Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA

Abhishek, Suman and Nakarakanti, Naveen Kumar and Deeksha, Waghela and Rajakumara, Eerappa (2021) Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. International Journal of Biological Macromolecules, 170. pp. 514-522. ISSN 01418130

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Abstract

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 stoichiometry 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.

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IITH Creators:

IITH Creators	ORCiD
Abhishek, Suman	UNSPECIFIED
Nakarakanti, Naveen Kumar	UNSPECIFIED
Deeksha, Waghela	UNSPECIFIED
Rajakumara, Eerappa	UNSPECIFIED

Item Type:

Article

Uncontrolled Keywords:

Article; binding affinity; computer simulation; controlled study; crystal structure; DNA methylation; isothermal titration calorimetry; metadynamics simulation; mouse; nonhuman; protein structure; SET and RING associated domain; stoichiometry; amino acid sequence; animal; CpG island; DNA methylation; metabolism; physiology; sequence alignment;5 methylcytosine; double stranded DNA; ubiquitin; ubiquitin like containing PHD and RING Finger domains 1; unclassified drug; 5 methylcytosine; CCAAT enhancer binding protein; complementary DNA; cytidylyl-3'-5'-guanosine; cytosine; dinucleoside phosphate; DNA; protein binding; ubiquitin protein ligase; Uhrf1 protein, mouse

Subjects:

Others > Biotechnology

Divisions:

Department of Biotechnology

Depositing User:

. LibTrainee 2021

Date Deposited:

29 Jun 2021 05:48

Last Modified:

29 Jun 2021 05:48

URI:

http://raiithold.iith.ac.in/id/eprint/8039