ArticleCell genomics2023
Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.Nucleic acids research · 2025Article
- Transcriptional coordination between intergenic RNA polymerase II-bound regions and nearby genes reveals functional specialization and disease associations in peripheral blood.Computational and structural biotechnology journal · 2025Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.bioRxiv : the preprint server for biology · 2024Article
- MUFFIN: a suite of tools for the analysis of functional sequencing data.NAR genomics and bioinformatics · 2024Article
- Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues.Cell genomics · 2023Article
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Authors and funding
6 authors.
Funding
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Abstract
Intergenic transcription in normal and cancerous tissues is pervasive but incompletely understood. To investigate this, we constructed an atlas of over 180,000 consensus RNA polymerase II (RNAPII)-bound intergenic regions from 900 RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments in normal and cancer samples. Through unsupervised analysis, we identified 51 RNAPII consensus clusters, many of which mapped to specific biotypes and revealed tissue-specific regulatory signatures. We developed a meta-clustering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Encyclopedia of DNA Elements (ENCODE). This analysis revealed strong tissue- and disease-specific interconnections between RNAPII occupancy and transcriptional activity. We demonstrate that intergenic transcription at RNAPII-bound regions is a novel per-cancer and pan-cancer biomarker. This biomarker displays genomic and clinically relevant characteristics, distinguishing cancer subtypes and linking to overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover intergenic transcriptional activity in normal and cancer tissues.
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