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Clusters of hairpins induce intrinsic transcription termination in bacteria

Gupta, S and Pal, D (2021) Clusters of hairpins induce intrinsic transcription termination in bacteria. In: Scientific Reports, 11 (1).

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Official URL: https://doi.org/10.1038/s41598-021-95435-3


Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87 of cases by predicting hairpin(s) and validate against 81 of cases for which the RNA-seq derived sites could be calculated. We identify 72 of these sites correctly, with 98 of them located � 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria. © 2021, The Author(s).

Item Type: Journal Article
Publication: Scientific Reports
Publisher: Nature Research
Additional Information: The copyright for this article belongs to Authors
Department/Centre: Division of Interdisciplinary Sciences > Computational and Data Sciences
Date Deposited: 16 Sep 2021 09:14
Last Modified: 16 Sep 2021 09:14
URI: http://eprints.iisc.ac.in/id/eprint/69723

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