The SNF2 family ATPase LSH promotes cell-autonomous de novo DNA methylation in somatic cells.

Ausma Termanis,Irina Stancheva,Natalia Torrea,Bernard Ramsahoye,Alastair Kerr,Jayne Culley

doi:10.1093/nar/gkw424

Abstract

Methylation of DNA at carbon 5 of cytosine is essential for mammalian development and implicated in transcriptional repression of genes and transposons. New patterns of DNA methylation characteristic of lineage-committed cells are established at the exit from pluripotency by de novo DNA methyltransferases enzymes, DNMT3A and DNMT3B, which are regulated by developmental signaling and require access to chromatin-organized DNA. Whether or not the capacity for de novo DNA methylation of developmentally regulated loci is preserved in differentiated somatic cells and can occur in the absence of exogenous signals is currently unknown. Here, we demonstrate that fibroblasts derived from chromatin remodeling ATPase LSH (HELLS)-null mouse embryos, which lack DNA methylation from centromeric repeats, transposons and a number of gene promoters, are capable of reestablishing DNA methylation and silencing of misregulated genes upon re-expression of LSH. We also show that the ability of LSH to bind ATP and the cellular concentration of DNMT3B are critical for cell-autonomous de novo DNA methylation in somatic cells. These data suggest the existence of cellular memory that persists in differentiated cells through many cell generations and changes in transcriptional state.

Highlights

Methylation of DNA at the fifth carbon of cytosine (5mC) is an abundant epigenetic modification in vertebrate genomes (1)
To investigate if the reduced levels of 5mC and the misexpression of normally silenced loci are reversible in the Lsh−/− mouse embryonic fibroblasts (MEFs) and if such reversal requires the catalytic activity of LSH, we introduced by lentiviral transduction a triple FLAG (3xFLAG)tagged full length LSH, either wild-type or ATP bindingdeficient mutant (25), carrying lysine 237 mutated to glutamine (K237Q), into the Lsh−/− MEFs
We asked in this study whether or not de novo DNA methylation can occur in somatic cells in the absence of exogenous signals

Summary

Introduction

Methylation of DNA at the fifth carbon of cytosine (5mC) is an abundant epigenetic modification in vertebrate genomes (1). DNA methylation is established during development and contributes to regulation of genomic imprinting, tissue-specific gene expression, silencing of retrotransposons and X chromosome inactivation in females (2,3). The deposition of new methyl groups to cytosine occurs by the action of two homologous enzymes, the de novo DNA methyltransferases DNMT3A and DNMT3B, while the propagation of 5mC through DNA replication requires the activity of maintenance DNA methyltransferase DNMT1 (4). DNMTs are critical in early mammalian development when, following a nearly global erasure of 5mC during the cleavage stages of pre-implantation embryo, new patterns of 5mC are established post-implantation in the developing epiblast (E6.5) (3,5,6). Several studies have identified DNMT3B as the main enzyme responsible for de novo DNA methylation during development (6,8–10). In Dnmt3b−/− embryos, the centromeric repeats, promoters of germ cell-specific genes and genes on the inactive X chromosome in female embryos remain hypomethylated

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