ArticleNature communications2021
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Review
- Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.BMC genomics · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Synthetic tunable promoters for flexible control of multi-gene expression in mammalian cells.Journal of advanced research · 2025Article
- Satellite DNA Genomics: The Ongoing Story.International journal of molecular sciences · 2025Review
- Isoform analysis of heterozygous putative splicing variants at the allele level using nanopore long-read sequencing.Scientific reports · 2025Article
- Potential Involvement of Myostatin in Smooth Muscle Differentiation in Pleomorphic Leiomyosarcoma.International journal of molecular sciences · 2025Article
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- Dysregulation of Transposon Transcription Profiles in Cancer Cells Resembles That of Embryonic Stem Cells.Current issues in molecular biology · 2024Article
- Sequencing and characterizing short tandem repeats in the human genome.Nature reviews. Genetics · 2024Review
- CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.Nature communications · 2024Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- The status of the human gene catalogue.Nature · 2023Review
- Short tandem repeats are important contributors to silencer elements in T cells.Nucleic acids research · 2023Article
- Characterization of genome-wide STR variation in 6487 human genomes.Nature communications · 2023Article
- The status of the human gene catalogue.ArXiv · 2023Article
- High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance.NAR genomics and bioinformatics · 2022Article
- Cap analysis of gene expression (CAGE) and noncoding regulatory elements.Seminars in immunopathology · 2022Review
- Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution.Molecular psychiatry · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
25 authors.
Funding
Abstract
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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