Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts.

Nucleic Acids Res.2017 Apr 07;45(6):3102-3115

Donghong Zhang ¹ , Bingruo Wu ¹ , Ping Wang ² , Yidong Wang ¹ , Pengfei Lu ¹ ,

Donghong Zhang ¹ , Bingruo Wu ¹ , Ping Wang ² , Yidong Wang ¹ , Pengfei Lu ¹ , Tamilla Nechiporuk ³ , Thomas Floss ⁴ , John M Greally ⁵ , Deyou Zheng ⁶ , Bin Zhou ⁷

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Author information

¹ Departments of Genetics, Pediatrics, and Medicine (Cardiology), Wilf Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
² Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
³ Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA.
⁴ German Research Center for Environmental Health, Neuherberg, Germany.
⁵ Departments of Genetics, Medicine (Hematology), and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
⁶ Departments of Genetics, Neurology, and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
⁷ Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

摘要

The dynamic interaction of DNA methylation and transcription factor binding in regulating spatiotemporal gene expression is essential for embryogenesis, but the underlying mechanisms remain understudied. In this study, using mouse models and integration of in vitro and in vivo genetic and epigenetic analyses, we show that the binding of REST (repressor element 1 (RE1) silencing transcription factor; also known as NRSF) to its cognate RE1 sequences is temporally regulated by non-CpG methylation. This process is dependent on DNA methyltransferase 3B (DNMT3B) and leads to suppression of adult cardiac genes in developing hearts. We demonstrate that DNMT3B preferentially mediates non-CpG methylation of REST-targeted genes in the developing heart. Downregulation of DNMT3B results in decreased non-CpG methylation of RE1 sequences, reduced REST occupancy, and consequently release of the transcription suppression during later cardiac development. Together, these findings reveal a critical gene silencing mechanism in developing mammalian hearts that is regulated by the dynamic interaction of DNMT3B-mediated non-CpG methylation and REST binding.

原始数据

保存测序数据

Sample name	Organism	Experiment title	Sample type	Library instrument	Attributes
Sample name	Organism	Experiment title	Sample type	Library instrument	age	genotype	source name	strain background	tissue
REST KO-3	Mus musculus	GSM2125447: REST KO-3; Mus musculus; RNA-Seq	RNA-Seq	Illumina HiSeq 2500	Embryonic 12.5 day	Rest gene knockout at cardiomyocyte by Troponin-T Cre	REST KO_E12.5_venticular	C57BL/6	heart; venticular
REST KO-2	Mus musculus	GSM2125446: REST KO-2; Mus musculus; RNA-Seq	RNA-Seq	Illumina HiSeq 2500	Embryonic 12.5 day	Rest gene knockout at cardiomyocyte by Troponin-T Cre	REST KO_E12.5_venticular	C57BL/6	heart; venticular
REST KO-1	Mus musculus	GSM2125445: REST KO-1; Mus musculus; RNA-Seq	RNA-Seq	Illumina HiSeq 2500	Embryonic 12.5 day	Rest gene knockout at cardiomyocyte by Troponin-T Cre	REST KO_E12.5_venticular	C57BL/6	heart; venticular
WT-3	Mus musculus	GSM2125444: WT-3; Mus musculus; RNA-Seq	RNA-Seq	Illumina HiSeq 2500	Embryonic 12.5 day	wild type	WT_E12.5_venticular	C57BL/6	heart; venticular
WT-2	Mus musculus	GSM2125443: WT-2; Mus musculus; RNA-Seq	RNA-Seq	Illumina HiSeq 2500	Embryonic 12.5 day	wild type	WT_E12.5_venticular	C57BL/6	heart; venticular