The interactions between transcription factors (TFs) and their DNA binding sites are central to gene regulatory networks. Genetic variation in TFs or their DNA binding sites can contribute to differences in traits among individuals. However, the role of interactions among such genetic variants remains poorly understood. Existing high-throughput technologies for assaying the DNA binding activities of TFs (or TF variants) are ?1-by-many? approaches, in which a given protein is assayed for its binding to a large library of different DNA sequences, or alternatively assay a large library of protein variants for activity from a given DNA sequence. A major hurdle in characterization of TF coding variants and DNA noncoding variants is the lack of a high-throughput ?many-by-many? technology that would enable testing of a large collection of TF coding variants for binding to a library of different DNA binding site sequences; such DNA binding site sequences could represent either a large collection of substitutions in a TF's DNA binding site motif, or alternatively putative cis-regulatory variants. The primary goal of this project is to develop novel technology, termed All-Variant Analysis of Transcription factor Affinity and Recognition (AVATAR), for highly parallel analysis of a library of TF coding variants for interaction with a library of variants in their DNA binding sites. We will prioritize human TFs that are associated with diseases and for which disease-associated mutations or naturally occurring polymorphisms predicted to have damaged DNA binding activity have been identified. Such technology would permit: more extensive experimental testing of putatively damaging TF coding variants whose precise effects on DNA binding activity are not currently predictable (unpublished results); an improved understanding of specificity- determining residues and TF-DNA `recognition rules' for various TF classes; and identification of potential genetic interactions between TF coding variants and noncoding variants in TF binding sites (TFBSs). !

Public Health Relevance

Genetic variation in transcription factors (TFs) or their DNA binding sites can contribute to differences in traits among individuals. However, the role of interactions among such genetic variants remains poorly understood. In this project, we will develop novel, high-throughput technology for the analysis of variation in TFs and their DNA binding sites, and will apply it to investigate human genetic variants. !

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21HG010200-02
Application #
9767247
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Pazin, Michael J
Project Start
2018-08-20
Project End
2021-05-31
Budget Start
2019-06-01
Budget End
2020-05-31
Support Year
2
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Brigham and Women's Hospital
Department
Type
DUNS #
030811269
City
Boston
State
MA
Country
United States
Zip Code
02115