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Items: 1 to 20 of 98

1.

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.

Andrey G, Schöpflin R, Jerković I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S.

Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6.

2.

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.

3.

Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements.

Infante CR, Park S, Mihala AG, Kingsley DM, Menke DB.

Dev Biol. 2013 Feb 1;374(1):234-44. doi: 10.1016/j.ydbio.2012.11.017. Epub 2012 Nov 27.

4.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP.

Genome Res. 2012 Jun;22(6):1069-80. doi: 10.1101/gr.129817.111. Epub 2012 Mar 15.

5.

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.

Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA.

Genome Res. 2014 Jun;24(6):920-9. doi: 10.1101/gr.168930.113. Epub 2014 Apr 21.

6.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

7.

Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

Waki H, Nakamura M, Yamauchi T, Wakabayashi K, Yu J, Hirose-Yotsuya L, Take K, Sun W, Iwabu M, Okada-Iwabu M, Fujita T, Aoyama T, Tsutsumi S, Ueki K, Kodama T, Sakai J, Aburatani H, Kadowaki T.

PLoS Genet. 2011 Oct;7(10):e1002311. doi: 10.1371/journal.pgen.1002311. Epub 2011 Oct 20.

8.

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.

9.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.

10.

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX.

Nucleic Acids Res. 2012 Sep;40(16):7690-704. Epub 2012 Jun 6.

11.

Locus-specific editing of histone modifications at endogenous enhancers.

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE.

Nat Biotechnol. 2013 Dec;31(12):1133-6. doi: 10.1038/nbt.2701. Epub 2013 Sep 8.

12.

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

Frank CL, Liu F, Wijayatunge R, Song L, Biegler MT, Yang MG, Vockley CM, Safi A, Gersbach CA, Crawford GE, West AE.

Nat Neurosci. 2015 May;18(5):647-56. doi: 10.1038/nn.3995. Epub 2015 Apr 6.

13.

A unique chromatin signature uncovers early developmental enhancers in humans.

Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.

Nature. 2011 Feb 10;470(7333):279-83. doi: 10.1038/nature09692. Epub 2010 Dec 15.

14.

Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization.

Varma G, Rawat P, Jalan M, Vinayak M, Srivastava M.

Mol Cell Biol. 2015 Oct;35(20):3504-16. doi: 10.1128/MCB.00514-15. Epub 2015 Aug 3.

15.

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.

Vokes SA, Ji H, Wong WH, McMahon AP.

Genes Dev. 2008 Oct 1;22(19):2651-63. doi: 10.1101/gad.1693008.

16.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

17.

CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart.

Gomez-Velazquez M, Badia-Careaga C, Lechuga-Vieco AV, Nieto-Arellano R, Tena JJ, Rollan I, Alvarez A, Torroja C, Caceres EF, Roy AR, Galjart N, Delgado-Olguin P, Sanchez-Cabo F, Enriquez JA, Gomez-Skarmeta JL, Manzanares M.

PLoS Genet. 2017 Aug 28;13(8):e1006985. doi: 10.1371/journal.pgen.1006985. eCollection 2017 Aug.

18.

Sequential histone modifications at Hoxd4 regulatory regions distinguish anterior from posterior embryonic compartments.

Rastegar M, Kobrossy L, Kovacs EN, Rambaldi I, Featherstone M.

Mol Cell Biol. 2004 Sep;24(18):8090-103.

19.

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201. Epub 2008 Oct 17.

20.

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs.

Janssens DH, Wu SJ, Sarthy JF, Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S.

Epigenetics Chromatin. 2018 Dec 21;11(1):74. doi: 10.1186/s13072-018-0243-8.

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