ArticleNature genetics2014
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
Article in Nature genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 446 papers.
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Who cites it
446 citing papers in PubMed, 739 citations in OpenAlex.
- Review
- Genome-wide mapping of theiScience · 2026Article
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility.bioRxiv : the preprint server for biology · 2026Article
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- Machine learning analysis of the human initiator region reveals key features of different types of core promoters.Genes & development · 2026Article
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Accurate de novo transcription unit annotation from run-on and sequencing data.PLoS computational biology · 2026Article
- Developmental expression of the skeletal muscle determination gene,bioRxiv : the preprint server for biology · 2026Article
- Regulation of RNA transcript elongation in metazoans and its relevance to disease.Nature reviews. Molecular cell biology · 2026Review
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- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule imaging reveals RNA polymerase II dynamics and TAF1-dependent promoter-proximal pause release.Nature communications · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- 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
386 more citing papers are in PubMed but not listed here.
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6 authors at 2 institutions in 1 country.
Funding
Abstract
Despite the conventional distinction between them, promoters and enhancers share many features in mammals, including divergent transcription and similar modes of transcription factor binding. Here we examine the architecture of transcription initiation through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B cell (GM12878) and chronic myelogenous leukemic (K562) ENCODE Tier 1 cell lines. Using a nuclear run-on protocol called GRO-cap, which captures TSSs for both stable and unstable transcripts, we conduct detailed comparisons of thousands of promoters and enhancers in human cells. These analyses identify a common architecture of initiation, including tightly spaced (110 bp apart) divergent initiation, similar frequencies of core promoter sequence elements, highly positioned flanking nucleosomes and two modes of transcription factor binding. Post-initiation transcript stability provides a more fundamental distinction between promoters and enhancers than patterns of histone modification and association of transcription factors or co-activators. These results support a unified model of transcription initiation at promoters and enhancers.
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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.