ArticleNature genetics2019
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements.
Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Genome-wide mapping of theiScience · 2026Article
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- The future objectives of the International Mouse Phenotyping Consortium (IMPC): functional evaluation of human disease-relevant cis-regulatory elements in the mouse genome.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Subtype-specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers.Molecular oncology · 2026Article
- Transcriptional interference revisited.Nature genetics · 2026Review
- GPR3 is an immediate-early gene-like GPCR regulating CREB-dependent neuronal differentiation.iScience · 2026Article
- Mapping and quantifying nascent transcript start sites using TT-TSS-seq.Genome research · 2026Article
- Article
- Introns as Protective Buffers Against Transposable Elements Invasion During Genome Gigantism in a Newt.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Multiomics Mendelian randomization identifies serpin family G member 1 as a chronic obstructive pulmonary disease modulator.Signal transduction and targeted therapy · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Role of eRNAs in Cardiovascular Diseases.Current cardiology reviews · 2026Review
- Epigenetic Regulation of G6PD Drives Metabolic Reprogramming in Intrahepatic Cholangiocarcinoma.Cancer science · 2025Article
- G-quadruplex structures as modulators of alternative promoter usage.NAR genomics and bioinformatics · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- RB1 controls differentiation through positive regulation of phosphoglycerate mutases.Cell death & disease · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
- A transcription coupling model for how enhancers communicate with their target genes.Nature structural & molecular biology · 2025Review
- Cell type-dependent directional transcription at enhancers.NAR genomics and bioinformatics · 2025Article
- Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers.Nature communications · 2025Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
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Abstract
Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell type-specific transcriptomes is not fully understood. We developed a simple and robust method, native elongating transcript-cap analysis of gene expression (NET-CAGE), to sensitively detect 5' ends of nascent RNAs in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously on stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 atlas of transcribed enhancers, with broad applicability to biomedical research.
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