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

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

doi:10.3390/ijms22189897

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.

Highlights

Short INterspersed Elements (SINEs) were discovered four decades ago
SINEs are nonautonomous as they encode no proteins and their spread in the genome relies on the reverse transcriptase of Long Interspersed Elements (LINEs)
Many of them were in tandem B2-B2, B1-B2, and B2-B1 repeats (18,757, 6368, and 17,757 dimeric copies, respectively). These were excluded from further analysis since we do not know if they emerged by integration of one SINE into the tail of another one or are complex SINEs retrotransposed from dimeric templates similar to Alu

Summary

Introduction

Short INterspersed Elements (SINEs) were discovered four decades ago. Initially, highly repetitive DNA regions dispersed in the human (Alu elements) and mouse (B1 and B2 elements) genomes were found [1,2]. SINEs are nonautonomous as they encode no proteins and their spread in the genome (amplification) relies on the reverse transcriptase of Long Interspersed Elements (LINEs). The majority of SINE families emerged by the reverse transcription of tRNA molecules [22]. Apart from the tRNA-derived head, most such SINEs have the central part (body) and tail [9]. The genomic sequences upstream of SINE copies can modulate their transcription [25,26], the pol III promoters reside within SINEs [9,12]. SINE sequences can be transcribed by RNA polymerase II as a part of gene introns; only the pol III-generated SINE transcripts can be templates for LINE reverse transcriptase that generate new genomic copies of SINEs

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Conclusion