Sequence-specific transcription factors (TFs) regulate gene expression through their interactions with DNA sequences in the genome. The overarching goal of this project is to continue developing approaches and data sets for understanding the DNA binding specificities of TFs, and to understand the effects of coding polymorphisms with TFs? DNA binding domains on their DNA binding preferences. Identification of TFs? DNA binding specificities is important in understanding transcriptional regulatory networks, in particular in the prediction of cis regulatory modules, inference of cis regulatory codes, and interpretation of in vivo TF binding data and gene expression data. Identification of the DNA binding effects of such polymorphic TF variants will be essential in studies aimed at understanding the gene regulatory effects resulting from natural genetic variation. This project will focus on human TFs associated with diseases, in particular Crohn?s disease, ulcerative colitis, diabetes, autism and other neuropsychiatric disorders. Our results will provide data that will likely be of importance to other systems, and more generally, our data, approaches, technologies, and database will be useful not only for human TFs but also for model organism studies. Specifically, we will: (1) develop systematic approaches for extracting fine-level features of TFs? DNA binding specificity when comparing very similar proteins;(2) generate clone resources and proteins for ~200 total human proteins (reference and polymorphic variants) with disease/trait associations;(3) determine the DNA binding specificities of the ~200 total reference and polymorphic TFs, and identify the effects of coding polymorphisms within TFs on their DNA binding specificities;(4) develop high-throughput, array-based technology for determining the effects of CpG DNA methylation on TF-DNA binding;(5) maintain the UniPROBE database that hosts high-resolution, universal protein binding microarray data on TFs? DNA binding specificities.

Public Health Relevance

This project is focused on better understanding the DNA binding specificities of regulatory transcription factors. In this project, we will transcription factors corresponding to the reference genome, and also those containing polymorphisms that may affect their DNA binding specificities. The findings from this project will provide data on the potential effects of transcription factor polymorphisms on gene regulation.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-F (02))
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Pazin, Michael J
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Brigham and Women's Hospital
United States
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Cheatle Jarvela, Alys M; Brubaker, Lisa; Vedenko, Anastasia et al. (2014) Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol 31:2672-88
Christodoulou, Danos C; Wakimoto, Hiroko; Onoue, Kenji et al. (2014) 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest 124:1364-70
Siggers, Trevor; Reddy, Jessica; Barron, Brian et al. (2014) Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 55:640-8
Zhao, Bo; Barrera, Luis A; Ersing, Ina et al. (2014) The NF-?B genomic landscape in lymphoblastoid B cells. Cell Rep 8:1595-606
Nakagawa, So; Gisselbrecht, Stephen S; Rogers, Julia M et al. (2013) DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci U S A 110:12349-54
Weirauch, Matthew T; Cote, Atina; Norel, Raquel et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol 31:126-34
Jiang, Bo; Liu, Jun S; Bulyk, Martha L (2013) Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. Bioinformatics 29:1390-8
Gordan, Raluca; Shen, Ning; Dror, Iris et al. (2013) Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep 3:1093-104
Siggers, Trevor; Chang, Abraham B; Teixeira, Ana et al. (2012) Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-?B family DNA binding. Nat Immunol 13:95-102
Guo, Xin; Bulyk, Martha L; Hartemink, Alexander J (2012) Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pac Symp Biocomput :104-15

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