ArticleBMC bioinformatics2020
ARTDeco: automatic readthrough transcription detection.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 44 citations in OpenAlex.
- Cross-domain signal grammars of transcription termination.Advanced biotechnology · 2026Review
- SERIPH: a two-step extraction protocol for selective enrichment of semi-extractable RNAs.RNA (New York, N.Y.) · 2026Article
- Dogcatcher2: Improved statistical detection of transcriptional readthrough and repetitive element analysis across sequencing platforms.bioRxiv : the preprint server for biology · 2026Article
- Transcription termination counteracts DNA damage after WEE1 inhibition.Nucleic acids research · 2026Article
- Regulatory Mechanisms and Functional Roles of Readthrough Transcripts in Tumorigenesis.International journal of molecular sciences · 2025Review
- Microtubule mechanotransduction refines cytomegalovirus interactions with and remodeling of host chromatin.Nature communications · 2025Article
- Comprehensive resource for transcription readthrough events in healthy human tissues.Scientific data · 2025Article
- Landscape of chimeric RNAs in COVID-19 patient blood.Genes & diseases · 2025Article
- HSV-1 ICP22 condensates impair host transcription by depleting promoter RNAPII Ser-2P occupation.Frontiers in microbiology · 2025Article
- Epstein-Barr virus induces host shutoff extensively via BGLF5-independent mechanisms.Cell reports · 2024Article
- A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals.Cell reports · 2024Article
- RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.Briefings in bioinformatics · 2024Article
- RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5.Genome biology · 2024Article
- Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.Molecular cell · 2024Article
- Article
- Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features.Communications biology · 2024Article
- Transcriptional Stress Induces the Generation of DoGs in Cancer Cells.Non-coding RNA · 2024Article
- The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery.Nature structural & molecular biology · 2023Article
- Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription.Science advances · 2023Article
- Inducible disruption ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription past the 3' end of genes, which can result in novel transcripts, changes in epigenetic states and altered 3D genome structure.
resultsWe developed Automatic Readthrough Transcription Detection (ARTDeco), a tool to detect and analyze multiple features of readthrough transcription from RNA-seq and other next-generation sequencing (NGS) assays that profile transcriptional activity. ARTDeco robustly quantifies the global severity of readthrough phenotypes, and reliably identifies individual genes that fail to terminate (readthrough genes), are aberrantly transcribed due to upstream termination failure (read-in genes), and novel transcripts created as a result of readthrough (downstream of gene or DoG transcripts). We used ARTDeco to characterize readthrough transcription observed during influenza A virus (IAV) infection, validating its specificity and sensitivity by comparing its performance in samples infected with a mutant virus that fails to block transcription termination. We verify ARTDeco's ability to detect readthrough as well as identify read-in genes from different experimental assays across multiple experimental systems with known defects in transcriptional termination, and show how these results can be leveraged to improve the interpretation of gene expression and downstream analysis. Applying ARTDeco to a gene expression data set from IAV-infected monocytes from different donors, we find strong evidence that read-in gene-associated expression quantitative trait loci (eQTLs) likely regulate genes upstream of read-in genes. This indicates that taking readthrough transcription into account is important for the interpretation of eQTLs in systems where transcription termination is blocked.
conclusionsARTDeco aids researchers investigating readthrough transcription in a variety of systems and contexts.
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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.