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Series GSE85518 Query DataSets for GSE85518
Status Public on Oct 31, 2016
Title B2 SINE expression during MHV68 infecton
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
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.
Overall design NIH 3T3 murine fibroblasts were infected with MHV68 for 24 hours. Total RNA from two biological replicates was primer extended for B2 SINE RNA. Primer extenstion products were converted in to sequencing libraries and ran on a MiSeq at the UC Berkeley QB3 Vncent J. Coates Genomics Sequencing Laboratory. Reads were aligned to he mouse mm10 reference genome using bwa. Reads mapping to known B2 SINEs (present in the repeatmasker tract of UCSC) were counted and normalizied RPKM values were computed using the BamUtil tool.
Contributor(s) Karijolich J, Glaunsinger B
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Submission date Aug 11, 2016
Last update date May 15, 2019
Contact name Yan Guo
Organization name Vanderbilt Cancer Center
Street address 639 Preston Research Bld
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (2)
GSM2274627 B2 SINE-seq replicate 1
GSM2274628 B2 SINE-seq replicate 2
BioProject PRJNA338698
SRA SRP081313

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Processed data provided as supplementary file

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