DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Taichi Umeyama, Takashi Ito

研究成果: Contribution to journalArticle査読

抄録

The genome exerts its functions through interactions with proteins. Hence, comprehensive identification of protein-occupied sites by genomic footprinting is critical to an in-depth understanding of genome functions. This unit describes the protocol of dimethyl sulfate-sequencing (DMS-seq). DMS is an alkylating reagent that methylates guanine and adenine in double-stranded DNA. DMS added to the culture medium readily enters the cell and methylates its DNA throughout the genome except for the regions bound by proteins, thereby obviating the need for nuclear isolation in genomic footprinting. Polyamine/AP-endonuclease treatment of DNA isolated from DMS-treated cells induces cleavages at the methylated sites. Deep sequencing of these fragments identifies protein-bound sites as peaks of protected fragments or troughs of cleavage sites. Furthermore, DMS displays an unexpected preference to nucleosome centers, enabling their direct detection without genetic manipulation. Therefore, DMS-seq provides a unique method for non-targeted profiling of in vivo protein-DNA interactions.

本文言語英語
論文番号e60
ジャーナルCurrent Protocols in Molecular Biology
123
1
DOI
出版ステータス出版済み - 7 2018

All Science Journal Classification (ASJC) codes

  • 分子生物学

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