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Items: 1 to 20 of 84

1.

A high-resolution map of active promoters in the human genome.

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B.

Nature. 2005 Aug 11;436(7052):876-80. Epub 2005 Jun 29.

2.

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

Kwon SY, Grisan V, Jang B, Herbert J, Badenhorst P.

PLoS Genet. 2016 Apr 5;12(4):e1005969. doi: 10.1371/journal.pgen.1005969. eCollection 2016 Apr.

3.

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.

Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K.

Cell Res. 2012 Mar;22(3):490-503. doi: 10.1038/cr.2012.15. Epub 2012 Jan 24.

4.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL.

Nature. 2013 Dec 12;504(7479):306-10. doi: 10.1038/nature12716. Epub 2013 Nov 10.

5.

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.

6.

Mediator, TATA-binding protein, and RNA polymerase II contribute to low histone occupancy at active gene promoters in yeast.

Ansari SA, Paul E, Sommer S, Lieleg C, He Q, Daly AZ, Rode KA, Barber WT, Ellis LC, LaPorta E, Orzechowski AM, Taylor E, Reeb T, Wong J, Korber P, Morse RH.

J Biol Chem. 2014 May 23;289(21):14981-95. doi: 10.1074/jbc.M113.529354. Epub 2014 Apr 11. Erratum in: J Biol Chem. 2016 May 6;291(19):9938.

7.

High-resolution mapping and characterization of open chromatin across the genome.

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE.

Cell. 2008 Jan 25;132(2):311-22. doi: 10.1016/j.cell.2007.12.014.

8.

Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila.

Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP.

Nucleic Acids Res. 2013 Mar 1;41(5):2963-80. doi: 10.1093/nar/gkt037. Epub 2013 Jan 28.

9.

Direct isolation and identification of promoters in the human genome.

Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B.

Genome Res. 2005 Jun;15(6):830-9. Epub 2005 May 17.

10.

A map of the cis-regulatory sequences in the mouse genome.

Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B.

Nature. 2012 Aug 2;488(7409):116-20. doi: 10.1038/nature11243.

11.

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B.

Nat Genet. 2007 Mar;39(3):311-8. Epub 2007 Feb 4.

PMID:
17277777
12.

A high-resolution map of the three-dimensional chromatin interactome in human cells.

Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B.

Nature. 2013 Nov 14;503(7475):290-4. doi: 10.1038/nature12644. Epub 2013 Oct 20.

13.

Genome-wide analysis of regions similar to promoters of histone genes.

Chowdhary R, Bajic VB, Dong D, Wong L, Liu JS.

BMC Syst Biol. 2010 May 28;4 Suppl 1:S4. doi: 10.1186/1752-0509-4-S1-S4.

14.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.

Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B.

Genome Res. 2008 Jan;18(1):46-59. Epub 2007 Nov 27.

15.

Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells.

Poletti V, Delli Carri A, Malagoli Tagliazucchi G, Faedo A, Petiti L, Mazza EM, Peano C, De Bellis G, Bicciato S, Miccio A, Cattaneo E, Mavilio F.

PLoS One. 2015 May 15;10(5):e0126590. doi: 10.1371/journal.pone.0126590. eCollection 2015.

16.

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.

Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y.

Genome Res. 2003 May;13(5):773-80.

17.

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.

18.

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.

Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL.

Mol Cell Biol. 2007 Jul;27(14):5090-104. Epub 2007 May 21.

19.

Integrative genome-wide chromatin signature analysis using finite mixture models.

Taslim C, Lin S, Huang K, Huang TH.

BMC Genomics. 2012;13 Suppl 6:S3. doi: 10.1186/1471-2164-13-S6-S3. Epub 2012 Oct 26.

20.

High-resolution profiling of histone methylations in the human genome.

Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.

Cell. 2007 May 18;129(4):823-37.

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