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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
.... Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture data sets and analyzed a collection of hundreds...
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Research: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
- A. Rasim Barutcu,
- Bryan R. Lajoie,
- Andrew J. Fritz,
- Rachel P. McCord,
- Jeffrey A. Nickerson,
- Andre J. van Wijnen,
- Jane B. Lian,
- Janet L. Stein,
- Job Dekker,
- Gary S. Stein,
- and Anthony N. Imbalzano
Genome Res. September 2016 26: 1188-1201; Published in Advance July 19, 2016, doi:10.1101/gr.201624.115
...-order chromatin structure in proliferating mammary epithelial cells Barutcu et al. SMARCA4 regulates chromatin interactions SMARCA4 regulates gene expression and higherorder chromatin structure in proliferating mammary epithelial cells A. Rasim Barutcu,1 Bryan R. Lajoie,2 Andrew J. Fritz,3 Rachel P. McCord,4...
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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
...of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron...
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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
...for the characterization of hundreds of limb-associated regulatory landscapes and a framework to interpret the chromatin folding dynamics observed during embryogenesis. [Supplemental material is available for this article.] Gene regulation in higher eukaryotes involves complex interactions between regulatory sequences...
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Research: Hormone-control regions mediate steroid receptor–dependent genome organization
- François Le Dily,
- Enrique Vidal,
- Yasmina Cuartero,
- Javier Quilez,
- A. Silvina Nacht,
- Guillermo P. Vicent,
- José Carbonell-Caballero,
- Priyanka Sharma,
- José Luis Villanueva-Cañas,
- Roberto Ferrari,
- Lara Isabel De Llobet,
- Gaetano Verde,
- Roni H.G. Wright,
- and Miguel Beato
Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
..., in particular ESR1, participate in the maintenance of a TAD structure that is permissive for the regulation of gene expression. Upon exposure to the hormones, further binding of the receptors can enhance or, in contrast, destabilize the interactions established between HCR and the promoters, leading to adequate...
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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
...that cohesin's main role in interphase genome organization is in mediating interactions within architectural chromosome compartments, rather than specifying compartments per se. However, it remains unclear how cohesin-mediated interactions contribute to the regulation of gene expression. We have found...
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Research: The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes
- Hui Fan,
- Pin Lv,
- Xiangru Huo,
- Jicheng Wu,
- Qianfeng Wang,
- Lu Cheng,
- Yun Liu,
- Qi-Qun Tang,
- Ling Zhang,
- Feng Zhang,
- Xiaoqi Zheng,
- Hao Wu,
- and Bo Wen
Genome Res. February 2018 28: 192-202; Published in Advance December 22, 2017, doi:10.1101/gr.224576.117
...active regions in the human . Cell Rep 17: 2042–2059. ↵Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, et al. 2013. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res...

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