Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

Abstract

DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a high-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences. We provide evidence that Lsh also controls genome-wide cytosine methylation at nonrepeat sequences and relate those changes to alterations in H4K4me3 modification and gene expression. Deletion of Lsh alters the allocation of cytosine methylation in chromosomal regions of 50 kb to 2 Mb and, in addition, leads to changes in the methylation profile at the 5′ end of genes. Furthermore, we demonstrate that loss of Lsh promotes—as well as prevents—cytosine methylation. Our data indicate that Lsh is an epigenetic modulator that is critical for normal distribution of cytosine methylation throughout the murine genome.

Cigarette smoke mediates epigenetic repression of miR-487b during pulmonary carcinogenesis

“…Genomic DNA was sonicated to produce fragments ranging in size from 300 to 1000 bp. Five micrograms of fragmented DNA was used for a standard MeDIP assay (29,67) and precipitated with 10 μl monoclonal antibody against 5-methylcytidine (Eurogentec) followed by incubation with protein A agarose beads. DNA was recovered by phenolchloroform extraction followed by ethanol precipitation.…”

SNF2 family ATPase LSH promotes phosphorylation of H2AX and efficient repair of DNA double-strand breaks in mammalian cells

“…In the Lsh 2/2 MEFs, the global levels of DNA methylation are reduced by ,50%, affecting many gene promoters and large chromosomal domains (Myant et al, 2011;Tao et al, 2011). Potentially, DNA hypomethylation may compromise the efficiency of DSBs repair either directly, by altering chromatin structure, or indirectly, by changing the expression of DNA repair genes.…”

“…Knockout of Lsh (Hells) gene in mice leads to postnatal lethality and 50-70% reduction in the global levels of DNA methylation, including repetitive sequences and large chromosomal domains throughout the genome (Dennis et al, 2001;Myant et al, 2011;Tao et al, 2011). In addition, Lsh 2/2 embryos exhibit defects in male and female meiosis, which are manifested by incomplete chromosome synapses and failure to load crossover-associated foci (De La Fuente et al, 2006;Zeng et al, 2011).…”

HELLS (Helicase, Lymphoid-Specific)

“…Knockout mice die perinatally with defects in lymphocyte proliferation, embryonic growth, and kidney development (Geiman et al, 2001;Geiman and Muegge, 2000). Loss leads to global DNA methylation changes including global hypomethylation at repetive sequences, as well as both hypo and hypermethylation of single copy genes (Myant et al, 2011;Tao et al, 2011b;Dunican et al, 2013;Yu et al, 2014). HELLS has been identified as a marker of mammalian stem cells with expression decreasing upon differentiation.…”

“…In addition, activation of lymphocytes leads to apoptosis intead of cell proliferation (Geiman et al, 2000). Molecular studies on this mouse led to identifying HELLS as a gene necessary for DNA methylation and important for correct chromatin packaging and histone methylation (Dennis et al, 2001;Yan et al, 2003b ;Huang et al, 2004;Myant et al, 2011;Tao et al, 2011b;Yu et al, 2014).…”