An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

Dong-Sung Lee; Jong-Yeon Shin; Peter D Tonge; Mira C Puri; Seungbok Lee; Hansoo Park; Won-Chul Lee; Samer M I Hussein; Thomas Bleazard; Ji-Young Yun; Jihye Kim; Mira Li; Nicole Cloonan; David Wood; Jennifer L Clancy; Rowland Mosbergen; Jae-Hyuk Yi; Kap-Seok Yang; Hyungtae Kim; Hwanseok Rhee; Christine A Wells; Thomas Preiss; Sean M Grimmond; Ian M Rogers; Andras Nagy; Jeong-Sun Seo

doi:10.1038/ncomms6619

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

Nat Commun. 2014 Dec 10:5:5619. doi: 10.1038/ncomms6619.

Authors

Dong-Sung Lee¹, Jong-Yeon Shin², Peter D Tonge³, Mira C Puri⁴, Seungbok Lee¹, Hansoo Park¹, Won-Chul Lee², Samer M I Hussein³, Thomas Bleazard⁵, Ji-Young Yun², Jihye Kim², Mira Li³, Nicole Cloonan⁶, David Wood⁷, Jennifer L Clancy⁸, Rowland Mosbergen⁹, Jae-Hyuk Yi¹⁰, Kap-Seok Yang¹¹, Hyungtae Kim¹¹, Hwanseok Rhee¹², Christine A Wells¹³, Thomas Preiss¹⁴, Sean M Grimmond¹⁵, Ian M Rogers¹⁶, Andras Nagy¹⁷, Jeong-Sun Seo¹⁸

Affiliations

¹ 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea [2] Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Korea [3] Department of Biochemistry, Seoul National University College of Medicine, Seoul 110-799, Korea.
² 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea [2] Life Science Institute, Macrogen Inc., Seoul 153-781, Korea.
³ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5.
⁴ 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5T 3H7.
⁵ Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PT, UK.
⁶ 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia [2] QIMR Berghofer Medical Research Institute, Genomic Biology Lab, 300 Herston Road, Herston, Queensland 4006, Australia.
⁷ Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
⁸ Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.
⁹ Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia.
¹⁰ Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea.
¹¹ Life Science Institute, Macrogen Inc., Seoul 153-781, Korea.
¹² Macrogen Bioinformatics Center, Macrogen, Seoul 153-781, Republic of Korea.
¹³ 1] Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia [2] College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland G12 8TA, UK.
¹⁴ 1] Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia [2] Molecular, Structural &Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia.
¹⁵ 1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia [2] Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Bearsden, Glasgow Scotland G61 1BD, UK.
¹⁶ 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2] Department of Physiology, University of Toronto, Toronto, Ontario, Canada M5T 3H7 [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada M5T3H7.
¹⁷ 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada M5T3H7 [3] Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada M5T 3H7.
¹⁸ 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea [2] Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Korea [3] Department of Biochemistry, Seoul National University College of Medicine, Seoul 110-799, Korea [4] Life Science Institute, Macrogen Inc., Seoul 153-781, Korea.

Abstract

Reprogramming of somatic cells to induced pluripotent stem cells involves a dynamic rearrangement of the epigenetic landscape. To characterize this epigenomic roadmap, we have performed MethylC-seq, ChIP-seq (H3K4/K27/K36me3) and RNA-Seq on samples taken at several time points during murine secondary reprogramming as part of Project Grandiose. We find that DNA methylation gain during reprogramming occurs gradually, while loss is achieved only at the ESC-like state. Binding sites of activated factors exhibit focal demethylation during reprogramming, while ESC-like pluripotent cells are distinguished by extension of demethylation to the wider neighbourhood. We observed that genes with CpG-rich promoters demonstrate stable low methylation and strong engagement of histone marks, whereas genes with CpG-poor promoters are safeguarded by methylation. Such DNA methylation-driven control is the key to the regulation of ESC-pluripotency genes, including Dppa4, Dppa5a and Esrrb. These results reveal the crucial role that DNA methylation plays as an epigenetic switch driving somatic cells to pluripotency.