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

Kazuhiro R Nitta,Junaid Akhtar,Bart Deplancke,Yimeng Yin,Arttu Jolma,Jarkko Toivonen,Jussi Taipale,Eileen E M Furlong,Teemu Kivioja,Korneel Hens,Ekaterina Morgunova

doi:10.7554/elife.04837

Abstract

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.

Highlights

It is estimated that the divergence between vertebrate and invertebrate lineages occurred over 600 million years ago (Hedges et al, 2006; Peterson et al, 2008)
A collection of cDNAs of DNA binding domains (DBDs) and full-length Drosophila transcription factors (TFs) were compiled based on annotations in FlyTF.org (Pfreundt et al, 2010) and Hens et al (2011), respectively
A total of 760 DBDs and 633 full length fruit fly TF constructs were expressed in E. coli as N-terminal thioredoxin-HIS tag fusion proteins, and subjected to the HT-SELEX process (Figure 1; Supplementary file 1A–C; see ‘Materials and methods’ for details)

Summary

Introduction

It is estimated that the divergence between vertebrate and invertebrate lineages occurred over 600 million years ago (Hedges et al, 2006; Peterson et al, 2008). Protein coding sequences have retained a relatively high level of similarity, whereas homology in gene-regulatory elements is not detectable, despite the fact that many developmental pathways and regulatory relationships between TFs and their target genes have been conserved (see e g., Goodrich et al, 1996; Pichaud and Desplan, 2002; Ciglar and Furlong, 2009). Lack of sequence conservation in gene regulatory elements despite their conserved function could be a consequence of divergence of the gene regulatory code between vertebrates and invertebrates. Several studies have indicated that primary TF DNA binding specificity evolves slowly, and is extremely conserved between mammalian species (see e g., Bohmann et al, 1987; Struhl, 1987; Merika and Orkin, 1993; Amoutzias et al, 2007; Wei et al, 2010; Jolma et al, 2013). The origin of most structural families of TFs dates well before the emergence of mammals, and even predates the

Methods

Results

Conclusion