We have previously shown that Lsh can influence the methylation pattern at retroviral sequences and endogenous genes, but the precise role of Lsh in the establishment of DNA methylation at a given site remained unclear. In particular it is not known whether Lsh, a member of the SNF2 family of chromatin remodeling proteins, can alter chromatin structure and how this can modulate DNA methylation. In order to study the molecular function of Lsh on chromatin, we established an in vitro ES cell based system. DNA methylation levels vary during development and are lowest in the inner cell mass of blastocysts before implantation. After implantation, a wave of de novo DNA methylation occurs and is associated with tissue differentiation. ES cells that differentiate in vitro show a similar wave of de novo methylation and can serve as suitable model to study the molecular function of Lsh in this process. We generated Lsh-/- ES cells and found that de novo methylation at several repeat sequences was incomplete in the absence of Lsh and fully restored when Lsh was re-introduced into Lsh-/- ES cells. This indicated that Lsh plays a critical in the establishment of DNA methylation during cellular differentiation. Furthermore, we found that Lsh is directly associated with those repeat sequences that are undergoing de novo methylation and that the presence of Lsh is required for association of the major DNA methyltransferase 3b to these loci. When we tested functional domains of Lsh, we discovered that the ATP binding site of Lsh is required for complete methylation and Dnmt3b association to these repeat target sequences. The ATP binding site is essential for ATP hydrolysis and chromatin remodeling function of SNF2 factors. Thus our results indicate that chromatin remodeling function of Lsh is required for effective DNA methylation. In order to assess chromatin structure we applied the nucleosomal occupancy assay. We detected lower nucleosomal density in Lsh-/- cells at repeat sequences compared to wild type controls. Nucleosomal density was restored to wild type levels upon re-introduction of Lsh into Lsh-/- cells. This indicated that nucleosomal occupancy at repeat sequences depends on the presence of Lsh. Finally, we could demonstrate that nucleosomal density depends on ATP function of Lsh indicating that Lsh performs chromatin remodeling at those repeat loci. Our results suggest that the primary molecular function of Lsh is chromatin remodeling via altering nucleosomal density at loci that are undergoing de novo methylation. Altered nucleosomal occupancy in turn modulates association of Dnmt3b with target sequences and hence supports de novo methylation. Our results connect two major epigenetic features, chromatin remodeling and DNA methylation, and provide mechanistic insights into the interplay of epigenetic pathways.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIABC010014-20
Application #
9153523
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
20
Fiscal Year
2015
Total Cost
Indirect Cost
Name
Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
Ren, Jianke; Hathaway, Nathaniel A; Crabtree, Gerald R et al. (2018) Tethering of Lsh at the Oct4 locus promotes gene repression associated with epigenetic changes. Epigenetics 13:173-181
Han, Yixing; Ren, Jianke; Lee, Eunice et al. (2017) Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells. Sci Rep 7:1136
He, Xiaozhen; Yan, Bin; Liu, Shuang et al. (2016) Chromatin Remodeling Factor LSH Drives Cancer Progression by Suppressing the Activity of Fumarate Hydratase. Cancer Res 76:5743-5755
Han, Yixing; Gao, Shouguo; Muegge, Kathrin et al. (2015) Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights 9:29-46
Jiang, Y; Yan, B; Lai, W et al. (2015) Repression of Hox genes by LMP1 in nasopharyngeal carcinoma and modulation of glycolytic pathway genes by HoxC8. Oncogene 34:6079-91
Ren, Jianke; Briones, Victorino; Barbour, Samantha et al. (2015) The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences. Nucleic Acids Res 43:1444-55
Terashima, Minoru; Barbour, Samantha; Ren, Jianke et al. (2015) Effect of high fat diet on paternal sperm histone distribution and male offspring liver gene expression. Epigenetics 10:861-71
Lungu, Cristiana; Muegge, Kathrin; Jeltsch, Albert et al. (2015) An ATPase-deficient variant of the SNF2 family member HELLS shows altered dynamics at pericentromeric heterochromatin. J Mol Biol 427:1903-15
Yu, Weishi; McIntosh, Carl; Lister, Ryan et al. (2014) Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Res 24:1613-23
Yu, Weishi; Briones, Victorino; Lister, Ryan et al. (2014) CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. Proc Natl Acad Sci U S A 111:5890-5

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