When genes move to new chromosomal locations they are often expressed at drastically different levels. We will use these chromosome position effects to investigate how different chromosomal locations affect the activity of cis-regulatory sequences (CRS). We propose to measure how the activities of a large and diverse collection of CRS change when they are moved to different chromosomal locations (Aim 1). To collect this data at scale we will introduce a new massively parallel reporter gene assay (MPRA).
We aim to address several questions. 1. What accounts for the differences in regulatory potential between chromosome positions? When the activity of a CRS changes because it moves to a new location, are the changes due to the new chromatin state, the activity of nearby enhancers, or both? 2. When are the regulatory effects of CRS and genome position independent and when do they interact in complex ways? Do interactions depend on the properties of CRS and the specific chromatin landscape? We also propose to complement our investigation of gene expression levels with a study of how genome position influences gene expression dynamics (Aim 2). By measuring the cell- to-cell patterns of mRNA generated by different CRS at different chromosome locations, we will uncover how chromosome environments alter the dynamics of expression. The successful completion of the aims of this proposal will result in a quantitative and molecular understanding of the combinatorial regulation of gene expression by CRS and chromatin environment. A clear understanding of how CRS function in the genome will help identify and interpret disease- causing genetic variants that affect cis-regulation.
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. 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.
|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