ArticleCurrent protocols in bioinformatics2019
Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway.
Article in Current protocols in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 48 citations in OpenAlex.
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- Functional and computational interrogation of juvenile idiopathic arthritis risk loci in CD4+ T cells.HGG advances · 2026Article
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.Nature communications · 2026Article
- KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival.Science advances · 2026Article
- Functional and Computational Interrogation of the Juvenile Idiopathic Arthritis Risk Loci Identifies Candidate Causal SNPs and Target Genes in CD4+ T cells.medRxiv : the preprint server for health sciences · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Dynamic regulation of murine RNA polymerase III transcription during heat shock stress.Genetics · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- PRC2 promotes canalisation during endodermal differentiation.PLoS genetics · 2025Article
- Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.Molecular cell · 2024Article
- KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription.Nature communications · 2024Article
- Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling.The EMBO journal · 2024Article
- Acute depletion of BRG1 reveals its primary function as an activator of transcription.Nature communications · 2024Article
- KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription.bioRxiv : the preprint server for biology · 2024Article
- Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome.Cell reports · 2024Article
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease†.Biology of reproduction · 2023Article
- Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells.Nucleic acids research · 2023Article
- Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model.BMC genomics · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Transcription is a chromatin mark that can be used effectively to identify the location of active enhancers and promoters, collectively known as transcriptional regulatory elements (TREs). We recently introduced dREG, a tool for the identification of TREs using run-on and sequencing (RO-seq) assays, including global run-on and sequencing (GRO-seq), precision run-on and sequencing (PRO-seq), and chromatin run-on and sequencing (ChRO-seq). In this protocol, we present step-by-step instructions for running dREG on an arbitrary run-on and sequencing dataset. Users provide dREG with bigWig files (in which each read is represented by a single base) representing the location of RNA polymerase in a cell or tissue sample of interest, and dREG returns a list of genomic regions that are predicted to be active TREs. Finally, we demonstrate the use of dREG regions in discovering transcription factors controlling response to a stimulus and predicting their target genes. Together, this protocol provides detailed instructions for running dREG on arbitrary run-on and sequencing data. © 2018 by John Wiley & Sons, Inc.
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