DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells

Daiki Tatsumi; Yohei Hayashi; Mai Endo; Hisato Kobayashi; Takumi Yoshioka; Kohei Kiso; Shinichiro Kanno; Yuji Nakai; Ikuma Maeda; Kentaro Mochizuki; Makoto Tachibana; Haruhiko Koseki; Akihiko Okuda; Akira Yasui; Tomohiro Kono; Yasuhisa Matsui

doi:10.1371/journal.pone.0205969

DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells

PLoS One. 2018 Nov 7;13(11):e0205969. doi: 10.1371/journal.pone.0205969. eCollection 2018.

Authors

Daiki Tatsumi^{1

2}, Yohei Hayashi^{1

2

3}, Mai Endo^{1

2}, Hisato Kobayashi⁴, Takumi Yoshioka⁵, Kohei Kiso^{1

6}, Shinichiro Kanno⁷, Yuji Nakai⁸, Ikuma Maeda¹, Kentaro Mochizuki^{1

2

9}, Makoto Tachibana¹⁰, Haruhiko Koseki^{11

12}, Akihiko Okuda¹³, Akira Yasui⁷, Tomohiro Kono⁵, Yasuhisa Matsui^{1

2

3

14}

Affiliations

¹ Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan.
² Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
³ The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chuo-ku, Tokyo, Japan.
⁴ NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.
⁵ Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.
⁶ Tohoku University School of Medicine, Sendai, Miyagi, Japan.
⁷ Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan.
⁸ Institute for Food Sciences, Hirosaki University, Hirosaki, Aomori, Japan.
⁹ Center for Environmental Conservation and Research Safety, Tohoku University, Sendai, Miyagi, Japan.
¹⁰ Department of Enzyme Chemistry, Institute for Enzyme Research, Tokushima University, Shinkura-cho, Tokushima, Japan.
¹¹ Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
¹² Core Research for Evolutional Science and Technology, Yokohama, Kanagawa, Japan.
¹³ Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan.
¹⁴ Center for Regulatory Epigenome and Diseases, Tohoku University School of Medicine, Sendai, Miyagi, Japan.

Abstract

In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell-related genes, is globally repressed. The transcription factor MAX represses germ cell-related gene expression in ESCs via PCGF6-polycomb repressive complex 1 (PRC1), which consists of several epigenetic factors. However, we predicted that MAX represses germ cell-related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell-related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell-related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell-related genes in ESCs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / metabolism*
Biomarkers / metabolism
Chemical Fractionation
Co-Repressor Proteins / metabolism*
DNA (Cytosine-5-)-Methyltransferases / metabolism*
DNA Methylation / genetics
Gene Expression Regulation*
Germ Cells / metabolism*
Histone-Lysine N-Methyltransferase / metabolism*
Histones / metabolism
Lysine / metabolism
Methylation
Mice
Mice, Knockout
Mouse Embryonic Stem Cells / metabolism*
Multiprotein Complexes / metabolism
Polycomb Repressive Complex 1 / metabolism
Protein Binding

Substances

Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
Biomarkers
Co-Repressor Proteins
Histones
Multiprotein Complexes
Pcgf6 protein, mouse
Max protein, mouse
DNA (Cytosine-5-)-Methyltransferases
Histone-Lysine N-Methyltransferase
SETDB1 protein, mouse
Polycomb Repressive Complex 1
Lysine

Grants and funding

This work was supported by a Grant-in-Aid (KAKENHI)(http://www.mext.go.jp/en/policy/science_technology/researchpromotion/title01/detail01/1374077.htm) in the Innovative Areas, “Sex spectrum” (grant #18H04875) to YH, KAKENHI in the Innovative Areas, “Mechanisms regulating gamete formation in animals” (grant #25114003) to YM from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and by AMED-CREST grant #17gm0510017h0005 to YM from the Japan Agency for Medical Research and Development (https://www.amed.go.jp/en/index.html). IM is employed by and received salary from HaploPharma Inc., Chuo-ku, Tokyo, Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.