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Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.

He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.

BMC Genomics. 2013 Jun 28;14:428. doi: 10.1186/1471-2164-14-428.


Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.

Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112.


Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.


Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.

Nie Y, Cheng X, Chen J, Sun X.

BMC Genomics. 2014 Jun 19;15:493. doi: 10.1186/1471-2164-15-493.


Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.

Chatterjee R, Zhao J, He X, Shlyakhtenko A, Mann I, Waterfall JJ, Meltzer P, Sathyanarayana BK, FitzGerald PC, Vinson C.

G3 (Bethesda). 2012 Oct;2(10):1243-56. doi: 10.1534/g3.112.004002. Epub 2012 Oct 1.


Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky DB.

PLoS Comput Biol. 2015 Aug 18;11(8):e1004429. doi: 10.1371/journal.pcbi.1004429. eCollection 2015 Aug.


Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.


Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.


Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo.

Truss M, Bartsch J, Schelbert A, Haché RJ, Beato M.

EMBO J. 1995 Apr 18;14(8):1737-51.


Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals.

Halder K, Halder R, Chowdhury S.

Mol Biosyst. 2009 Dec;5(12):1703-12. doi: 10.1039/b905132e. Epub 2009 May 29.


COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.

Ha N, Polychronidou M, Lohmann I.

PLoS One. 2012;7(12):e52055. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.


Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.


The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.


Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast.

Afek A, Sela I, Musa-Lempel N, Lukatsky DB.

Biophys J. 2011 Nov 16;101(10):2465-75. doi: 10.1016/j.bpj.2011.10.012. Epub 2011 Nov 15.


In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.

Gossett AJ, Lieb JD.

PLoS Genet. 2012;8(6):e1002771. doi: 10.1371/journal.pgen.1002771. Epub 2012 Jun 21.


Multiple distinct stimuli increase measured nucleosome occupancy around human promoters.

Pham CD, Sims HI, Archer TK, Schnitzler GR.

PLoS One. 2011;6(8):e23490. doi: 10.1371/journal.pone.0023490. Epub 2011 Aug 11.


Glucocorticoid receptor-glucocorticoid response element binding stimulates nucleosome disruption by the SWI/SNF complex.

Ostlund Farrants AK, Blomquist P, Kwon H, Wrange O.

Mol Cell Biol. 1997 Feb;17(2):895-905.


C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements.

Grøntved L, John S, Baek S, Liu Y, Buckley JR, Vinson C, Aguilera G, Hager GL.

EMBO J. 2013 May 29;32(11):1568-83. doi: 10.1038/emboj.2013.106. Epub 2013 May 10.


High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

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