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Mining histone methyltransferases and demethylases from whole genome sequence

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Abstract

Epigenetic regulation through post-translational modification of histones, especially methylation, is well conserved in evolution. Although there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have utilized a novel work-flow to identify one or more domains as high-priority domain (HPD), if present in at least 50% of the genes of a given functional class in the reference genome, namely, that of Drosophila melanogaster. Based on this approach, we have mined histone methyltransferases and demethylases from the whole genome sequence of Aedes aegypti (Diptera), the pea aphid Acyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera), the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum (Coleoptera). We identified 38 clusters consisting of arginine methyltransferases, lysine methyltransferases and demethylases using OrthoFinder, and the presence of HPD was queried in these sequences using InterProScan. This approach led us to identify putative novel members and currently inaccurate ones. Other than the high-priority domains, these proteins contain shared and unique domains that can mediate protein–protein interaction. Phylogenetic analysis indicates that there is different extent of protein sequence similarity; average similarity between histone lysine methyltransferases varies from 41% (for active mark) to 48% (for repressive mark), arginine methyltransferases is 51%, and demethylases is 52%. The method utilized here facilitates reliable identification of desired functional class in newly sequenced genomes.

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Abbreviations

HPD:

high-priority domain

KMT:

lysine methyltransferases

PRMT:

protein arginine methyltransferases

PTM:

post-translational modification

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Acknowledgements

The authors gratefully acknowledge the funding for the work through research grant to VB from the Council for Scientific and Industrial Research (CSIR), (EpiHeD: BSC0118/2012-17) and SERB No. 60 (0102)/12/EMR-II), India. We acknowledge DBT Bioinformatics facility at ACBR and the UGC SAP-II support. PG acknowledges CSIR; SK and AN acknowledge University Grants Commission, India, for support through Senior Research Fellowship and D.S. Kothari Post-doctoral fellowship.

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Authors and Affiliations

  1. Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110 007, India

    Parul Gulati, Surbhi Kohli, Ankita Narang & Vani Brahmachari

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  1. Parul Gulati
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  2. Surbhi Kohli
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  3. Ankita Narang
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  4. Vani Brahmachari
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Correspondence to Vani Brahmachari.

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This article is part of the Topical Collection: Chromatin Biology and Epigenetics.

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Gulati, P., Kohli, S., Narang, A. et al. Mining histone methyltransferases and demethylases from whole genome sequence. J Biosci 45, 9 (2020). https://doi.org/10.1007/s12038-019-9982-3

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