Detecting endogenous retrovirus-driven tissue-specific gene transcription

Genome Biology and Evolution
Mihaela PavlicevLouis Muglia

Abstract

Transposable elements (TEs) comprise approximately half of the human genome, and several independent lines of investigation have demonstrated their role in rewiring gene expression during development, evolution, and oncogenesis. The identification of their regulatory effects has largely been idiosyncratic, by linking activity with isolated genes. Their distribution throughout the genome raises critical questions-do these elements contribute to broad tissue- and lineage-specific regulation? If so, in what manner, as enhancers, promoters, RNAs? Here, we devise a novel approach to systematically dissect the genome-wide consequences of TE insertion on gene expression, and test the hypothesis that classes of endogenous retrovirus long terminal repeats (LTRs) exert tissue-specific regulation of adjacent genes. Using correlation of expression patterns across 18 tissue types, we reveal the tissue-specific uncoupling of gene expression due to 62 different LTR classes. These patterns are specific to the retroviral insertion, as the same genes in species without the LTRs do not exhibit the same effect. Although the LTRs can be transcribed themselves, the most highly transcribed TEs do not have the largest effects on adjacent regulation of...Continue Reading

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Citations

Jan 29, 2016·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Luis P Villarreal
Jun 20, 2018·BMC Genomics·Marco TrizzinoChristopher D Brown
Sep 20, 2019·Nature Reviews. Genetics·Myriam HembergerWendy Dean
Sep 24, 2020·RNA Biology·Maria Elena Vilar AlvarezIgor Vorechovsky
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Dec 26, 2019·PeerJ·Macarena ArroyoM Gonzalo Claros
Oct 20, 2020·Reproductive Medicine and Biology·Shun ShibataTakahiro Arima
May 31, 2021·Brain Structure & Function·Borros Arneth
Jul 29, 2021·Molecular Biology and Evolution·Ming-An SunTodd S Macfarlan

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Methods Mentioned

BETA
RNASeq

Software Mentioned

RNASeq
HumanBodyMap
Cufflinks
UCSC table browser
Bowtie2

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