Perspectives on Gene Regulatory Network Evolution

Abstract

Animal development proceeds through the activity of genes and their cis-regulatory modules, working together in sets of gene regulatory networks (GRNs). Emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here different aspects of GRN evolution and argue that developmental system drift, in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution. Advances in methods to discover related cis-regulatory modules in diverse insect species, a critical requirement for detailed GRN characterization, are also described.

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

“…Despite the many similarities, there are also several differences in gene usage between the adult and embryonic skeletogenic programs in sea urchins. With respect to effector genes, for example, distinct members of the sm30 gene family are expressed in embryos and adults (Livingston et al, 2006 Halfon, 2017). Developmental systems drift may also contribute to taxonspecific differences in the embryonic skeletogenic GRN.…”

Thermal Response of Epigenetic Genes Informs Turtle Sex Determination with and without Sex Chromosomes

“…A similar trend was seen in Apalone , except that more genes were upregulated at stages 15 and 19 compared to Chrysemys . Why this occurs is unclear, but perhaps it is partly explained by developmental systems drift where gene regulatory networks diverge neutrally but maintain the production of conserved phenotypes [Halfon, 2017]. That is, the divergence of relict thermosensitive transcription in Apalone as observed here and previously [Valenzuela, 2008a, b;Radhakrishnan et al, 2017b] via genetic drift would not have been opposed by natural selection, because GSD evolution in this lineage would have rendered sexual development independent of the thermal response of these genes to environmental signals.…”

Characterization of a novel Drosophila melanogaster cis‐regulatory module that drives gene expression to the larval tracheal system and adult thoracic musculature

“…cis-regulatory module, dorsal longitudinal muscles, Drosophila melanogaster, tracheal system 1 | INTRODUCTION Gene regulatory networks (GNRs) depict the molecular genetic control of a given cell function (Halfon, 2017). More specifically, GNRs describe the interactions that occur between cis-regulatory modules (CRMs), the regulatory DNA, and transcription factors.…”

“…More specifically, GNRs describe the interactions that occur between cis-regulatory modules (CRMs), the regulatory DNA, and transcription factors. GNRs evolve at the level of both transcription factors and CRMs, and the identification of CRMs is an essential step toward understanding the mechanisms underlying their evolution (Halfon, 2017). Combinations of multiple transcription factors acting together in a given cell type activate specific sets of CRMs that results in the establishment of patterns of differential gene expression during development (Martin, Organista, & de Celis, 2016;Rebeiz, Patel, & Hinman, 2015).…”

“…Combinations of multiple transcription factors acting together in a given cell type activate specific sets of CRMs that results in the establishment of patterns of differential gene expression during development (Martin, Organista, & de Celis, 2016;Rebeiz, Patel, & Hinman, 2015). GNRs evolve at the level of both transcription factors and CRMs, and the identification of CRMs is an essential step toward understanding the mechanisms underlying their evolution (Halfon, 2017).…”