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

Abstract

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.

RETRACTED ARTICLE: REST regulates the cell cycle for cardiac development and regeneration

“…It binds a cis -element of 21 nucleotide base pairs, named RE1 motif 22 , to silence the expression of neuronal genes in the non-neuronal cells required for neurogenesis 23 , 24 . We have recently reported REST acting as a transcription repressor in mouse embryonic hearts 20 . In this study, we reveal that suppression of the cell cycle inhibitor gene p21 by REST is critically required during cardiac development and regeneration to maintain cardiomyocyte proliferation.…”

“…Several transcription factors, such as GATA4 12 , TBX20 13 , BRG1 14 , YAP 15 , 16 , ERBB2 17 , PITX2 18 , and MEIS1 19 have been shown to be essential for cardiomyocyte proliferation during development and for regeneration following neonatal heart injury. Transcriptional repressor element-1 silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF), is widely expressed in the embryonic tissues 20 , 21 . It binds a cis -element of 21 nucleotide base pairs, named RE1 motif 22 , to silence the expression of neuronal genes in the non-neuronal cells required for neurogenesis 23 , 24 .…”

Non-CpG Methylation Revised

“…Due to technical advances and, in particular, unbiased epigenetic approaches, we can now state that non-CpG methylation occurs at higher frequencies than previously expected, ranging from 25% to 35% in mice and humans, particularly in adult mammalian somatic cells including the adult mammalian brain, skeletal muscle, and hematopoietic cells [2,21,22]. In parallel to this new awareness of the non-CpG methylation frequency in differentiated tissues and adult tissues in mammals, recent results increasingly highlight its functional role [23][24][25][26][27] as well as the identity of several genes that are functionally regulated by non-CpG methylation [28][29][30][31][32].…”

SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions

“…Methylation sensitive transcription factors examined here include CREB, cMYC, USF, NFkB, E2F, MYC, and ZFX (Tate and Bird, 1993;Weng et al , 2013;Zhu et al , 2016;Stadler et al , 2011) . Methylation insensitive transcription factors examined here include SP1, REST, CEBPa, FOXA1, RXRA, and ARNT2 (Tate and Bird, 1993;Zhang et al , 2017;Stadler et al , 2011;Zhu et al , 2016;Bartke et al , 2010;Hu et al , 2013) . As expected, transcription factors previously associated with methylation sensitivity show a larger average difference in SEM scores between C and M, and G and W nucleotides compared to transcription factors previously defined as insensitive (Figure 2).…”