Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea

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.

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Figure 1: Sequence and structural determinants of transcription terminators in M. mazei.
Figure 2: Multiple terminators control gene boundaries in M. mazei.
Figure 3: Determinants of transcription terminators in S. acidocaldarius.
Figure 4: Abundant overlapping termination suggests possible role in gene regulation.

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Acknowledgements

The authors thank M. Shamir, S. Doron, A. Millman and A. Lopatina for discussions. R.S. was supported, in part, by the Israel Science Foundation (personal grant no. 1303/12 and I-CORE grant no. 1796/12), the ERC-StG programme (grant no. 260432), the Abisch–Frenkel Foundation, the Pasteur–Weizmann council grant, the Minerva Foundation, the Leona M. and Harry B. Helmsley Charitable Trust and by a DIP grant from the Deutsche Forschungs Gemeinschaft (DFG). D.P. was funded by the DFG (Schm1052/9-2).

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D.D., R.A.S. and R.S conceived and designed the research studies. D.D. and D.P. performed the experiments. D.D. and R.S. analysed the data. D.D., RA.S., D.P. and R.S. wrote the manuscript.

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Correspondence to Rotem Sorek.

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The authors declare no competing financial interests.

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Supplementary Figures 1-4, Supplementary Table Legends 1-9, Supplementary References (PDF 702 kb)

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Dar, D., Prasse, D., Schmitz, R. et al. Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea. Nat Microbiol 1, 16143 (2016). https://doi.org/10.1038/nmicrobiol.2016.143

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