Quantitative analysis reveals increased histone modifications and a broad nucleosome-free region bound by histone acetylases in highly expressed genes in human CD4+ T cells

Genome-wide mapping of nucleosomes and histone modifications revealed meaningful patterns. Despite advances in resolving the associations between chromatin and transcription, quantitative chromatin dynamics have not been well defined. We quantitatively determined differences in histone modifications, nucleosome positions, DNA methylation, and transcription factor binding in highly expressed and repressed genes in human CD4+ T cells. We showed that the first (− 1) nucleosome upstream of the transcription start site (TSS) is shifted to the 5′ direction, thus forming a broad nucleosome-free region (NFR) near the TSS in highly expressed genes in CD4+ T cells. Moreover, the transcription factor YY1 and histone acetyltransferases bind the NFR with high affinity. Most of histone acetylations drastically increase in transcription activation (> 5 folds). We also suggested that single nucleotide polymorphisms (SNPs) occur at a much lower frequency in highly expressed genes than in repressed genes. Our analysis quantitatively revealed details of chromatin dynamics.

► We quantitatively determined epigenetic dynamics.
► A broad nucleosome-free region (NFR) is near the TSS in highly expressed genes.
► Most of histone acetylations drastically increase in transcription activation.
► SNP occurs at a low frequency in highly expressed genes.