Repetitive DNA methylome analysis by small-scale and single-cell shotgun bisulfite sequencing

Hisato Kobayashi*, Tasuku Koike, Akihiko Sakashita, Keisuke Tanaka, Soichiro Kumamoto, Tomohiro Kono

*この研究の対応する著者

研究成果: Article査読

7 被引用数 (Scopus)

抄録

Whole-genome shotgun bisulfite sequencing (WG-SBS) is currently the most powerful tool available for understanding genomewide cytosine methylation with single-base resolution; however, the high sequencing cost limits its widespread application, particularly for mammalian genomes. We mapped high- to low-coverage SBS short reads of mouse and human female developing germ cells to consensus sequences of repetitive elements that were multiplied in the respective host genome. This mapping strategy effectively identified active and evolutionarily young retrotransposon subfamilies and centromeric satellite repeats that were resistant to DNA demethylation during the investigated progressive stages of germ cell development. Notably, quantities of only tens of thousands of uniquely mapped reads provided sufficient sensitivity to allow for methylation analyses of multiple retrotransposons and satellite repeats in mice. Furthermore, we produced SBS results from single female murine germ cells by an improved multiplexing and amplification-free SBS method (scPBAT). The scPBAT results quantitatively provided ≥5× sequencing coverage for at least 30 repeats, and the individual methylation patterns detected were similar to the bulk cell-based results. Our single-cell methylome sequencing technique will allow researchers to investigate intergenic methylation characteristics from limited amounts of mammalian cells as well as cells from other organisms with genomic annotations.

本文言語English
ページ(範囲)1209-1222
ページ数14
ジャーナルGenes to Cells
21
11
DOI
出版ステータスPublished - 2016 11月 1
外部発表はい

ASJC Scopus subject areas

  • 遺伝学
  • 細胞生物学

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