ArticleNature biotechnology2022
A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Genome-wide mapping of theiScience · 2026Article
- Regulatory activity and evolutionary co-option of cis-regulatory elements underlying bear hibernation.Molecular biology and evolution · 2026Article
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- The nascent transcriptome delineates the regulatory landscape in human health and disease.bioRxiv : the preprint server for biology · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts.Nature methods · 2026Article
- H3K9me3 controls epidermis morphogenesis by regulating RNA Pol II dynamics at developmental promoters and enhancers.Nature communications · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis.Science advances · 2026Article
- STARR-CRAAVT: A platform to identify cell type-specific regulatory elements for next-generation gene therapy.iScience · 2026Article
- A Double-Negative Prostate Cancer Subtype Is Vulnerable to SWI/SNF-Targeting Degrader Molecules.Cancer research · 2026Article
- CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease.Nature neuroscience · 2026Article
- Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.Science (New York, N.Y.) · 2026Article
- Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.Developmental cell · 2026Article
- Dual promoter-enhancer activities reflect a unified regulatory logic.Nature communications · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- SEdb 3.0: a comprehensive super-enhancer database across multiple species.Nucleic acids research · 2026Article
6 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. Here, we compared 13 genome-wide RNA sequencing (RNA-seq) assays in K562 cells and show that nuclear run-on followed by cap-selection assay (GRO/PRO-cap) has advantages in enhancer RNA detection and active enhancer identification. We also introduce a tool, peak identifier for nascent transcript starts (PINTS), to identify active promoters and enhancers genome wide and pinpoint the precise location of 5' transcription start sites. Finally, we compiled a comprehensive enhancer candidate compendium based on the detected enhancer RNA (eRNA) transcription start sites (TSSs) available in 120 cell and tissue types, which can be accessed at https://pints.yulab.org . With knowledge of the best available assays and pipelines, this large-scale annotation of candidate enhancers will pave the way for selection and characterization of their functions in a time- and labor-efficient manner.
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