Identification of regulatory elements from nascent transcription using dREG.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
02 2019
02 2019
Historique:
received:
13
05
2018
accepted:
18
12
2018
pubmed:
24
12
2018
medline:
30
5
2019
entrez:
22
12
2018
Statut:
ppublish
Résumé
Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns of actively elongating RNA polymerase. We previously introduced dREG to identify TIRs using PRO-seq data. Here, we introduce an efficient new implementation of dREG that uses PRO-seq data to identify both uni- and bidirectionally transcribed TIRs with 70% improvement in accuracy, three- to fourfold higher resolution, and >100-fold increases in computational efficiency. Using a novel strategy to identify TIRs based on their statistical confidence reveals extensive overlap with orthogonal assays, yet also reveals thousands of additional weakly transcribed TIRs that were not identified by H3K27ac ChIP-seq or DNase-seq. Novel TIRs discovered by dREG were often associated with RNA polymerase III initiation, bound by pioneer transcription factors, or located in broad domains marked by repressive chromatin modifications. Our results suggest that transcription initiation can be a powerful tool for expanding the catalog of functional elements.
Identifiants
pubmed: 30573452
pii: gr.238279.118
doi: 10.1101/gr.238279.118
pmc: PMC6360809
doi:
Substances chimiques
Heterochromatin
0
Transcription Factors
0
RNA Polymerase III
EC 2.7.7.6
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
293-303Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG009309
Pays : United States
Informations de copyright
© 2019 Wang et al.; Published by Cold Spring Harbor Laboratory Press.
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