@article{0118eee946444b8b8d7f1c90dc5eef40,
title = "Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation",
abstract = "Genome-wide de novo DNA methylation occurs in mouse gonocytes, arrested male embryonic germ cells. However, how the methylome gets established in the genome of arrested cells remains unexplored. Yamanaka et al. report that multiple chromatin reprogramming pathways allow the access of methyltransferases to DNA in gonocytes.",
keywords = "ATAC-seq, de novo DNA methylation, gene cluster, gene desert, gonocyte, transposon",
author = "Soichiro Yamanaka and Hidenori Nishihara and Hidehiro Toh and {Eijy Nagai}, {Luis Augusto} and Kosuke Hashimoto and Park, {Sung Joon} and Aoi Shibuya and Suzuki, {Ana Maria} and Yujiro Tanaka and Kenta Nakai and Piero Carninci and Hiroyuki Sasaki and Haruhiko Siomi",
note = "Funding Information: We thank all members of the Siomi laboratory, especially Drs. Yuka Iwasaki and Hirotsugu Ishizu, for discussions and comments on this work. We also thank Drs. Kei-ichiro Ishiguro ( Kumamoto University ), Yoshiyuki Seki ( Kwansei Gakuin University ), and Satoshi Namekawa ( Cincinnati Children{\textquoteright}s Hospital Medical Center ) for critical reading of the manuscript. We are also grateful to Dr. Kuniya Abe ( RIKEN ) for shearing the Ddx4-Venus TG mouse. Finally, we thank Edanz ( www.edanzediting.co.jp ) for editing the English text of a draft of this manuscript. This work was partly performed in the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University . We are grateful to the Collaborative Research Resources, School of Medicine, Keio University for technical support and reagents. Computations were partially performed on the supercomputer system of SIROKANE at the Human Genome Center, The Institute of Medical Sciences, University of Tokyo , and that of the Institute of Statistical Mathematics. S.Y. is supported by Takeda Science Foundation and Keio Gijuku Academic Development Funds. This work was supported by Grants-in-Aid for Scientific Research on Innovative Areas ( 25112010 to H. Sasaki, 16H01403 to K.N., 18H04710 to S.P., and 26112513 and 16H01411 to S.Y.) from the Japan Society for the Promotion of Science (JSPS). A Grant-in-Aid for Challenging Exploratory Research ( 17K19424 ) to H.N. and a Grant-in-Aid for Young Scientists (A) ( 26710011 ) to S.Y. from JSPS also supported the present work. K.H. is supported by a research grant from MEXT to the RIKEN Center for Integrative Medical Sciences. H. Siomi was supported by a Grant-in-Aid for Scientific Research (S) ( 25221003 ) from JSPS and is a recipient of funding for the Project for Elucidating and Controlling Mechanisms of Aging and Longevity ( 1005442 ) from the Japan Agency for Medical Research and Development (AMED). Funding Information: We thank all members of the Siomi laboratory, especially Drs. Yuka Iwasaki and Hirotsugu Ishizu, for discussions and comments on this work. We also thank Drs. Kei-ichiro Ishiguro (Kumamoto University), Yoshiyuki Seki (Kwansei Gakuin University), and Satoshi Namekawa (Cincinnati Children's Hospital Medical Center) for critical reading of the manuscript. We are also grateful to Dr. Kuniya Abe (RIKEN) for shearing the Ddx4-Venus TG mouse. Finally, we thank Edanz (www.edanzediting.co.jp) for editing the English text of a draft of this manuscript. This work was partly performed in the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University. We are grateful to the Collaborative Research Resources, School of Medicine, Keio University for technical support and reagents. Computations were partially performed on the supercomputer system of SIROKANE at the Human Genome Center, The Institute of Medical Sciences, University of Tokyo, and that of the Institute of Statistical Mathematics. S.Y. is supported by Takeda Science Foundation and Keio Gijuku Academic Development Funds. This work was supported by Grants-in-Aid for Scientific Research on Innovative Areas (25112010 to H. Sasaki, 16H01403 to K.N. 18H04710 to S.P. and 26112513 and 16H01411 to S.Y.) from the Japan Society for the Promotion of Science (JSPS). A Grant-in-Aid for Challenging Exploratory Research (17K19424) to H.N. and a Grant-in-Aid for Young Scientists (A) (26710011) to S.Y. from JSPS also supported the present work. K.H. is supported by a research grant from MEXT to the RIKEN Center for Integrative Medical Sciences. H. Siomi was supported by a Grant-in-Aid for Scientific Research (S) (25221003) from JSPS and is a recipient of funding for the Project for Elucidating and Controlling Mechanisms of Aging and Longevity (1005442) from the Japan Agency for Medical Research and Development (AMED). S.Y. and H. Siomi conceived of the project and designed the experiments. S.Y. H.N. H.T. K.H. L.A.E.N. and S.-J.P. performed the computational analysis. H.N. analyzed the detailed transposon profiles for ATAC-seq and ChIP-seq. A.S. A.M.S. and Y.T. helped with the DNA library preparation for ATAC-seq, nanoCAGE-seq, and ChIP-seq, respectively. K.N. helped the Hi-C data analysis. P.C. helped the acquisition and the analysis of nanoCAGE-seq data. H. Sasaki helped the analysis of DNA methylation profiles and revised the paper. S.Y. and H. Siomi wrote the paper with the inputs from all authors. All authors commented on and agreed with the contents of this paper. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",
year = "2019",
month = oct,
day = "7",
doi = "10.1016/j.devcel.2019.07.023",
language = "English",
volume = "51",
pages = "21--34.e5",
journal = "Developmental Cell",
issn = "1534-5807",
publisher = "Cell Press",
number = "1",
}