Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Deciphering Transcriptional Regulation of Human Core Promoters

Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger, Eran Segal
doi: https://doi.org/10.1101/174904
Shira Weingarten-Gabbay
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: shira.gabbay@weizmann.ac.il eran.segal@weizmann.ac.il
Ronit Nir
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
3Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shai Lubliner
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eilon Sharon
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
4Department of Genetics, Stanford University, Stanford, California, USA
5Department of Biology, Stanford University, Stanford, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yael Kalma
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
6IVF Lab and Wolfe PGD-Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adina Weinberger
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eran Segal
1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: shira.gabbay@weizmann.ac.il eran.segal@weizmann.ac.il
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted August 30, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Deciphering Transcriptional Regulation of Human Core Promoters
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Deciphering Transcriptional Regulation of Human Core Promoters
Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger, Eran Segal
bioRxiv 174904; doi: https://doi.org/10.1101/174904
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Deciphering Transcriptional Regulation of Human Core Promoters
Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger, Eran Segal
bioRxiv 174904; doi: https://doi.org/10.1101/174904

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3514)
  • Biochemistry (7367)
  • Bioengineering (5347)
  • Bioinformatics (20326)
  • Biophysics (10046)
  • Cancer Biology (7777)
  • Cell Biology (11353)
  • Clinical Trials (138)
  • Developmental Biology (6453)
  • Ecology (9980)
  • Epidemiology (2065)
  • Evolutionary Biology (13357)
  • Genetics (9373)
  • Genomics (12614)
  • Immunology (7725)
  • Microbiology (19104)
  • Molecular Biology (7465)
  • Neuroscience (41153)
  • Paleontology (301)
  • Pathology (1235)
  • Pharmacology and Toxicology (2142)
  • Physiology (3180)
  • Plant Biology (6880)
  • Scientific Communication and Education (1276)
  • Synthetic Biology (1900)
  • Systems Biology (5328)
  • Zoology (1091)