ArticleNucleic acids research2019
SQuIRE reveals locus-specific regulation of interspersed repeat expression.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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Who cites it
133 citing papers in PubMed.
- Comprehensive characterization of transposable element expression reveals regulatory circuitry and clinical implications in cancers.Science advances · 2026Article
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- Microglia activation by derepression of endogenous retroviruses drives inflammation and cellular senescence.Nature neuroscience · 2026Article
- UHRF1 overexpression generates distinct senescent states with different Tp53 dependencies.EMBO reports · 2026Article
- Hijacking pre-tRNA enables LTR-retrotransposon-initiated constitutive heterochromatin formation.Science advances · 2026Article
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Article
- Distinct endogenous retroviruses are expressed in mutational subtypes of clear cell renal cell carcinoma and are linked to improved clinical outcomes.Cell reports · 2026Article
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Intermittent fasting rewires tissue-specific gene-transposable element regulatory networks.PNAS nexus · 2026Article
- Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA.Cell reports · 2026Article
- Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.Nature communications · 2026Article
- Cyanine-modified ssODNs enhance CRISPR-Cas9 HDR in stem cell embryo models via chromatin and chemical modulation.Nature communications · 2026Article
- Review
- mNature communications · 2026Article
- Chromatin reorganization drives overexpression of a Btaf1 variant underpinning hematopoietic aging.Nature communications · 2026Article
- Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8.Nucleic acids research · 2026Article
- Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.Nature communications · 2026Article
- Expression of endogenous retroviral elements is associated with extracellular matrix remodeling in prostate cancer.Mobile DNA · 2026Article
- RNA variation as the driver of genomic efficiency and phenotypic complexity.International journal of biological sciences · 2026Review
73 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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.
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