Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is large...

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Bibliographic Details
Published in:Nucleic acids research 2017-06, Vol.45 (10), p.6194-6208
Main Authors: Karijolich, John, Zhao, Yang, Alla, Ravi, Glaunsinger, Britt
Format: Article
Language:English
Subjects:
Animals
Biological Transport - genetics
Cell Cycle Proteins - genetics
Gene Expression Regulation - genetics
Gene Knockdown Techniques
Herpesviridae Infections - genetics
Mice
NIH 3T3 Cells
Nuclear Matrix-Associated Proteins - metabolism
Retroelements - physiology
Rhadinovirus
RNA
RNA Interference
RNA Polymerase III - genetics
RNA, Messenger - genetics
RNA, Messenger - metabolism
RNA-Binding Proteins - metabolism
Sequence Analysis, DNA
Short Interspersed Nucleotide Elements - genetics
Stress, Physiological - genetics
Subcellular Fractions - metabolism
Transcription, Genetic
Tumor Virus Infections - genetics
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Summary:Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx180