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Items: 1 to 20 of 106

1.

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY.

Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25.

2.

Enhancers looping to target genes.

Trynka G.

Nat Genet. 2017 Oct 27;49(11):1564-1565. doi: 10.1038/ng.3982.

PMID:
29074944
3.

Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders.

Jeng MY, Mumbach MR, Granja JM, Satpathy AT, Chang HY, Chang ALS.

J Invest Dermatol. 2019 Mar;139(3):605-614. doi: 10.1016/j.jid.2018.09.011. Epub 2018 Oct 10.

4.

Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A.

Nature. 2017 Sep 7;549(7670):111-115. doi: 10.1038/nature23875. Epub 2017 Aug 30. Erratum in: Nature. 2018 Jul;559(7715):E13.

5.

Systematic mapping of functional enhancer-promoter connections with CRISPR interference.

Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM.

Science. 2016 Nov 11;354(6313):769-773. Epub 2016 Sep 29.

6.

Mutations in the noncoding genome.

Scacheri CA, Scacheri PC.

Curr Opin Pediatr. 2015 Dec;27(6):659-64. doi: 10.1097/MOP.0000000000000283. Review.

7.

Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.

Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KG.

Genome Med. 2016 Jul 19;8(1):76. doi: 10.1186/s13073-016-0329-5.

8.

Identifying functional noncoding variants from genome-wide association studies for cardiovascular disease and related traits.

Smith AJ, Humphries SE, Talmud PJ.

Curr Opin Lipidol. 2015 Apr;26(2):120-6. doi: 10.1097/MOL.0000000000000158. Review.

PMID:
25692342
9.

Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes.

Weinstein JS, Lezon-Geyda K, Maksimova Y, Craft S, Zhang Y, Su M, Schulz VP, Craft J, Gallagher PG.

Blood. 2014 Dec 11;124(25):3719-29. doi: 10.1182/blood-2014-06-582700. Epub 2014 Oct 20.

10.

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.

Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M.

Genome Biol. 2017 Jul 21;18(1):137. doi: 10.1186/s13059-017-1273-4.

11.

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.

12.

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.

Schwartz AM, Demin DE, Vorontsov IE, Kasyanov AS, Putlyaeva LV, Tatosyan KA, Kulakovskiy IV, Kuprash DV.

Gene. 2017 Feb 20;602:50-56. doi: 10.1016/j.gene.2016.11.032. Epub 2016 Nov 19.

PMID:
27876533
13.

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.

Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ.

Genome Biol. 2018 Oct 8;19(1):160. doi: 10.1186/s13059-018-1531-0.

14.

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.

15.

Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes.

Blinka S, Reimer MH Jr, Pulakanti K, Rao S.

Cell Rep. 2016 Sep 27;17(1):19-28. doi: 10.1016/j.celrep.2016.09.002.

16.

Functional Analysis of a Novel Genome-Wide Association Study Signal in SMAD3 That Confers Protection From Coronary Artery Disease.

Turner AW, Martinuk A, Silva A, Lau P, Nikpay M, Eriksson P, Folkersen L, Perisic L, Hedin U, Soubeyrand S, McPherson R.

Arterioscler Thromb Vasc Biol. 2016 May;36(5):972-83. doi: 10.1161/ATVBAHA.116.307294. Epub 2016 Mar 10.

PMID:
26966274
17.

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.

Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC.

Genome Res. 2014 Jan;24(1):1-13. doi: 10.1101/gr.164079.113. Epub 2013 Nov 6.

18.

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.

19.

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity.

Schmidl C, Klug M, Boeld TJ, Andreesen R, Hoffmann P, Edinger M, Rehli M.

Genome Res. 2009 Jul;19(7):1165-74. doi: 10.1101/gr.091470.109. Epub 2009 Jun 3.

20.

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants.

Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N; NISC Comparative Sequencing Program, Black BL, Visel A, Pennacchio LA, Collins FS; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors; NISC Comparative Sequencing Program Authors.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17921-6. doi: 10.1073/pnas.1317023110. Epub 2013 Oct 14.

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