Dar, D., Prasse, D., Schmitz-Streit, Ruth and Sorek, R. (2016) Widespread formation of alternative 3 ' UTR isoforms via transcription termination in archaea. Nature Microbiology, 1 (10). DOI 10.1038/nmicrobiol.2016.143.

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Abstract

Transcription termination sets the 3' end boundaries of RNAs and plays key roles in gene regulation. Although termination has been well studied in bacteria, the signals that mediate termination in archaea remain poorly understood. Here, we applied term-seq to comprehensively map RNA 3' termini, with single-base precision, in two phylogenetically distant archaea: Methanosarcina mazei and Sulfolobus acidocaldarius. Comparison of RNA 3' ends across hundreds of genes revealed the sequence composition of transcriptional terminators in each organism, highlighting both common and divergent characteristics between the different archaeal phyla. We find that, in contrast to bacteria, a considerable portion of archaeal genes are controlled by multiple consecutive terminators, generating several alternative 3' untranslated region isoforms for >30% of the genes. These alternative isoforms often present marked length differences, implying that archaea can employ regulation via alternative 3' untranslated regions, similar to eukaryotes. Although most of the terminators are intergenic, we discover numerous cases in which termination of one gene occurs within the coding region of a downstream gene, implying that leaky termination may tune inter-transcript stoichiometry in multi-gene operons. These results provide the first high-throughput maps of transcriptional terminators in archaea and point to an evolutionary path linking bacterial and eukaryal non-coding regulatory strategies.

Document Type:	Article
Keywords:	Archaeal genes, Gene regulation, Non-coding RNAs, Transcriptomics
Research affiliation:	Kiel University Kiel University > Kiel Marine Science OceanRep > The Future Ocean - Cluster of Excellence
Refereed:	Yes
Open Access Journal?:	No
Publisher:	Nature Research
Projects:	Future Ocean
Date Deposited:	19 Mar 2017 08:04
Last Modified:	23 Sep 2019 21:56
URI:	https://oceanrep.geomar.de/id/eprint/36048

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