
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Research: Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
- Elizabeth Ing-Simmons,
- Vlad C. Seitan,
- Andre J. Faure,
- Paul Flicek,
- Thomas Carroll,
- Job Dekker,
- Amanda G. Fisher,
- Boris Lenhard,
- and Matthias Merkenschlager
Genome Res. April 2015 25: 504-513; Published in Advance February 12, 2015, doi:10.1101/gr.184986.114
..., Schuijers J, Lee TI, Zhao K, et al. 2014. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159: 374–387. Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. 2012. Cohesin regulates tissue-specific expression by stabilizing...
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Research: The genomic landscape of cohesin-associated chromatin interactions
- Laura E. DeMare,
- Jing Leng,
- Justin Cotney,
- Steven K. Reilly,
- Jun Yin,
- Richard Sarro,
- and James P. Noonan
Genome Res. August 2013 23: 1224-1234; Published in Advance May 23, 2013, doi:10.1101/gr.156570.113
...-shaped complex consisting of the core subunits SMC1A, SMC3, SCC1 (also known as RAD21), and SA1/SA2 (Nasmyth and Haering 2009). Although cohesin does not bind DNA directly, it colocalizes with tissue-specific transcription factors on chromatin (Schmidt et al. 2010; Nitzsche et al. 2011) and is thought...
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Research: Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- Vlad C. Seitan,
- Andre J. Faure,
- Ye Zhan,
- Rachel Patton McCord,
- Bryan R. Lajoie,
- Elizabeth Ing-Simmons,
- Boris Lenhard,
- Luca Giorgetti,
- Edith Heard,
- Amanda G. Fisher,
- Paul Flicek,
- Job Dekker,
- and Matthias Merkenschlager
Genome Res. December 2013 23: 2066-2077; Published in Advance September 3, 2013, doi:10.1101/gr.161620.113
...between cohesin-bound sites, whereas alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...with open and closed chromatin, respectively (Lieberman-Aiden et al. 2009; Dixon et al. 2015). Although 95% of all compartments were conserved across different tissues (Fig. 2A,B), we found tissue-specific compartments to be enriched for both induced and spontaneous SV (Fig. 2B), and enrichment of induced...
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Research: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
- Bum-Kyu Lee,
- Akshay A. Bhinge,
- Anna Battenhouse,
- Ryan M. McDaniell,
- Zheng Liu,
- Lingyun Song,
- Yunyun Ni,
- Ewan Birney,
- Jason D. Lieb,
- Terrence S. Furey,
- Gregory E. Crawford,
- and Vishwanath R. Iyer
Genome Res. January 2012 22: 9-24; Published in Advance November 16, 2011, doi:10.1101/gr.127597.111
...Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells Bum-Kyu Lee 1 , Akshay A. Bhinge 1 , Anna Battenhouse 1 , Ryan M. McDaniell 1 , Zheng Liu 1...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...studied so far, genes encoding tissue-specific transcription factors are regulated by a high number of enhancers (Bejerano et al. 2004; Woolfe et al. 2005; Hong et al. 2008; Visel et al. 2008; Heintzman et al. 2009; Visel et al. 2009a). Furthermore, predicted enhancers are enriched in the same genomic...
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Research: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
- Guillaume Andrey,
- Robert Schöpflin,
- Ivana Jerković,
- Verena Heinrich,
- Daniel M. Ibrahim,
- Christina Paliou,
- Myriam Hochradel,
- Bernd Timmermann,
- Stefan Haas,
- Martin Vingron,
- and Stefan Mundlos
Genome Res. February 2017 27: 223-233; Published in Advance December 6, 2016, doi:10.1101/gr.213066.116
...by the Cohesin-CTCF interactions, as formulated in the loop extrusion model, and variable ones could be the product of a “roadblock” of the Cohesin translocating complex induced by the presence of tissue-specific transcription factors and associated protein complexes (Sanborn et al. 2015; Fudenberg et al. 2016...

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