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Results: 1 to 20 of 45

1.

DNA specificity determinants associate with distinct transcription factor functions.

Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ.

PLoS Genet. 2009 Dec;5(12):e1000778. doi: 10.1371/journal.pgen.1000778. Epub 2009 Dec 18.

PMID:
20019798
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Chromatin poises miRNA- and protein-coding genes for expression.

Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K.

Genome Res. 2009 Oct;19(10):1742-51. doi: 10.1101/gr.090951.109. Epub 2009 Aug 27. Erratum in: Genome Res. 2009 Dec;19(12):2343.

PMID:
19713549
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.

Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G.

Nat Genet. 2009 Aug;41(8):941-5. doi: 10.1038/ng.409. Epub 2009 Jul 26.

PMID:
19633671
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Transcription independent insulation at TFIIIC-dependent insulators.

Valenzuela L, Dhillon N, Kamakaka RT.

Genetics. 2009 Sep;183(1):131-48. doi: 10.1534/genetics.109.106203. Epub 2009 Jul 13.

PMID:
19596900
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Distinctive chromatin in human sperm packages genes for embryo development.

Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR.

Nature. 2009 Jul 23;460(7254):473-8. doi: 10.1038/nature08162. Epub 2009 Jun 14.

PMID:
19525931
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Developmental programming of CpG island methylation profiles in the human genome.

Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, Simon I, Yakhini Z, Cedar H.

Nat Struct Mol Biol. 2009 May;16(5):564-71. doi: 10.1038/nsmb.1594. Epub 2009 Apr 19.

PMID:
19377480
[PubMed - indexed for MEDLINE]
7.

C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts.

Bortolin-Cavaillé ML, Dance M, Weber M, Cavaillé J.

Nucleic Acids Res. 2009 Jun;37(10):3464-73. doi: 10.1093/nar/gkp205. Epub 2009 Apr 1.

PMID:
19339516
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
19295514
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

PMID:
19160518
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

PMID:
19122651
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.

Nix DA, Courdy SJ, Boucher KM.

BMC Bioinformatics. 2008 Dec 5;9:523. doi: 10.1186/1471-2105-9-523.

PMID:
19061503
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.

Genome Res. 2009 Jan;19(1):24-32. doi: 10.1101/gr.082800.108. Epub 2008 Dec 3.

PMID:
19056695
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Non-coding RNA production by RNA polymerase III is implicated in cancer.

Marshall L, White RJ.

Nat Rev Cancer. 2008 Dec;8(12):911-4. doi: 10.1038/nrc2539. Epub 2008 Nov 6. Erratum in: Nat Rev Cancer. 2012 Oct;12(10):732.

PMID:
18987635
[PubMed - indexed for MEDLINE]
14.

RNA polymerases I and III, non-coding RNAs and cancer.

White RJ.

Trends Genet. 2008 Dec;24(12):622-9. doi: 10.1016/j.tig.2008.10.003. Epub 2008 Nov 6. Review.

PMID:
18980784
[PubMed - indexed for MEDLINE]
15.

TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae.

Simms TA, Dugas SL, Gremillion JC, Ibos ME, Dandurand MN, Toliver TT, Edwards DJ, Donze D.

Eukaryot Cell. 2008 Dec;7(12):2078-86. doi: 10.1128/EC.00128-08. Epub 2008 Oct 10.

PMID:
18849469
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

PMID:
18787082
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Combinatorial patterns of histone acetylations and methylations in the human genome.

Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K.

Nat Genet. 2008 Jul;40(7):897-903. doi: 10.1038/ng.154. Epub 2008 Jun 15.

PMID:
18552846
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Dynamic regulation of nucleosome positioning in the human genome.

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

Cell. 2008 Mar 7;132(5):887-98. doi: 10.1016/j.cell.2008.02.022.

PMID:
18329373
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
18243105
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III.

Listerman I, Bledau AS, Grishina I, Neugebauer KM.

PLoS Genet. 2007 Nov;3(11):e212.

PMID:
18039033
[PubMed - indexed for MEDLINE]
Free PMC Article

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