scholarly journals A systems biology approach uncovers the core gene regulatory network governing iridophore fate choice from the neural crest

PLoS Genetics ◽  
2018 ◽  
Vol 14 (10) ◽  
pp. e1007402 ◽  
Author(s):  
Kleio Petratou ◽  
Tatiana Subkhankulova ◽  
James A. Lister ◽  
Andrea Rocco ◽  
Hartmut Schwetlick ◽  
...  
Keyword(s):  
Systems Biology ◽  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Core Gene ◽  
The Core ◽  
Gene Regulatory

scholarly journals Migrating into Genomics with the Neural Crest

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Marianne E. Bronner
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Neural Crest Cells ◽  
Embryonic Cell ◽  
Putative Gene ◽  
Peripheral Neurons ◽  
Neural Plate Border ◽  
The Central Nervous System ◽  
Gene Regulatory

Neural crest cells are a fascinating embryonic cell type, unique to vertebrates, which arise within the central nervous system but emigrate soon after its formation and migrate to numerous and sometimes distant locations in the periphery. Following their migratory phase, they differentiate into diverse derivatives ranging from peripheral neurons and glia to skin melanocytes and craniofacial cartilage and bone. The molecular underpinnings underlying initial induction of prospective neural crest cells at the neural plate border to their migration and differentiation have been modeled in the form of a putative gene regulatory network. This review describes experiments performed in my laboratory in the past few years aimed to test and elaborate this gene regulatory network from both an embryonic and evolutionary perspective. The rapid advances in genomic technology in the last decade have greatly expanded our knowledge of important transcriptional inputs and epigenetic influences on neural crest development. The results reveal new players and new connections in the neural crest gene regulatory network and suggest that it has an ancient origin at the base of the vertebrate tree.

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 Ancient Evolutionary Origin of the Neural Crest Gene Regulatory Network

2007 ◽  
Vol 13 (3) ◽  
pp. 405-420 ◽  
Author(s):  
Tatjana Sauka-Spengler ◽  
Daniel Meulemans ◽  
Matthew Jones ◽  
Marianne Bronner-Fraser
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Evolutionary Origin ◽  
Gene Regulatory

scholarly journals A direct role for murine Cdx proteins in the trunk neural crest gene regulatory network

Development ◽  
2016 ◽  
Vol 143 (8) ◽  
pp. 1363-1374 ◽  
Author(s):  
Oraly Sanchez-Ferras ◽  
Guillaume Bernas ◽  
Omar Farnos ◽  
Aboubacrine M. Touré ◽  
Ouliana Souchkova ◽  
...  
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Direct Role ◽  
Trunk Neural Crest ◽  
Gene Regulatory

scholarly journals Genetic signatures of evolution of the pluripotency gene regulating network across mammals

2020 ◽  
Author(s):  
Yoshinori Endo ◽  
Ken-ichiro Kamei ◽  
Miho Inoue-Murayama
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Network Evolution ◽  
Downstream Targets ◽  
The Core ◽  
Regulatory Circuit ◽  
Pluripotency Gene ◽  
Gene Regulatory

AbstractMammalian pluripotent stem cells (PSCs) have distinct molecular and biological characteristics, but we lack a comprehensive understanding of regulatory network evolution in mammals. Here, we applied a comparative genetic analysis of 134 genes constituting the pluripotency gene regulatory network across 48 mammalian species covering all the major taxonomic groups. We found evolutionary conservation in JAK-STAT and PI3K-Akt signaling pathways, suggesting equivalent capabilities in self-renewal and proliferation of mammalian PSCs. On the other hand, we discovered rapid evolution of the downstream targets of the core regulatory circuit, providing insights into variations of characteristics. Our data indicate that the variations in the PSCs characteristics may be due to positive selections in the downstream targets of the core regulatory circuit. We further reveal that positively selected genes can be associated with species unique adaptation that is not dedicated to regulation of PSCs. These results provide important insight into the evolution of the pluripotency gene regulatory network underlying variations in characteristics of mammalian PSCs.

scholarly journals Using Genomic Resources for Linkage Analysis in Peromyscus with an Application for Characterizing Dominant Spot

2020 ◽  
Author(s):  
Zhenhua Shang ◽  
David J Horovitz ◽  
Ronald H McKenzie ◽  
Jessica L Keisler ◽  
Michael R Felder ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Neural Crest ◽  
Candidate Gene ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cholesterol Metabolism ◽  
Deer Mouse ◽  
Genomic Resources ◽  
Hybrid Offspring ◽  
Gene Regulatory

Abstract Background: Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring, coupled with developing genomic resources, enables researchers to conduct linkage analysis studies to identify genomic loci associated with specific traits. Results: We used available genomic data to identify DNA polymorphisms between P. maniculatus and P. polionotus and used the polymorphic data to identify the range of genetic complexity that underlies physiological and behavioral differences between the species, including cholesterol metabolism and genes associated with autism. In addition, we used the polymorphic data to conduct a candidate gene linkage analysis for the Dominant spot trait and determined that Dominant spot is linked to a region of chromosome 20 that contains a strong candidate gene, Sox10. During the linkage analysis, we found that the spot size varied quantitively in affected Peromyscus based on genetic background. Conclusions: The expanding genomic resources for Peromyscus facilitate their use in linkage analysis studies, enabling the identification of loci associated with specific traits. More specifically, we have linked a coat color spotting phenotype, Dominant spot, with Sox10, a member the neural crest gene regulatory network, and that there are likely two genetic modifiers that interact with Dominant spot. These results establish Peromyscus as a model system for identifying new alleles of the neural crest gene regulatory network.

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