Journal
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
Volume 170, Issue -, Pages 514-522Publisher
ELSEVIER
DOI: 10.1016/j.ijbiomac.2020.12.149
Keywords
Metadynamics; Non-CpG DNA methylation; UHRF1
Funding
- Department of Biotechnology (DBT)
- Science and Engineering Research Board, Department of Science and Technology, Government of India
- Ministry of Human Resource Development, Government of India
- University Grants Commission, Government of India
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UHRF1 SRA can recognize non-mCpG DNA, with contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition. While the binding affinity for fully-mCpG is weaker, UHRF1 SRA exhibits higher affinity for fully-mCpHpG.
Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. Recently, UHRF1 has been found to contribute to de novo non-CpG methylation, however, whether UHRF1 could recognize non-mCpG is unknown. Here, we have demonstrated through calorimetric measurements that the UHRF1 SRA can recognize mCpH and fully-mCpHpG, types of non-mCpG. Our ITC binding studies endorse the preferential reading of hemi-mCpG by UHRF1 SRA and also show 6-fold weaker binding for fully-mCpG than hemi-mCpG. Despite presence of symmetrical (5-methyl cytosine) 5mCs, stoichiometry of 1:1 for UHRF1 SRA binding to fully-mCpG indicates that UHRF1 SRA may not form a stable complex with fully-mCpG DNA. Contrarily, UHRF1 SRA recognizes fully-mCpHpG with a sloichiomeny of 2:1 protein to DNA duplex with binding affinity higher than fully-mCpG. Our crystal structure of UHRF1 SRA bound to fully-mCpHpG DNA reveals dual flip-out mechanism of 5mC recognition. Metadynamics studies corroborates with ITC data that UHRF1 SRA could not form a stable complex with fully-mCpG DNA. Altogether, this study demonstrates that UHRF1 SRA recognizes non-mCpG DNA and exhibits contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition. (C) 2020 Elsevier B.V. All rights reserved.
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