Combinatorial patterns of histone acetylations and methylations in the human genome

By Zhibin Wang, Chongzhi Zang, J. Rosenfeld, Dustin E. Schones, A. Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q. Zhang and 1 more. Nature Genetics, 2008

2,429 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9239150fd983c8254d5326e24fdb758fb82881a8

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In Molecular Biology

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Citations in the corpus

• ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014, methodology): “For example, we only know the sequence specificity of less than half (Matys et al. 2003; Wasserman and Sandelin 2004; Pachkov et al. 2007) of the ; 1500 (Vaquerizas et al. 2009) TFs in mammalian genomes.”
• Next-Generation Genomics: an Integrative Approach (2010, neutral): “can determine the genome-wide localization of histone modification”
• Histone modification levels are predictive for gene expression (2010, methodology): “These modifications colocalize and their levels are well correlated (17).”
• CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing (2009, methodology): “Only H3K27me3 is known to be required for Polycomb silencing and has a genome-wide distribution pattern distinct from that of H3K27me1/2 in human T cells (Wang et al., 2008).”
• A clustering approach for identification of enriched domains from histone modification ChIP-Seq data (2009, neutral): “Availability: http://home.gwu.edu/∼wpeng/Software.htm Contact: wpeng@gwu.edu Supplementary information: Supplementary data are available at Bioinformatics online.”
• seqMINER: an integrated ChIP-seq data interpretation platform (2010, background): “Finally, it becomes clear that definition of genomic regulatory elements cannot rely on a single feature, but need integration of multiple sources of information to be properly identified (16,17).”
• Epigenetics: A Molecular Link Between Environmental Factors and Type 2 Diabetes (2009, background): “However, different models have recently been proposed, including the histone code hypothesis, where multiple histone modifications act in combination to regulate transcription (15,16).”
• Chromatin organization marks exon-intron structure (2009, methodology): “To assess this, we analyzed genome-wide ChIP-seq data sets containing data on sequences bound by histones with 38 modifications in human activated T cell”
• Ensembl 2009 (2008, background): “Since the first release reported last year (14), we have updated the regulatory build three times, each time adding more data (35,36) and a more sophisticated analysis of the chromatin conformation and modification data.”
• Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. (2008, methodology): “In a recent study, we mapped the acetylation of 18 histone lysines in CD4 T cells (Wang et al. 2008).”
• Distinct roles of GCN5/PCAF‐mediated H3K9ac and CBP/p300‐mediated H3K18/27ac in nuclear receptor transactivation (2011, methodology): “This is probably because H3K27ac and H3K27me2 are mutually exclusive and H3K27ac is enriched around the TSSs while H3K27me2 is broadly distributed (Wang et al, 2008b).”