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Characterizing protein-DNA binding event subtypes in ChIP-exo data.

Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S.

Bioinformatics. 2019 Mar 15;35(6):903-913. doi: 10.1093/bioinformatics/bty703.


In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets.

Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ.

Nucleic Acids Res. 2018 Sep 19;46(16):8385-8403. doi: 10.1093/nar/gky692.


Simplified ChIP-exo assays.

Rossi MJ, Lai WKM, Pugh BF.

Nat Commun. 2018 Jul 20;9(1):2842. doi: 10.1038/s41467-018-05265-7.


The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally.

García-Molinero V, García-Martínez J, Reja R, Furió-Tarí P, Antúnez O, Vinayachandran V, Conesa A, Pugh BF, Pérez-Ortín JE, Rodríguez-Navarro S.

Epigenetics Chromatin. 2018 Mar 29;11(1):13. doi: 10.1186/s13072-018-0184-2.


Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.

Rossi MJ, Lai WKM, Pugh BF.

Genome Res. 2018 Apr;28(4):497-508. doi: 10.1101/gr.229518.117. Epub 2018 Mar 21.


Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock.

Vinayachandran V, Reja R, Rossi MJ, Park B, Rieber L, Mittal C, Mahony S, Pugh BF.

Genome Res. 2018 Feb 14. doi: 10.1101/gr.226761.117. [Epub ahead of print]


Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4.

Miller JE, Zhang L, Jiang H, Li Y, Pugh BF, Reese JC.

G3 (Bethesda). 2018 Jan 4;8(1):315-330. doi: 10.1534/g3.117.300415.


Correspondence: DNA shape is insufficient to explain binding.

Rossi MJ, Lai WKM, Pugh BF.

Nat Commun. 2017 Jun 5;8:15643. doi: 10.1038/ncomms15643. No abstract available. Erratum in: Nat Commun. 2017 Jun 05;8:15723.


Understanding nucleosome dynamics and their links to gene expression and DNA replication.

Lai WKM, Pugh BF.

Nat Rev Mol Cell Biol. 2017 Sep;18(9):548-562. doi: 10.1038/nrm.2017.47. Epub 2017 May 24. Review.


Genome-wide uniformity of human 'open' pre-initiation complexes.

Lai WK, Pugh BF.

Genome Res. 2017 Jan;27(1):15-26. doi: 10.1101/gr.210955.116. Epub 2016 Nov 10.


The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6.

Van Oss SB, Shirra MK, Bataille AR, Wier AD, Yen K, Vinayachandran V, Byeon IL, Cucinotta CE, Héroux A, Jeon J, Kim J, VanDemark AP, Pugh BF, Arndt KM.

Mol Cell. 2016 Nov 17;64(4):815-825. doi: 10.1016/j.molcel.2016.10.008. Epub 2016 Nov 10.


Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.

Jeronimo C, Langelier MF, Bataille AR, Pascal JM, Pugh BF, Robert F.

Mol Cell. 2016 Nov 3;64(3):455-466. doi: 10.1016/j.molcel.2016.09.002. Epub 2016 Oct 20.


Genomic Nucleosome Organization Reconstituted with Pure Proteins.

Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P.

Cell. 2016 Oct 20;167(3):709-721.e12. doi: 10.1016/j.cell.2016.09.045.


Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly.

Aguilar-Gurrieri C, Larabi A, Vinayachandran V, Patel NA, Yen K, Reja R, Ebong IO, Schoehn G, Robinson CV, Pugh BF, Panne D.

EMBO J. 2016 Jul 1;35(13):1465-82. doi: 10.15252/embj.201694105. Epub 2016 May 25.


The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.

Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS.

Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001.


RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription.

Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, Przytycka TM, Kouzine F, Lewis BA, Zhao K, Levens D.

Cell. 2016 Apr 7;165(2):357-71. doi: 10.1016/j.cell.2016.02.036.


Genomic Organization of Human Transcription Initiation Complexes.

Pugh BF, Venters BJ.

PLoS One. 2016 Feb 11;11(2):e0149339. doi: 10.1371/journal.pone.0149339. eCollection 2016.


Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.

de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Bou Dargham D, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, Gut M, Gut I, Werner M, Deleuze JF, Olaso R, Aude JC, Chantalat S, Pugh BF, Gérard M.

Nature. 2016 Feb 4;530(7588):113-6. doi: 10.1038/nature16505. Epub 2016 Jan 27.


Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution.

Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF.

Mol Cell Biol. 2015 Oct 26;36(1):157-72. doi: 10.1128/MCB.00806-15. Print 2016 Jan 1.


Molecular mechanisms of ribosomal protein gene coregulation.

Reja R, Vinayachandran V, Ghosh S, Pugh BF.

Genes Dev. 2015 Sep 15;29(18):1942-54. doi: 10.1101/gad.268896.115.


The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.

Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A.

Cell. 2015 Aug 27;162(5):1016-28. doi: 10.1016/j.cell.2015.07.059.


Protein-DNA binding in high-resolution.

Mahony S, Pugh BF.

Crit Rev Biochem Mol Biol. 2015;50(4):269-83. doi: 10.3109/10409238.2015.1051505. Epub 2015 Jun 3. Review.


ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells.

Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chan-Salis KY, Gu Y, Chen G, Thomas C, Pugh BF, Wang Y.

Mol Cancer Ther. 2015 Apr;14(4):877-88. doi: 10.1158/1535-7163.MCT-14-1093-T. Epub 2015 Jan 22.


Subnucleosomal structures and nucleosome asymmetry across a genome.

Rhee HS, Bataille AR, Zhang L, Pugh BF.

Cell. 2014 Dec 4;159(6):1377-88. doi: 10.1016/j.cell.2014.10.054.


Retraction: Genomic organization of human transcription initiation complexes.

Venters BJ, Pugh BF.

Nature. 2014 Sep 18;513(7518):444. doi: 10.1038/nature13588. Epub 2014 Jul 23. No abstract available.


A comprehensive and high-resolution genome-wide response of p53 to stress.

Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF.

Cell Rep. 2014 Jul 24;8(2):514-27. doi: 10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17.


Genomic organization of human transcription initiation complexes.

Venters BJ, Pugh BF.

Nature. 2013 Oct 3;502(7469):53-8. doi: 10.1038/nature12535. Epub 2013 Sep 18. Retraction in: Venters BJ, Pugh BF. Nature. 2014 Sep 18;513(7518):444.


SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes.

Yen K, Vinayachandran V, Pugh BF.

Cell. 2013 Sep 12;154(6):1246-56. doi: 10.1016/j.cell.2013.08.043.


Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing.

Li J, Liu Y, Rhee HS, Ghosh SK, Bai L, Pugh BF, Gilmour DS.

Mol Cell. 2013 Jun 6;50(5):711-22. doi: 10.1016/j.molcel.2013.05.016.


A genome-wide map of CTCF multivalency redefines the CTCF code.

Nakahashi H, Kieffer Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh BF, Lobanenkov V, Hager GL, Casellas R.

Cell Rep. 2013 May 30;3(5):1678-1689. doi: 10.1016/j.celrep.2013.04.024. Epub 2013 May 23.


Molecular biology: The ends justify the means.

Pugh BF.

Nature. 2013 May 2;497(7447):48-9. doi: 10.1038/nature12098. Epub 2013 Apr 24. No abstract available.


ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy.

Rhee HS, Pugh BF.

Curr Protoc Mol Biol. 2012 Oct;Chapter 21:Unit 21.24. doi: 10.1002/0471142727.mb2124s100.


Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.

Wal M, Pugh BF.

Methods Enzymol. 2012;513:233-50. doi: 10.1016/B978-0-12-391938-0.00010-0.


Genome-wide nucleosome specificity and directionality of chromatin remodelers.

Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF.

Cell. 2012 Jun 22;149(7):1461-73. doi: 10.1016/j.cell.2012.04.036.


The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae.

Bryant JM, Govin J, Zhang L, Donahue G, Pugh BF, Berger SL.

Mol Cell Biol. 2012 Jul;32(14):2771-83. doi: 10.1128/MCB.00282-12. Epub 2012 May 14.


Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.

Lee JS, Garrett AS, Yen K, Takahashi YH, Hu D, Jackson J, Seidel C, Pugh BF, Shilatifard A.

Genes Dev. 2012 May 1;26(9):914-9. doi: 10.1101/gad.186841.112.


Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.

Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glöckner G, Schuster SC, Pugh BF.

Genome Res. 2012 Jun;22(6):1098-106. doi: 10.1101/gr.131649.111. Epub 2012 Mar 20.


Genome-wide structure and organization of eukaryotic pre-initiation complexes.

Rhee HS, Pugh BF.

Nature. 2012 Jan 18;483(7389):295-301. doi: 10.1038/nature10799. Erratum in: Nature. 2012 Jul 5;487(7405):128.


Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.

Rhee HS, Pugh BF.

Cell. 2011 Dec 9;147(6):1408-19. doi: 10.1016/j.cell.2011.11.013.


Genome-wide function of H2B ubiquitylation in promoter and genic regions.

Batta K, Zhang Z, Yen K, Goffman DB, Pugh BF.

Genes Dev. 2011 Nov 1;25(21):2254-65. doi: 10.1101/gad.177238.111.


A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling.

Sen P, Ghosh S, Pugh BF, Bartholomew B.

Nucleic Acids Res. 2011 Nov;39(21):9155-66. doi: 10.1093/nar/gkr622. Epub 2011 Aug 10.


Variety of genomic DNA patterns for nucleosome positioning.

Ioshikhes I, Hosid S, Pugh BF.

Genome Res. 2011 Nov;21(11):1863-71. doi: 10.1101/gr.116228.110. Epub 2011 Jul 12.


Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin.

Zhang Z, Pugh BF.

PLoS One. 2011;6(6):e20511. doi: 10.1371/journal.pone.0020511. Epub 2011 Jun 27.


A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.

Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF.

Science. 2011 May 20;332(6032):977-80. doi: 10.1126/science.1200508.


Stable and dynamic nucleosome states during a meiotic developmental process.

Zhang L, Ma H, Pugh BF.

Genome Res. 2011 Jun;21(6):875-84. doi: 10.1101/gr.117465.110. Epub 2011 Apr 22.


Genome-wide transcriptional dependence on conserved regions of Mot1.

Venters BJ, Irvin JD, Gramlich P, Pugh BF.

Mol Cell Biol. 2011 Jun;31(11):2253-61. doi: 10.1128/MCB.01464-10. Epub 2011 Mar 28.


A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces.

Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C, Pugh BF.

Mol Cell. 2011 Feb 18;41(4):480-92. doi: 10.1016/j.molcel.2011.01.015.


High-resolution genome-wide mapping of the primary structure of chromatin.

Zhang Z, Pugh BF.

Cell. 2011 Jan 21;144(2):175-86. doi: 10.1016/j.cell.2011.01.003.


Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae.

Ghosh S, Pugh BF.

Mol Cell Biol. 2011 Jan;31(1):190-202. doi: 10.1128/MCB.00317-10. Epub 2010 Oct 18.


A preoccupied position on nucleosomes.

Pugh BF.

Nat Struct Mol Biol. 2010 Aug;17(8):923. doi: 10.1038/nsmb0810-923. No abstract available.


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