RT Journal Article
SR Electronic
T1 Identification of regulatory elements from nascent transcription using dREG
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 321539
DO 10.1101/321539
A1 Zhong Wang
A1 Tinyi Chu
A1 Lauren A. Choate
A1 Charles G. Danko
YR 2018
UL http://biorxiv.org/content/early/2018/11/17/321539.abstract
AB 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% improvements in accuracy, 3-4-fold 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-I-hypersensitivity. 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. We provide a web interface to dREG that can be used by the scientific community (http://dREG.DNASequence.org).