Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Deplus, R.; Blanchon, L.; Rajavelu, A.; Boukaba, A.; Defrance, M.; Luciani, J.; Rothé, F.; Dedeurwaerder, S.; Denis, H.; Brinkman, A. B; Simmer, F.; Müller, F.; Bertin, B.; Berdasco, M.; Putmans, P.; Calonne, E.; Litchfield, D. W; Launoit, Y. d.; Jurkowski, T. P; Stunnenberg, H. G; Bock, C.; Sotiriou, C.; Fraga, M. F; Esteller, M.; Jeltsch, A.; and Fuks, F. CellReports, 8(3):743 – 753, 2014. - CK2 phosphorylates de-novo methyltransferase Dnmt3a - global DNA methylation levels increase when CK2 is knocked down - Methylation levels in non-repetitive protion of the genome highly correlated/conserved, but repeats show significant differences - KD cells hypermeth in SINEs (Alus), hypometh in LINE, LTRs and satellites compared to control - hypermeth in Alus confirmed by bisulfite sequencing - SINEs are highly rich in CpGs - could relate to altered targeting: CK2 depleted cells are less targeted to heterochromatin than control (immunofluorescence) - CK2 \textbackslashtextasciitilde Dnmt phosphorylation \textbackslashtextasciitilde reduced Dnmt activity \textbackslashtextasciitilde low global DNA methylation \textbackslashtextasciitilde heterochromatin localization - speculation: CK2 mediated phosphorylation of Dnmt singals keeps euchromatic regions open while still silencing of heterochromatin regions. When CK2 is knocked down, (Dnmts localize away from heterochromatin and) methylation spreads more into euchromatic regions (Alus)
doi  abstract   bibtex   
DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. Using mass spectrometry and a phosphospecific Dnmt3a antibody, we demonstrate that CK2 phosphorylates endogenous Dnmt3a at two key residues located near its PWWP domain, thereby downregulating the ability of Dnmt3a to methylate DNA. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs. This modulation can be directly attributed to CK2-mediated phosphorylation of Dnmt3a. We also find that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function and by uncovering a mechanism for the regulation of methylation at repetitive elements, our results shed light on the origin of DNA methylation patterns.
@article{Deplus:2014, 
title = {{Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a.}}, 
author = {Deplus, Rachel and Blanchon, Loïc and Rajavelu, Arumugam and Boukaba, Abdelhalim and Defrance, Matthieu and Luciani, Judith and Rothé, Françoise and Dedeurwaerder, Sarah and Denis, Helene and Brinkman, Arie B and Simmer, Femke and Müller, Fabian and Bertin, Benjamin and Berdasco, Maria and Putmans, Pascale and Calonne, Emilie and Litchfield, David W and Launoit, Yvan de and Jurkowski, Tomasz P and Stunnenberg, Hendrik G and Bock, Christoph and Sotiriou, Christos and Fraga, Mario F and Esteller, Manel and Jeltsch, Albert and Fuks, François}, 
journal = {CellReports}, 
doi = {10.1016/j.celrep.2014.06.048}, 
abstract = {{DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. Using mass spectrometry and a phosphospecific Dnmt3a antibody, we demonstrate that CK2 phosphorylates endogenous Dnmt3a at two key residues located near its PWWP domain, thereby downregulating the ability of Dnmt3a to methylate DNA. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs. This modulation can be directly attributed to CK2-mediated phosphorylation of Dnmt3a. We also find that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function and by uncovering a mechanism for the regulation of methylation at repetitive elements, our results shed light on the origin of DNA methylation patterns.}}, 
pages = {743 -- 753}, 
number = {3}, 
volume = {8}, 
language = {English}, 
note = {- CK2 phosphorylates de-novo methyltransferase Dnmt3a
- global DNA methylation levels increase when CK2 is knocked down
- Methylation levels in non-repetitive protion of the genome highly correlated/conserved, but repeats show significant differences
- KD cells hypermeth in SINEs (Alus), hypometh in LINE, LTRs and satellites compared to control
- hypermeth in Alus confirmed by bisulfite sequencing
- SINEs are highly rich in CpGs
- could relate to altered targeting: CK2 depleted cells are less targeted to heterochromatin than control (immunofluorescence)
- CK2 \textbackslashtextasciitilde Dnmt phosphorylation \textbackslashtextasciitilde reduced Dnmt activity \textbackslashtextasciitilde low global DNA methylation \textbackslashtextasciitilde heterochromatin localization
- speculation: CK2 mediated phosphorylation of Dnmt singals keeps euchromatic regions open while still silencing of heterochromatin regions. When CK2 is knocked down, (Dnmts localize away from heterochromatin and) methylation spreads more into euchromatic regions (Alus)}, 
local-url = {file://localhost/Users/fm/Documents/Papers%20Library/2014/CellReports/2014_Deplus_CellReports.pdf}, 
year = {2014}, 
rating = {4}
}
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