ArticleScientific reports2015
Identifying transcription start sites and active enhancer elements using BruUV-seq.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Emerging insights into enhancer RNAs: biogenesis, function, mechanism, and disease implication.Briefings in bioinformatics · 2026Review
- Role of eRNAs in Cardiovascular Diseases.Current cardiology reviews · 2026Review
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
- Cockayne syndrome B protein is implicated in transcription and associated chromatin dynamics in homeostatic and genotoxic conditions.Aging cell · 2025Article
- Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress.Blood · 2023Article
- Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis.Nucleic acids research · 2023Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types.Genome research · 2022Article
- Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis.Molecular cancer · 2020Review
- Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing.NAR genomics and bioinformatics · 2020Article
- Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions.Nature communications · 2020Article
- Methods for the analysis of transcriptome dynamics.Toxicology research · 2019Review
- Finding ARIEL under the sea of T-ALL circuits.Blood · 2019Article
- Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation.Molecular neurobiology · 2018Article
- Enhancer-derived RNA: A Primer.Genomics, proteomics & bioinformatics · 2017Review
- Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53.Scientific reports · 2017Article
- Gene length as a biological timer to establish temporal transcriptional regulation.Cell cycle (Georgetown, Tex.) · 2017Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5'-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3'-5' degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells.
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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.