ArticlePLoS computational biology2019
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 50 citations in OpenAlex.
- Review
- Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Transposable element expression is associated with sex chromosome number in humans.PLoS genetics · 2025Article
- Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level.Scientific reports · 2024Article
- Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation.Epigenetics & chromatin · 2023Article
- Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat.BMC genomics · 2023Article
- LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq.Nucleic acids research · 2023Article
- Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM.Methods in molecular biology (Clifton, N.J.) · 2023Article
- TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments.Bioinformatics (Oxford, England) · 2022Article
- SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution.Mobile DNA · 2022Article
- Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data.Biology · 2022Article
- LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation.International journal of molecular sciences · 2021Review
- STK11/LKB1 Loss of Function Is Associated with Global DNA Hypomethylation andCancer research · 2021Article
- Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.Genome research · 2021Article
- Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats.BMC biology · 2020Article
- Measuring and interpreting transposable element expression.Nature reviews. Genetics · 2020Review
- Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation.Development (Cambridge, England) · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.