PT  - JOURNAL ARTICLE
AU  - Weingarten-Gabbay, Shira
AU  - Nir, Ronit
AU  - Lubliner, Shai
AU  - Sharon, Eilon
AU  - Kalma, Yael
AU  - Weinberger, Adina
AU  - Segal, Eran
TI  - Deciphering Transcriptional Regulation of Human Core Promoters
AID  - 10.1101/174904
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 174904
4099  - http://biorxiv.org/content/early/2017/08/30/174904.short
4100  - http://biorxiv.org/content/early/2017/08/30/174904.full
AB  - 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.