• Vani Brahmachari

      Articles written in Journal of Biosciences

    • Modified bases in transfer RNA

      Vani Brahmachari T Ramakrishnan

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      Transfer RNA is uniquely enriched with modified bases. A large body of information has accumulated about the occurrence, nature and distribution of modified bases in tRNA. But similar investigations on the enzymes involved in this post-transcriptional modification have been hampered by the instability of the enzymes and lack of suitable substrates. The present review summarises briefly, the occurrence and methods of detection of modified bases, the enzymes involved in their formation and also certain suggestive evidence for the role of modification in cellular metabolism.

    • Mining histone methyltransferases and demethylases from whole genome sequence

      PARUL GULATI SURBHI KOHLI ANKITA NARANG VANI BRAHMACHARI

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      Epigenetic regulation through post-translational modification of histones, especially methylation, is wellconserved in evolution. Although there are several insect genomes sequenced, an analysis with a focus on theirepigenetic repertoire is limited. We have utilized a novel work-flow to identify one or more domains as highprioritydomain (HPD), if present in at least 50% of the genes of a given functional class in the referencegenome, namely, that of Drosophila melanogaster. Based on this approach, we have mined histone methyltransferasesand demethylases from the whole genome sequence of Aedes aegypti (Diptera), the pea aphidAcyrthosiphon 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 anddemethylases 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 highprioritydomains, 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; averagesimilarity between histone lysine methyltransferases varies from 41% (for active mark) to 48% (for repressivemark), arginine methyltransferases is 51%, and demethylases is 52%. The method utilized here facilitatesreliable identification of desired functional class in newly sequenced genomes.

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