ArticleGenome biology2017
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 62 citations in OpenAlex.
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- scCensus: Off-target scRNA-seq reads reveal meaningful biology.bioRxiv : the preprint server for biology · 2024Article
- Integration of single-cell transcriptomics and epigenetic analysis reveals enhancer-controlled TIMP1 as a regulator of ferroptosis in colorectal cancer.Genes & genomics · 2024Article
- Amplifying gene expression with RNA-targeted therapeutics.Nature reviews. Drug discovery · 2023Review
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
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- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.BMC biology · 2022Article
- The contribution of evolutionarily volatile promoters to molecular phenotypes and human trait variation.Genome biology · 2022Article
- Prediction of histone post-translational modification patterns based on nascent transcription data.Nature genetics · 2022Article
- Natural antisense transcripts as drug targets.Frontiers in molecular biosciences · 2022Review
- The non-coding genome in genetic brain disorders: new targets for therapy?Essays in biochemistry · 2021Review
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Using CRISPR to understand and manipulate gene regulation.Development (Cambridge, England) · 2021Review
- Mechanisms of enhancer action: the known and the unknown.Genome biology · 2021Review
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
- Genome-Wide Estrogen Receptor Activity in Breast Cancer.Endocrinology · 2021Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEnhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo.
resultsHere, we show that bidirectional transcription initiation is a pervasive feature of accessible chromatin, including at enhancers, promoters, and other DNase hypersensitive regions not marked with canonical histone modification profiles. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured both in enhancer assays and at endogenous loci. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect evidence of purifying selection on the resulting enhancer RNAs within the human population.
conclusionsOur results indicate that bidirectional transcription initiation from accessible chromatin is not sufficient for, nor specific to, enhancer activity. Transcription initiating at enhancers may be a frequent by-product of promiscuous RNA polymerase initiation at accessible chromatin and is unlikely to generally play a functional role in enhancer activity.
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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.