Deciphering Transcriptional Regulation of Human Core Promoters
Open accessPreprint — published as 10.1101/gr.236075.118 · Paper page
Abstract
Despite its pivotal role in regulating transcription, our understanding of core promoter function, architecture, and cis-regulatory elements is lacking. Here, we devised a highthroughput assay to quantify the activity of ∼15,000 fully designed core promoters that we integrated and expressed from a fixed location within the human genome. We find that core promoters drive transcription unidirectionally, and that sequences originating from promoters exhibit stronger activity than sequences originating from enhancers. Testing multiple combinations and distances of core promoter elements, we observe a positive effect of TATA and Initiator, a negative effect of BREu and BREd, and a 10bp periodicity in the optimal distance between the TATA and the Initiator. By comprehensively screening TF binding-sites, we show that site orientation has little effect, that the effect of binding site number on expression is factor-specific, and that there is a striking agreement between the effect of binding site multiplicity in our assay and the tendency of the TF to appear in homotypic clusters throughout the genome. Overall, our results systematically assay the elements that drive expression in core- and proximal-promoter regions and shed light on organization principles of regulatory regions in the human genome.
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Cites
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- Authors
- Weingarten-Gabbay, S., Nir, R., Lubliner, S., Sharon, E., Kalma, Y., Weinberger, A., & Segal, E.
- Affiliations
- Weizmann Institute of Science (IL)
- Tel Aviv Sourasky Medical Center (IL)
- Corresponding author
- Weingarten-Gabbay, Shira
- Segal, Eran
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2017-08-10
- OpenAlex
- W2744618343
- Cited by
- 6
- References
- 6
- Citations by year
- 2019: 3 · 2018: 3
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- core promoter, transcriptional regulation, cis-regulatory elements, TATA box, initiator element, BRe, transcription factor binding sites, enhancers, proximal promoter, human genome organization
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