Human gene-centered transcription factor networks for enhancers and disease variants
Program in Systems Biology; Program in Molecular Medicine
Computational Biology | Genomics | Molecular Biology | Molecular Genetics | Systems Biology
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.
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Citation: Cell. 2015 Apr 23;161(3):661-73. doi: 10.1016/j.cell.2015.03.003. Link to article on publisher's site
Fuxman Bass, Juan; Sahni, Nidhi; Shrestha, Shaleen; Garcia-Gonzalez, Aurian; Mori, Akihiro; Bhat, Numana; Yi, Song; Hill, David E.; Vidal, Marc; and Walhout, Albertha J. M., "Human gene-centered transcription factor networks for enhancers and disease variants" (2015). Program in Systems Biology Publications and Presentations. 58.