Sirt1 Regulates DNA Methylation and Differentiation Potential of Embryonic Stem Cells by Antagonizing Dnmt3l

Jinbeom Heo; Jisun Lim; Seungun Lee; Jaeho Jeong; Hyunsook Kang; YongHwan Kim; Jeong Wook Kang; Hwan Yeul Yu; Eui Man Jeong; Kyunggon Kim; Magda Kucia; Sabine J Waigel; Wolfgang Zacharias; Yinlu Chen; In-Gyu Kim; Mariusz Z Ratajczak; Dong-Myung Shin

doi:10.1016/j.celrep.2017.01.074

Sirt1 Regulates DNA Methylation and Differentiation Potential of Embryonic Stem Cells by Antagonizing Dnmt3l

Cell Rep. 2017 Feb 21;18(8):1930-1945. doi: 10.1016/j.celrep.2017.01.074.

Authors

Jinbeom Heo¹, Jisun Lim², Seungun Lee¹, Jaeho Jeong¹, Hyunsook Kang¹, YongHwan Kim¹, Jeong Wook Kang¹, Hwan Yeul Yu³, Eui Man Jeong⁴, Kyunggon Kim⁵, Magda Kucia⁶, Sabine J Waigel⁷, Wolfgang Zacharias⁷, Yinlu Chen⁷, In-Gyu Kim⁴, Mariusz Z Ratajczak⁸, Dong-Myung Shin⁹

Affiliations

¹ Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; Department of Physiology, University of Ulsan College of Medicine, Seoul 05505, Korea.
² Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; Department of Physiology, University of Ulsan College of Medicine, Seoul 05505, Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
³ Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea.
⁴ Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
⁵ Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; Clinical Proteomics Core Lab, Asan Institute for Life Sciences, Seoul 05505, Korea.
⁶ Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
⁷ Department of Medicine and Department of Pharmacology and Toxicology, Genomics Facility, University of Louisville, Louisville, KY 40202, USA.
⁸ Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Regenerative Medicine, Warsaw Medical University, Warsaw 02-091, Poland. Electronic address: mzrata01@louisville.edu.
⁹ Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; Department of Physiology, University of Ulsan College of Medicine, Seoul 05505, Korea. Electronic address: d0shin03@amc.seoul.kr.

PMID: 28228259
DOI: 10.1016/j.celrep.2017.01.074

Abstract

Embryonic stem cell (ESC) abnormalities in genome methylation hamper the utility of their therapeutic derivatives; however, the underlying mechanisms are unknown. Here, we show that the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase, Sirt1, selectively prevents abnormal DNA methylation of some developmental genes in murine ESCs by antagonizing Dnmt3l. Transcriptome and DNA methylome analyses demonstrated that Sirt1-null (Sirt1^-/-) ESCs repress expression of a subset of imprinted and germline genes concomitant with increased DNA methylation of regulatory elements. Dnmt3l was highly expressed in Sirt1^-/- ESCs, and knockdown partially rescued abnormal DNA methylation of the Sirt1 target genes. The Sirt1 protein suppressed transcription of Dnmt3l and physically interacted with the Dnmt3l protein, deacetylating and destabilizing Dnmt3l protein. Sirt1 deficiency delayed neurogenesis and spermatogenesis. These differentiation delays were significantly or partially abolished by reintroduction of Sirt1 cDNA or Dnmt3l knockdown. This study sheds light on mechanisms that restrain DNA methylation of developmentally vital genes operating in ESCs.

Keywords: DNA methylation; Dnmt3l; Sirt1; embryonic stem cell; epigenetic stability; genomic imprinting.

Publication types

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

MeSH terms

Animals
Cell Differentiation / physiology*
Cells, Cultured
DNA (Cytosine-5-)-Methyltransferases / antagonists & inhibitors*
DNA Methylation / physiology*
Embryonic Stem Cells / metabolism*
Embryonic Stem Cells / physiology*
Gene Expression Regulation / physiology
Mice
Mice, Inbred NOD
Mice, SCID
NAD / metabolism
Neurogenesis / physiology
Sirtuin 1 / metabolism*
Spermatogenesis / physiology
Transcription, Genetic / physiology

Substances

NAD
Dnmt3l protein, mouse
DNA (Cytosine-5-)-Methyltransferases
Sirt1 protein, mouse
Sirtuin 1