Identification of Genetic Variants That Affect Histone Modifications in Human Cells

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Science  17 Oct 2013:
DOI: 10.1126/science.1242429

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Histone modifications are important markers of function and chromatin state, yet the DNA sequence elements that direct them to specific genomic locations are poorly understood. Here, we identify hundreds of quantitative trait loci, genome-wide, that impact histone modification or RNA polymerase (PolII) occupancy in Yoruba lymphoblastoid cell lines (LCLs). In many cases the same variant is associated with quantitative changes in multiple histone marks and PolII, as well as in DNaseI sensitivity and nucleosome positioning. Transcription factor binding site polymorphisms are correlated overall with differences in local histone modification, and we identify specific transcription factors whose binding leads to histone modification in LCLs. Furthermore, variants that impact chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters.

  • * These authors contributed equally to this work.

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