DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Taichi Umeyama, Takashi Ito

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Umeyama and Ito develop DMS-seq for nuclear isolation-free genomic footprinting by exploiting the cell-permeable nature of dimethyl sulfate (DMS). DMS-seq detects trans-acting factors bound to cis-regulatory elements, as well as non-canonical chromatin particles in nucleosome-free regions. It also has the unique potential to directly locate nucleosome centers.

Original languageEnglish
Pages (from-to)289-300
Number of pages12
JournalCell Reports
Volume21
Issue number1
DOIs
Publication statusPublished - Oct 3 2017

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

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