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Identification of regulatory elements from nascent transcription using dREG

Zhong Wang, Tinyi Chu, Lauren A. Choate, Charles G. Danko
doi: https://doi.org/10.1101/321539
Zhong Wang
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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Tinyi Chu
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
2Graduate field of Computational Biology, Cornell University, Ithaca, NY 14853.
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Lauren A. Choate
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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Charles G. Danko
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
3Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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  • For correspondence: dankoc@gmail.com
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Abstract

Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns of transcription initiation. We previously introduced dREG to identify TIRs using PROseq 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 or bound by transcription factors that recognize DNA concurrently with a nucleosome. We provide a web interface to dREG that can be used by the scientific community (http://dREG.DNASequence.org).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 14, 2018.
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Identification of regulatory elements from nascent transcription using dREG
Zhong Wang, Tinyi Chu, Lauren A. Choate, Charles G. Danko
bioRxiv 321539; doi: https://doi.org/10.1101/321539
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Identification of regulatory elements from nascent transcription using dREG
Zhong Wang, Tinyi Chu, Lauren A. Choate, Charles G. Danko
bioRxiv 321539; doi: https://doi.org/10.1101/321539

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