Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins

Abstract

Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life1, but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the genus Heliocidaris that exhibit highly divergent life histories and in an outgroup species. Signatures of positive selection and changes in chromatin status within putative gene regulatory elements are both enriched on the branch leading to the derived life history, and particularly so near core dGRN genes; in contrast, positive selection within protein-coding regions have at most a modest enrichment in branch and function. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near dGRN genes with conserved roles in cell fate specification. Experimentally perturbing the function of three key transcription factors reveals profound evolutionary changes in the earliest events that pattern the embryo, disrupting regulatory interactions previously conserved for ∼225 million years. Together, these results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change and that even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.

Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins

“…4d ). This protein has gene regulatory functions in diverse biological contexts ranging from antioxidant response and cellular defense to metabolism and stem cell quiescence (Tonelli, et al 2018), which in this case, could be related to derived embryonic detoxification and physiological systems (Tsushima, et al 1995; Davidson, et al 2019) or early cell lineage specification programs (Wray and Raff 1989, 1990; Davidson, et al 2021) of He . Taken together, regulatory elements tasked with wiring the ancestral sea urchin dGRN have accumulated a disproportionate number of mutations on the He branch.…”

“…These analyses provide a simultaneous comparison of gene regulatory mechanisms in two ways: (1) availability of CREs to transcription factor binding associated with differential chromatin configuration (accessibility) and (2) affinity of transcription factor binding to CREs via changes in nucleotide sequence, as evidenced by motif analysis and signatures of positive selection. Importantly, the genomes of these sea urchin species were assembled and annotated using an identical set of sequencing technology and methodology (Davidson, et al 2020; Davidson, et al 2021), minimizing technical bias and permitting high resolution identification of changes in regulatory element activity.…”

“…These trimmed and filtered alignments serve as “query” sequences of tests for selection. To generate a neutral reference for comparison, ten orthologous, neutral sites were randomly selected from a curated set of ∼88,000 putatively neutral sequences (Davidson, et al 2021) (Data S2) and concatenated into a single neutral reference sequence. Then, substitution rates of both the query and randomly concatenated neutral reference were estimated using phyloFit (Siepel and Haussler 2004), and the zeta score was calculated as the ratio of the query substitution rate to the neutral reference substitution rate.…”

“…These trimmed and filtered alignments serve as “query” sequences of tests for selection. To generate a neutral reference for comparison, ten orthologous, neutral sites were randomly selected from a curated set of ∼88,000 putatively neutral sequences (Davidson, et al 2021) (Data S2) and concatenated into a single neutral reference sequence. A global neutral reference, rather than a local reference, was implemented to more conservatively estimate signatures of positive selection as recent work has demonstrated a local neutral reference may more likely overestimate positive selection – an especially acute issue in smaller, gene-dense genomes (Berrio et al, 2020).…”

“…For instance, dorso-ventral and left-right axis establishment occurs considerably earlier in this species (Henry, et al 1990), concordant with accelerated rudiment development and metamorphosis (Williams and Anderson 1975). At other embryonic domains, specification of cell lineages such as those responsible for mesenchymal tissue types have been delayed, lost, or spatially rearranged (Wray and Raff 1990; Klueg, et al 1997; Wilson, Andrews, Rudolf Turner, et al 2005; Davidson, et al 2021). Recent transcriptomic studies have shown that expression profiles of key developmental gene regulatory network (dGRN) genes in this species have diverged from the highly conserved expression patterns in planktotrophic species (Israel, et al 2016), and many of these regulatory changes are predicted to be based in cis (Wang, et al 2020).…”