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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. Wang Z, et al. Among authors: barski a. Nat Genet. 2008 Jul;40(7):897-903. doi: 10.1038/ng.154. Epub 2008 Jun 15. Nat Genet. 2008. PMID: 18552846 Free PMC article.
Our data indicate that a large number of patterns are associated with promoters and enhancers. In particular, we identify a common modification module consisting of 17 modifications detected at 3,286 promoters. ...
Our data indicate that a large number of patterns are associated with promoters and enhancers. In particular, we identify a co …
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. Barski A, et al. Cell. 2007 May 18;129(4):823-37. doi: 10.1016/j.cell.2007.05.009. Cell. 2007. PMID: 17512414
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. Schones DE, et al. Among authors: barski a. Cell. 2008 Mar 7;132(5):887-98. doi: 10.1016/j.cell.2008.02.022. Cell. 2008. PMID: 18329373
Furthermore, the first nucleosome downstream of a start site exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. ...Our data pr …
Furthermore, the first nucleosome downstream of a start site exhibits differential positioning in active and silent genes. TCR signal …
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Jothi R, et al. Among authors: barski a. Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6. Nucleic Acids Res. 2008. PMID: 18684996 Free PMC article.
Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. ...Using tag density as an indicator of DNA-binding affinity, we have identified cor …
Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding site …
Genomic location analysis by ChIP-Seq.
Barski A, Zhao K. Barski A, et al. J Cell Biochem. 2009 May 1;107(1):11-8. doi: 10.1002/jcb.22077. J Cell Biochem. 2009. PMID: 19173299 Free PMC article. Review.
The interaction of a multitude of transcription factors and other chromatin proteins with the genome can influence gene expression and subsequently cell differentiation and function. ...Now protein binding can be mapped in a truly genome-wide manner with extremely h …
The interaction of a multitude of transcription factors and other chromatin proteins with the genome can influence gene expression an …
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.
Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Wang Z, et al. Among authors: barski a. Cell. 2009 Sep 4;138(5):1019-31. doi: 10.1016/j.cell.2009.06.049. Epub 2009 Aug 20. Cell. 2009. PMID: 19698979 Free PMC article.
As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. ...Inactive genes that are primed by MLL-mediated histone H3K4 methylation are subject to a dynamic cycle of acetylation and deacetylation …
As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. ...In …
Chromatin poises miRNA- and protein-coding genes for expression.
Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Barski A, et al. Genome Res. 2009 Oct;19(10):1742-51. doi: 10.1101/gr.090951.109. Epub 2009 Aug 27. Genome Res. 2009. PMID: 19713549 Free PMC article.
Active chromatin modifications were already in place for a majority of inducible protein-coding genes, even while the genes were silent in resting cells. ...
Active chromatin modifications were already in place for a majority of inducible protein-coding genes, even while the genes were sile …
Epigenomics of T cell activation, differentiation, and memory.
Cuddapah S, Barski A, Zhao K. Cuddapah S, et al. Among authors: barski a. Curr Opin Immunol. 2010 Jun;22(3):341-7. doi: 10.1016/j.coi.2010.02.007. Epub 2010 Mar 11. Curr Opin Immunol. 2010. PMID: 20226645 Free PMC article. Review.
In this review we discuss recent data suggesting that naïve T cell activation, differentiation, and lineage commitment result in epigenetic changes and a fine balance between different histone modifications is required. ...
In this review we discuss recent data suggesting that naïve T cell activation, differentiation, and lineage commitment result in epigenetic …
Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes.
Barski A, Chepelev I, Liko D, Cuddapah S, Fleming AB, Birch J, Cui K, White RJ, Zhao K. Barski A, et al. Nat Struct Mol Biol. 2010 May;17(5):629-34. doi: 10.1038/nsmb.1806. Epub 2010 Apr 25. Nat Struct Mol Biol. 2010. PMID: 20418881 Free PMC article.
Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions.
Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K. Cuddapah S, et al. Among authors: barski a. Mol Cell Biol. 2011 Feb;31(4):700-9. doi: 10.1128/MCB.00740-10. Epub 2010 Dec 20. Mol Cell Biol. 2011. PMID: 21173166 Free PMC article.
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