Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- 1Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
- 2Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA;
- 3Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27708, USA;
- 4Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina 27606, USA;
- 5Department of Computer Science, Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
Abstract
Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e., paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are coexpressed in the cell and thus can compete for target sites across the genome. However, this competition is rarely taken into account when studying the in vivo binding patterns of eukaryotic TFs. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data show that Cbf1 and Pho4 greatly influence each other's occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs’ expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275145.120.
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Freely available online through the Genome Research Open Access option.
- Received December 15, 2020.
- Accepted May 6, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
