Clusters of hairpins induce intrinsic transcription termination in bacteria

Abstract 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...

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Autores principales:	Swati Gupta, Debnath Pal
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7eb152a9f02f45f69e7a19cd13756b0f
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spelling	oai:doaj.org-article:7eb152a9f02f45f69e7a19cd13756b0f2021-12-02T16:28:06ZClusters of hairpins induce intrinsic transcription termination in bacteria10.1038/s41598-021-95435-32045-2322https://doaj.org/article/7eb152a9f02f45f69e7a19cd13756b0f2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95435-3https://doaj.org/toc/2045-2322Abstract 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.Swati GuptaDebnath PalNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Swati Gupta Debnath Pal Clusters of hairpins induce intrinsic transcription termination in bacteria
description	Abstract 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.
format	article
author	Swati Gupta Debnath Pal
author_facet	Swati Gupta Debnath Pal
author_sort	Swati Gupta
title	Clusters of hairpins induce intrinsic transcription termination in bacteria
title_short	Clusters of hairpins induce intrinsic transcription termination in bacteria
title_full	Clusters of hairpins induce intrinsic transcription termination in bacteria
title_fullStr	Clusters of hairpins induce intrinsic transcription termination in bacteria
title_full_unstemmed	Clusters of hairpins induce intrinsic transcription termination in bacteria
title_sort	clusters of hairpins induce intrinsic transcription termination in bacteria
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7eb152a9f02f45f69e7a19cd13756b0f
work_keys_str_mv	AT swatigupta clustersofhairpinsinduceintrinsictranscriptionterminationinbacteria AT debnathpal clustersofhairpinsinduceintrinsictranscriptionterminationinbacteria
_version_	1718383938169208832

Clusters of hairpins induce intrinsic transcription termination in bacteria

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