Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators

Vassetzky, Nikita S.; Borodulina, Olga R.; Ustyantsev, Ilia G.; Kosushkin, Sergei A.; Kramerov, Dmitri A.

doi:10.3390/ijms22189897

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Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators

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Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia

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These authors contributed equally to this work.

Academic Editor: Vijay Kumar Thakur

Int. J. Mol. Sci. 2021, 22(18), 9897; https://doi.org/10.3390/ijms22189897

Received: 16 August 2021 / Revised: 5 September 2021 / Accepted: 6 September 2021 / Published: 13 September 2021

(This article belongs to the Section Molecular Biology)

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Abstract

Short Interspersed Elements (SINEs) are eukaryotic non-autonomous retrotransposons transcribed by RNA polymerase III (pol III). The 3′-terminus of many mammalian SINEs has a polyadenylation signal (AATAAA), pol III transcription terminator, and A-rich tail. The RNAs of such SINEs can be polyadenylated, which is unique for pol III transcripts. Here, B2 (mice and related rodents), Dip (jerboas), and Ves (vespertilionid bats) SINE families were thoroughly studied. They were divided into subfamilies reliably distinguished by relatively long indels. The age of SINE subfamilies can be estimated, which allows us to reconstruct their evolution. The youngest and most active variants of SINE subfamilies were given special attention. The shortest pol III transcription terminators are TCTTT (B2), TATTT (Ves and Dip), and the rarer TTTT. The last nucleotide of the terminator is often not transcribed; accordingly, the truncated terminator of its descendant becomes nonfunctional. The incidence of complete transcription of the TCTTT terminator is twice higher compared to TTTT and thus functional terminators are more likely preserved in daughter SINE copies. Young copies have long poly(A) tails; however, they gradually shorten in host generations. Unexpectedly, the tail shortening below A₁₀ increases the incidence of terminator elongation by Ts thus restoring its efficiency. This process can be critical for the maintenance of SINE activity in the genome. View Full-Text

Keywords: SINE; retroposon; retrotransposon; RNA polymerase III; transcription terminator; polyadenylation

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Vassetzky, N.S.; Borodulina, O.R.; Ustyantsev, I.G.; Kosushkin, S.A.; Kramerov, D.A. Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators. Int. J. Mol. Sci. 2021, 22, 9897. https://doi.org/10.3390/ijms22189897

AMA Style

Vassetzky NS, Borodulina OR, Ustyantsev IG, Kosushkin SA, Kramerov DA. Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators. International Journal of Molecular Sciences. 2021; 22(18):9897. https://doi.org/10.3390/ijms22189897

Chicago/Turabian Style

Vassetzky, Nikita S., Olga R. Borodulina, Ilia G. Ustyantsev, Sergei A. Kosushkin, and Dmitri A. Kramerov. 2021. "Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators" International Journal of Molecular Sciences 22, no. 18: 9897. https://doi.org/10.3390/ijms22189897

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Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators

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