The long-term goal of this project is to understand the combinatorial rules that govern the interactions between transcription factor binding sites (TFBS). Through these rules, combinations of TFBS specify an enormous diversity of complex gene expression patterns. Normal growth and development depends on the tight control of TFBS over levels of gene expression in both time and space, and aberrant regulation of gene expression underlies many genetic diseases. Although much progress has been made identifying TFBS, and the transcription factors (TFs) that bind to them, much less is known about how TFBS interact with each other to generate specific patterns of gene expression. This lack of knowledge is manifested in the inability to predict the expression patterns specified by novel combinations of TFBS, and the inability to distinguish true regulatory regions in the genome from spurious clusters of TFBS. The proposal addresses these problems through experiments designed to unravel the mechanisms that govern TFBS interactions. Large libraries of simplified synthetic promoters will be constructed and assayed for expression and TF occupancy. The data from these libraries will be analyzed with a thermodynamic model that describes the physical interactions between TFBS, TFs and RNA polymerase. The models produced from synthetic promoters will be explicitly tested on genomic promoters.
In Aim 1 this system will be used to study the extent to which the simple occupancy of TFBS by TFs determines complex patterns of gene expression.
In Aim 2 the system will be extended to determine the effects of additional variables on combinatorial cis-regulation, including the strength of the TATA box, chromosomal location, and chromatin modifications. The successful completion of the aims of this proposal will result in a quantitative and molecular understanding of the rules underlying combinatorial cis-regulation. Such an understanding is necessary to empower biomedical applications, such as stem cell engineering, that are based on manipulating gene expression patterns. The results produced from this proposal will also help guide the annotation of the large regions of non-coding DNA in the genome that specify gene expression patterns. Finally, a clear understanding of TFBS interactions will help the identification and interpretation of disease causing genetic variants that affect cis-regulation.

Public Health Relevance

In addition to serving as a """"""""parts list"""""""" of genes, the genome also encodes information that controls precisely where, when, and to what levels genes are produced (expressed). Strict control of gene expression is critical for normal growth and development, and aberrant gene expression underlies many genetic diseases, including cancer. Successful completion of the experiments in this proposal will illuminate the processes through which information in the genome controls precise patterns of gene expression, and will help us interpret disease causing genetic variants that alter normal patterns of gene expression.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM092910-03
Application #
8403073
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Krasnewich, Donna M
Project Start
2011-01-01
Project End
2014-12-31
Budget Start
2013-01-01
Budget End
2013-12-31
Support Year
3
Fiscal Year
2013
Total Cost
$337,350
Indirect Cost
$115,409
Name
Washington University
Department
Genetics
Type
Schools of Medicine
DUNS #
068552207
City
Saint Louis
State
MO
Country
United States
Zip Code
63130
Cottrell, Kyle A; Chaudhari, Hemangi G; Cohen, Barak A et al. (2018) PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs. Nat Commun 9:301
Maricque, Brett B; Chaudhari, Hemangi G; Cohen, Barak A (2018) A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity. Nat Biotechnol :
Staller, Max V; Holehouse, Alex S; Swain-Lenz, Devjanee et al. (2018) A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Syst 6:444-455.e6
Chaudhari, Hemangi G; Cohen, Barak A (2018) Local sequence features that influence AP-1 cis-regulatory activity. Genome Res 28:171-181
Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye et al. (2017) Causal Genetic Variation Underlying Metabolome Differences. Genetics 206:2199-2206
Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica et al. (2017) Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Nat Commun 8:14550
White, Michael A; Kwasnieski, Jamie C; Myers, Connie A et al. (2016) A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors. Cell Rep 17:1247-1254
Fiore, Chris; Cohen, Barak A (2016) Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Res 26:778-86
Maricque, Brett B; Dougherty, Joseph D; Cohen, Barak A (2016) A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells. Nucleic Acids Res :
Savic, Daniel; Roberts, Brian S; Carleton, Julia B et al. (2015) Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites. Genome Res 25:1791-800

Showing the most recent 10 out of 19 publications