ArticleNature genetics2018
Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.
Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- Accurate de novo transcription unit annotation from run-on and sequencing data.PLoS computational biology · 2026Article
- 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
- 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
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.Nature communications · 2026Article
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- Small RNA Analysis in Cancer Cells.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Transcriptional pause release at enhancers mediates cell identity.NAR cancer · 2025Review
- Disruption of TAD hierarchy promotes LTR co-option in cancer.Nature genetics · 2025Article
- Article
- Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.Nature structural & molecular biology · 2025Article
- Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing.Bio-protocol · 2025Article
- An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs.Nature genetics · 2025Article
- Training deep learning models on personalized genomic sequences improves variant effect prediction.bioRxiv : the preprint server for biology · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Eukaryotic RNA polymerase II (Pol II) has been found at both promoters and distal enhancers, suggesting additional functions beyond mRNA production. To understand this role, we sequenced nascent RNAs at single-molecule resolution to unravel the interplay between Pol II initiation, capping and pausing genome-wide. Our analyses identify two pause classes that are associated with different RNA capping profiles. More proximal pausing is associated with less complete capping, less elongation and a more enhancer-like complement of transcription factors than later pausing. Unexpectedly, transcription start sites (TSSs) are predominantly found in constellations composed of multiple divergent pairs. TSS clusters are intimately associated with precise arrays of nucleosomes and correspond with boundaries of transcription factor binding and chromatin modification at promoters and enhancers. TSS architecture is largely unchanged during the dramatic transcriptional changes induced by heat shock. Together, our results suggest that promoter- and enhancer-associated Pol II is a regulatory nexus for integrating information across TSS ensembles.
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