ArticleNucleic acids research2022
Locus-specific chromatin profiling of evolutionarily young transposable elements.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 14 citations in OpenAlex.
- Fiber-TEnCATS reveals haplotype-specific chromatin accessibility and DNA methylation at human L1HS loci.bioRxiv : the preprint server for biology · 2026Article
- Locus-specific LINE-1 mRNA expression reflects cell-type- and stimulus-specific senescence states.Nucleic acids research · 2026Article
- Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer's disease.GeroScience · 2025Article
- Transposable elements as genome regulators in normal and malignant haematopoiesis.Blood cancer journal · 2025Review
- Regulation and function of transposable elements in cancer genomes.Cellular and molecular life sciences : CMLS · 2024Review
- Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites.Cell genomics · 2024Article
- Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes.PLoS genetics · 2023Article
- LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq.Nucleic acids research · 2023Article
- SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution.Mobile DNA · 2022Article
- ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.Bioinformatics (Oxford, England) · 2022Article
- Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements.Frontiers in genetics · 2022Review
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.
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