ArticleGenome biology2014
Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
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- Review
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- Genomic patterns of transcription-replication interactions in mouse primary B cells.Nucleic acids research · 2022Article
- Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver.PLoS genetics · 2021Article
- LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.Nature communications · 2021Article
- Characterizing Genetic Regulatory Elements in Ovine Tissues.Frontiers in genetics · 2021Article
- Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells.Nucleic acids research · 2020Article
- BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.Epigenetics & chromatin · 2019Article
- Metastasis Suppressor NME1 Directly Activates Transcription of theAnticancer research · 2018Article
- Dynamic turnover of paused Pol II complexes at human promoters.Genes & development · 2018Article
- Rapid Response and Slow Recovery of the H3K4me3 Epigenomic Marker in the Liver after Light-mediated Phase Advances of the Circadian Clock.Journal of biological rhythms · 2018Article
- Identification of active miRNA promoters from nuclear run-on RNA sequencing.Nucleic acids research · 2017Article
- PHF13: A new player involved in RNA polymerase II transcriptional regulation and co-transcriptional splicing.Transcription · 2017Article
- Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.Biophysical journal · 2017Article
- Genome-wide uniformity of human 'open' pre-initiation complexes.Genome research · 2017Article
- Regulatory cis-elements are located in accessible promoter regions of the CAT2 promoter and affect activating histone modifications in Arabidopsis thaliana.Plant molecular biology · 2017Article
- Linking Core Promoter Classes to Circadian Transcription.PLoS genetics · 2016Article
- Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.eLife · 2015Article
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4 authors.
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Abstract
backgroundIn mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states.
resultsHere, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3.
conclusionsWe thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.
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