Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development

Abstract

Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs by using ChIP-sequencing and associates these orthologs with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although nonoverlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low-affinity binding motifs is significantly depressed in sea urchins compared with sea star, but both motif types are associated with genes from a range of functional categories. Only a small fraction (∼10%) of genes are predicted to be orthologous targets. Collectively, these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms and that the targets and the binding motifs in associated cis-regulatory sequences are dispersed throughout the hierarchy of the GRN, rather than being biased toward terminal process or discrete functional blocks, which suggests extensive evolutionary tinkering.Tbrain | echinoderm | binding site affinity | ChIP-seq

Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis

“…ChIP was performed as previously described (Cary et al, 2017;Cheatle Jarvela et al, 2014;Mortazavi et al, 2006), with some modifications (see supplementary Materials and Methods). Three independent cultures of S. purpuratus were collected and processed at the mesenchyme blastula stage (24 hpf ) ( Fig.…”

From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms

“…Thus, Alx1 provides a particularly striking example of a specific evolutionary change in transcription factor sequence that has led to a major shift in developmental function (see Lynch & Wagner, ). Another transcription factor in the PMC GRN, Tbr , has also undergone significant protein sequence changes, as evidenced by subtly different DNA binding preferences of the sea star and sea urchin orthologs both in vivo and in vitro (Cary, Cheatle Jarvela, Francolini, & Hinman, ; Cheatle‐Jarvela et al, ).…”

Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression

“…Recent manipulations of enhancer sequences across multiple organisms have emphasized the importance of low- and medium-affinity protein – DNA interactions in generating specific developmental expression patterns without ectopic induction ( Lorberbaum et al, 2016 ; Crocker et al, 2015 ; Cary et al, 2017 ; Farley et al, 2015 ). In addition to sub-optimized protein – DNA interactions, these studies have also noted that the clustering of multiple low-affinity sites (or multiple enhancers) is capable of restoring robust activation while maintaining specificity.…”