SQuIRE reveals locus-specific regulation of interspersed repeat expression.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
18 03 2019
18 03 2019
Historique:
accepted:
03
01
2019
revised:
18
12
2018
received:
05
06
2018
pubmed:
10
1
2019
medline:
12
10
2019
entrez:
10
1
2019
Statut:
ppublish
Résumé
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
Identifiants
pubmed: 30624635
pii: 5280934
doi: 10.1093/nar/gky1301
pmc: PMC6411935
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e27Subventions
Organisme : NCI NIH HHS
ID : F30 CA221175
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM124531
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA009110
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
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