Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.
The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.|Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Joseph S
JS
Harrison
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, United States.
Evan M
EM
Cornett
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Dennis
D
Goldfarb
Department of Biochemistry, University of Washington, Seattle, United States.
Paul A
PA
DaRosa
Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Zimeng M
ZM
Li
Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Feng
F
Yan
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, United States.
Bradley M
BM
Dickson
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Angela H
AH
Guo
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Daniel V
DV
Cantu
Structural Genomics Consortium, University of Toronto, Toronto, Canada.
Lilia
L
Kaustov
Structural Genomics Consortium, University of Toronto, Toronto, Canada.
Peter J
PJ
Brown
Structural Genomics Consortium, University of Toronto, Toronto, Canada.
Cheryl H
CH
Arrowsmith
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Dorothy A
DA
Erie
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, United States.|Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Michael B
MB
Major
Department of Biochemistry, University of Washington, Seattle, United States.
Rachel E
RE
Klevit
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Krzysztof
0000-0001-7159-617X
K
Krajewski
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.|Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Brian
B
Kuhlman
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States.|Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.
Brian D
BD
Strahl
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, United States.
Scott B
0000-0003-1631-5392
SB
Rothbart
D022762:CCAAT-Enhancer-Binding Proteins / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism*; D006801:Humans; D011485:Protein Binding; D044767:Ubiquitin-Protein Ligases; D054875:Ubiquitination; D014918:Wills
D022762:CCAAT-Enhancer-Binding Proteins; D006657:Histones; D004247:DNA; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; C000619380:DNMT1 protein, human; C406364:UHRF1 protein, human; D044767:Ubiquitin-Protein Ligases
DNA methylation; UHRF1; biochemistry; biophysics; epigenetics; histone post-translational modifications; human; structural biology; ubiquitin; ubiquitylation