Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1
Joseph S Harrison,
Evan M Cornett,
Dennis Goldfarb,
Paul A DaRosa,
Zimeng M Li,
Feng Yan,
Bradley M Dickson,
Angela H Guo,
Daniel V Cantu,
Lilia Kaustov,
Peter J Brown,
Cheryl H Arrowsmith,
Dorothy A Erie,
Michael B Major,
Rachel E Klevit,
Krzysztof Krajewski,
Brian Kuhlman,
Brian D Strahl,
Scott B Rothbart
Affiliations
Joseph S Harrison
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
Evan M Cornett
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, United States
Dennis Goldfarb
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, United States
Paul A DaRosa
Department of Biochemistry, University of Washington, Seattle, United States
Zimeng M Li
Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, United States
Feng Yan
Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
Bradley M Dickson
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, United States
Angela H Guo
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States
Daniel V Cantu
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States
Lilia Kaustov
Structural Genomics Consortium, University of Toronto, Toronto, Canada
Peter J Brown
Structural Genomics Consortium, University of Toronto, Toronto, Canada
Cheryl H Arrowsmith
Structural Genomics Consortium, University of Toronto, Toronto, Canada
Dorothy A Erie
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
Michael B Major
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
Rachel E Klevit
Department of Biochemistry, University of Washington, Seattle, United States
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States
Brian 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 Strahl
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
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.
