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Items: 1 to 20 of 260

1.

The long-range interaction landscape of gene promoters.

Sanyal A, Lajoie BR, Jain G, Dekker J.

Nature. 2012 Sep 6;489(7414):109-13. doi: 10.1038/nature11279.

2.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

3.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

4.

Genome-wide map of regulatory interactions in the human genome.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP.

Genome Res. 2014 Dec;24(12):1905-17. doi: 10.1101/gr.176586.114. Epub 2014 Sep 16.

5.

The genomic landscape of cohesin-associated chromatin interactions.

DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP.

Genome Res. 2013 Aug;23(8):1224-34. doi: 10.1101/gr.156570.113. Epub 2013 May 23.

6.

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q.

Cell. 2015 Aug 13;162(4):900-10. doi: 10.1016/j.cell.2015.07.038.

7.

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.

Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M.

Genome Res. 2013 Dec;23(12):2066-77. doi: 10.1101/gr.161620.113. Epub 2013 Sep 3.

8.

Mediator and cohesin connect gene expression and chromatin architecture.

Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA.

Nature. 2010 Sep 23;467(7314):430-5. doi: 10.1038/nature09380. Epub 2010 Aug 18. Erratum in: Nature. 2011 Apr 14;472(7342):247.

9.

3D Chromosome Regulatory Landscape of Human Pluripotent Cells.

Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, Weintraub AS, Hnisz D, Pegoraro G, Lee TI, Misteli T, Jaenisch R, Young RA.

Cell Stem Cell. 2016 Feb 4;18(2):262-75. doi: 10.1016/j.stem.2015.11.007. Epub 2015 Dec 10.

10.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8.

11.

Chromosome conformation elucidates regulatory relationships in developing human brain.

Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH.

Nature. 2016 Oct 27;538(7626):523-527. doi: 10.1038/nature19847. Epub 2016 Oct 19.

12.

Genomic approaches for the discovery of CFTR regulatory elements.

Ott CJ, Harris A.

Transcription. 2011 Jan-Feb;2(1):23-7. doi: 10.4161/trns.2.1.13693.

13.

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M.

Genome Res. 2015 Apr;25(4):504-13. doi: 10.1101/gr.184986.114. Epub 2015 Feb 12.

14.

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders.

Uusküla-Reimand L, Hou H, Samavarchi-Tehrani P, Rudan MV, Liang M, Medina-Rivera A, Mohammed H, Schmidt D, Schwalie P, Young EJ, Reimand J, Hadjur S, Gingras AC, Wilson MD.

Genome Biol. 2016 Aug 31;17(1):182. doi: 10.1186/s13059-016-1043-8.

15.

Cohesin mediates chromatin interactions that regulate mammalian β-globin expression.

Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR Jr, Calof AL, Lander AD, Groudine MT, Yokomori K.

J Biol Chem. 2011 May 20;286(20):17870-8. doi: 10.1074/jbc.M110.207365. Epub 2011 Mar 29.

16.
17.

CTCF and cohesin: linking gene regulatory elements with their targets.

Merkenschlager M, Odom DT.

Cell. 2013 Mar 14;152(6):1285-97. doi: 10.1016/j.cell.2013.02.029. Review.

18.

Genomics: ENCODE explained.

Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E.

Nature. 2012 Sep 6;489(7414):52-5. doi: 10.1038/489052a. No abstract available.

PMID:
22955614
19.

Cohesin mediates transcriptional insulation by CCCTC-binding factor.

Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, Tsutsumi S, Nagae G, Ishihara K, Mishiro T, Yahata K, Imamoto F, Aburatani H, Nakao M, Imamoto N, Maeshima K, Shirahige K, Peters JM.

Nature. 2008 Feb 14;451(7180):796-801. doi: 10.1038/nature06634. Epub 2008 Jan 30.

PMID:
18235444
20.

Cell type specificity of chromatin organization mediated by CTCF and cohesin.

Hou C, Dale R, Dean A.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3651-6. doi: 10.1073/pnas.0912087107. Epub 2010 Feb 2.

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