Significant new insights have emerged from the analysis of a gene regulatory network (GRN) that underlies the development of the endoskeleton of the sea urchin embryo. Comparative studies have revealed ways in which this GRN has been modified (and conserved) during echinoderm evolution, and point to mechanisms associated with the evolution of a new cell lineage. The skeletogenic GRN has also re...

The neural crest is a multipotent stem cell–like population that gives rise to a wide range of derivatives in the vertebrate embryo including elements of the craniofacial skeleton and peripheral nervous system as well as melanocytes. The neural crest forms in a series of regulatory steps that include induction and specification of the prospective neural crest territory–neural plat...

A wealth of physical interaction data between transcription factors (TFs) and DNA has been generated, but these interactions often do not have apparent regulatory consequences. Thus, equating physical interaction data with gene regulatory networks (GRNs) is problematic. Here, we comprehensively assay TF activity, rather than binding, to construct a network of gene regulatory interactions in the...

The Gene Regulatory Network (GRN) specifies the series of regulatory interactions between different genes. A target gene is interacted by a signal which is originated from the expression of its regulator gene. A gene is known to be expressed when it synthesizes a protein and the degree of synthesizing the protein determines the level of its expression. The same gene can behave as a 'target' in ...

Motivated by studying synchronization mechanisms in gene regulatory networks (GRNs) and their relation to evolutionary events such as genetic duplication redundancy, we consider two types of mathematical dynamical models GRNs that depict general additive (SUM model) or multiplicative (MULT regulations. By a synchrony pattern mean clusters synchronized genes whose states coincide for all time. T...

Evolutionary change in animal morphology results from alteration of the functional organization of the gene regulatory networks (GRNs) that control development of the body plan. A major mechanism of evolutionary change in GRN structure is alteration of cis-regulatory modules that determine regulatory gene expression. Here we consider the causes and consequences of GRN evolution. Although some G...

Despite a long-standing interest in the genetic basis of morphological diversity, the molecular mechanisms that give rise to developmental variation are incompletely understood. Here, we use comparative transcriptomics coupled with the construction of gene coexpression networks to predict a gene regulatory network (GRN) for leaf development in tomato and two related wild species with strikingly...

Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrow...

Of the five echinoderm classes, only the modern sea urchins (euechinoids) generate a precociously specified embryonic micromere lineage that ingresses before gastrulation and then secretes the biomineral embryonic skeleton. The gene regulatory network (GRN) underlying the specification and differentiation of this lineage is now known. Many of the same differentiation genes as are used in the bi...

Abstract Heart formation in the zebrafish involves a rapid, complex series of morphogenetic events three-dimensional space that spans cardiac lineage specification through to chamber and maturation. This process is tightly orchestrated by gene regulatory network (GRN), which ensures precise spatio-temporal deployment genes critical for heart formation. Alterations timing or spatial localisation...