Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

By K. Nitta, A. Jolma, Yimeng Yin, E. Morgunova, Teemu Kivioja, Junaid Akhtar, K. Hens, Jarkko Toivonen, B. Deplancke, E. Furlong and 1 more. 2015

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Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells. DOI: http://dx.doi.org/10.7554/eLife.04837.001

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “Although not all 40 bp sequences were interrogated due to the limiting amount of DNA, TFs do not generally bind to exact matches of 40 bp (80 bits of information); using the amounts of DNA used, HT-SELEX allows for identification of motifs whose information content is in the order of ~40 bits, excee”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “…in enhancer activity, as enhancer elements are subject to high rates of turnover (Arnold et al., 2014; Villar et al., 2015) while both coactivator-TF interfaces and TF DNA-binding specificities appear to be well conserved over evolutionary timescales (Minezaki et al., 2006; Nitta et al., 2015).”
The Human Transcription Factors. (2018, unknown): “TF orthologs between human and Drosophila often display virtually identical sequence specificity (Nitta et al., 2015).”