A special issue of Developmental Biology will appear on June 1, devoted entirely to papers on developmental gene regulatory networks and related subjects. Its advent signals the interdisciplinary revolution that is sweeping across the landscape of bioscience, as there emerges a new level of understanding of biological systems. A system-level synthesis of genomics, developmental biology, evolutionary biology, computational biology, and gene regulation molecular biology underlies gene regulatory network analysis.

Genomics ◽  
2002 ◽  
Vol 79 (6) ◽  
pp. 749
Keyword(s):  
Developmental Biology ◽  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
System Level ◽  
Special Issue ◽  
Developmental Gene ◽  
Gene Regulatory ◽  
Level Of Understanding

Using ascidian embryos to study the evolution of developmental gene regulatory networks

2005 ◽  
Vol 83 (1) ◽  
pp. 75-89 ◽  
Author(s):  
Angela C Cone ◽  
Robert W Zeller
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Regulatory Mechanisms ◽  
Developmental Gene ◽  
Regulatory Architecture ◽  
Ascidian Embryos ◽  
Gene Regulatory ◽  
Mode Of Development ◽  
Ascidian Embryo

Ascidians are ideally positioned taxonomically at the base of the chordate tree to provide a point of comparison for developmental regulatory mechanisms that operate among protostomes, non-chordate deuterostomes, invertebrate chordates, and vertebrates. In this review, we propose a model for the gene regulatory network that gives rise to the ascidian notochord. The purpose of this model is not to clarify all of the interactions between molecules of this network, but to provide a working schematic of the regulatory architecture that leads to the specification of endoderm and the patterning of mesoderm in ascidian embryos. We describe a series of approaches, both computational and biological, that are currently being used, or are in development, for the study of ascidian embryo gene regulatory networks. It is our belief that the tools now available to ascidian biologists, in combination with a streamlined mode of development and small genome size, will allow for more rapid dissection of developmental gene regulatory networks than in more complex organisms such as vertebrates. It is our hope that the analysis of gene regulatory networks in ascidians can provide a basic template which will allow developmental biologists to superimpose the modifications and novelties that have arisen during deuterostome evolution.

scholarly journals Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses

2015 ◽  
Vol 112 (30) ◽  
pp. E4075-E4084 ◽  
Author(s):  
Eric M. Erkenbrack ◽  
Eric H. Davidson
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Strongylocentrotus Purpuratus ◽  
Late Paleozoic ◽  
Monophyletic Clade ◽  
Developmental Gene ◽  
Permian Extinction ◽  
Gene Regulatory ◽  
Functional Analyses

Evolution of animal body plans occurs with changes in the encoded genomic programs that direct development, by alterations in the structure of encoded developmental gene-regulatory networks (GRNs). However, study of this most fundamental of evolutionary processes requires experimentally tractable, phylogenetically divergent organisms that differ morphologically while belonging to the same monophyletic clade, plus knowledge of the relevant GRNs operating in at least one of the species. These conditions are met in the divergent embryogenesis of the two extant, morphologically distinct, echinoid (sea urchin) subclasses, Euechinoidea and Cidaroidea, which diverged from a common late Paleozoic ancestor. Here we focus on striking differences in the mode of embryonic skeletogenesis in a euechinoid, the well-known model Strongylocentrotus purpuratus (Sp), vs. the cidaroid Eucidaris tribuloides (Et). At the level of descriptive embryology, skeletogenesis in Sp and Et has long been known to occur by distinct means. The complete GRN controlling this process is known for Sp. We carried out targeted functional analyses on Et skeletogenesis to identify the presence, or demonstrate the absence, of specific regulatory linkages and subcircuits key to the operation of the Sp skeletogenic GRN. Remarkably, most of the canonical design features of the Sp skeletogenic GRN that we examined are either missing or operate differently in Et. This work directly implies a dramatic reorganization of genomic regulatory circuitry concomitant with the divergence of the euechinoids, which began before the end-Permian extinction.

scholarly journals Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm

RSC Advances ◽  
2017 ◽  
Vol 7 (37) ◽  
pp. 23222-23233 ◽  
Author(s):  
Wei Liu ◽  
Wen Zhu ◽  
Bo Liao ◽  
Haowen Chen ◽  
Siqi Ren ◽  
...  
Keyword(s):  
Systems Biology ◽  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Network Structure ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Central Problem ◽  
Expression Data ◽  
Redundancy Reduction ◽  
Gene Regulatory

Inferring gene regulatory networks from expression data is a central problem in systems biology.

scholarly journals Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids

Development ◽  
2018 ◽  
Vol 145 (24) ◽  
pp. dev167288 ◽  
Author(s):  
Eric M. Erkenbrack ◽  
Eric H. Davidson ◽  
Isabelle S. Peter
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Regulatory State ◽  
Developmental Gene ◽  
Gene Regulatory

Modeling Evolution of Developmental Gene Regulatory Networks

2021 ◽  
pp. 1013-1029
Author(s):  
Renske M. A. Vroomans ◽  
Kirsten H. W. J. ten Tusscher
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Gene ◽  
Gene Regulatory

scholarly journals Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks

2009 ◽  
Vol 25 (15) ◽  
pp. 1898-1904 ◽  
Author(s):  
Chang H. Seo ◽  
Jeong-Rae Kim ◽  
Man-Sun Kim ◽  
Kwang-Hyun Cho
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Gene ◽  
Hub Genes ◽  
Positive Feedbacks ◽  
Gene Regulatory

Developmental gene regulatory networks in the zebrafish embryo

2009 ◽  
Vol 1789 (4) ◽  
pp. 279-298 ◽  
Author(s):  
Tzu-Min Chan ◽  
William Longabaugh ◽  
Hamid Bolouri ◽  
Hua-Ling Chen ◽  
Wen-Fang Tseng ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Zebrafish Embryo ◽  
Developmental Gene ◽  
Gene Regulatory
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