Precise Mnase-Sequencing of Mouse Cells Reveals Distinct Nucleosome Organization at Active Promoters

Authors

• TA Johnson
• RV Chereji
• DA Stavreva
• MJ Guertin
• GL Hager
• DJ Clark

Abstract

Nucleosome organization is a primary characteristic of chromatin and may be important for controlling transcription. We precisely mapped nucleosomes in mouse cells by paired-end sequencing of Mnase digested nuclei. Comparing previously published data for Dnase-Seq and ChIP-Seq, we show that genes with promoter Dnase I hypersensitive sites (DHS) and RNA polymerase II (RNAP) peaks have distinct nucleosome organization around the transcription start site. These phased nucleosomes also contain the histone variant H2AZ. Gene promoters lacking DHS and RNAP show no obvious nucleosomal organization. The data show that DHS do not consistently correlate with areas void of nucleosomes. Also, many areas of the genome with very low nucleosome occupancy show no accessibility to Dnase I. Mnase acts as a general cutter of chromatin whereas Dnase I recognizes characteristics of “accessible chromatin” and cuts there more often. The data suggest that Dnase I recognizes more than a simple lack of nucleosomes but also one or more epigenetic marks common to the regulatory parts of the genome. We detect local chromatin remodeling events after glucocorticoid treatment by observing changes in nucleosome occupancy at glucocorticoid receptor (GR) binding sites. GR binding sites occur more often within the core particle DNA of nucleosomes and exhibit a loss of the nucleosome occupancy upon hormone treatment. Our findings suggest many models of nucleosome organization and chromatin structure need revision. Transcription factors controlling gene expression regularly, even preferably, access nucleosome-occupied DNA and do not simply interact on the “naked” genomic DNA.

Scientific Focus Area: Genetics and Genomics

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