scholarly journals Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms

genesis ◽  
2014 ◽  
Vol 52 (3) ◽  
pp. 193-207 ◽  
Author(s):  
Veronica F. Hinman ◽  
Alys M. Cheatle Jarvela
Keyword(s):  
Gene Regulatory Network ◽  
Comparative Studies ◽  
Regulatory Network ◽  
Network Evolution ◽  
Developmental Gene ◽  
Gene Regulatory

scholarly journals LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e67434 ◽  
Author(s):  
Mingyi Wang ◽  
Jerome Verdier ◽  
Vagner A. Benedito ◽  
Yuhong Tang ◽  
Jeremy D. Murray ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Comparative Studies ◽  
Regulatory Network ◽  
Prediction Server ◽  
Network Prediction ◽  
Gene Regulatory

scholarly journals Gene Regulatory Network Evolution Through Augmenting Topologies

2015 ◽  
Vol 19 (6) ◽  
pp. 823-837 ◽  
Author(s):  
Sylvain Cussat-Blanc ◽  
Kyle Harrington ◽  
Jordan Pollack
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Network Evolution ◽  
Gene Regulatory

scholarly journals The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network

PLoS Biology ◽  
2013 ◽  
Vol 11 (10) ◽  
pp. e1001696 ◽  
Author(s):  
David A. Garfield ◽  
Daniel E. Runcie ◽  
Courtney C. Babbitt ◽  
Ralph Haygood ◽  
William J. Nielsen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Gene Expression Variation ◽  
Developmental Gene ◽  
Expression Variation ◽  
Gene Regulatory ◽  
The Impact

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 Interpreting ruminant specific conserved non-coding elements by developmental gene regulatory network

2021 ◽  
Author(s):  
Xiangyu Pan ◽  
Zhaoxia Ma ◽  
Xinqi Sun ◽  
Hui Li ◽  
Tingting Zhang ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Complex Traits ◽  
Systematic Approach ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Developmental Gene ◽  
Gene Regulatory ◽  
Evo Devo ◽  
Interpretation Method

Biologists long recognized that the genetic information encoded in DNA leads to trait innovation via gene regulatory network (GRN) in development. Here, we generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep and revealed 1,601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we developed a Conserved Non-coding Element interpretation method by gene Regulatory network (CNEReg) to define toolkit transcription factors (TTF) and model its regulation on rumen specific gene via batteries of active-RSCNEs during development. Our developmental GRN reveals 18 TTFs and 313 active-RSCNEs regulating the functional modules of the rumen and identifies OTX1, SOX21, HOXC8, SOX2, TP63, PPARG and 16 active-RSCNEs that functionally distinguish the rumen from the esophagus. We argue that CNEReg is an attractive systematic approach to integrate evo-devo concepts with omics data to understand how gene regulation evolves and shapes complex traits.

scholarly journals Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

2012 ◽  
Vol 8 (7) ◽  
pp. e1002589 ◽  
Author(s):  
Anton Crombach ◽  
Karl R. Wotton ◽  
Damjan Cicin-Sain ◽  
Maksat Ashyraliyev ◽  
Johannes Jaeger
Keyword(s):  
Reverse Engineering ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Developmental Gene ◽  
Gene Regulatory

scholarly journals Genetic Signatures of Evolution of the Pluripotency Gene Regulating Network across Mammals

2020 ◽  
Vol 12 (10) ◽  
pp. 1806-1818
Author(s):  
Yoshinori Endo ◽  
Ken-ichiro Kamei ◽  
Miho Inoue-Murayama
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Regulatory Elements ◽  
Network Evolution ◽  
Pluripotency Gene ◽  
Fundamental Biological Process ◽  
Gene Regulatory ◽  
Taxonomic Groups

Abstract Mammalian pluripotent stem cells (PSCs) have distinct molecular and biological characteristics among species, but to date we lack a comprehensive understanding of regulatory network evolution in mammals. Here, we carried out a comparative genetic analysis of 134 genes constituting the pluripotency gene regulatory network across 48 mammalian species covering all the major taxonomic groups. We report that mammalian genes in the pluripotency regulatory network show a remarkably high degree of evolutionary stasis, suggesting the conservation of fundamental biological process of mammalian PSCs across species. Nevertheless, despite the overall conservation of the regulatory network, we discovered rapid evolution of the downstream targets of the core regulatory elements and specific amino acid residues that have undergone positive selection. Our data indicate development of lineage-specific pluripotency regulating networks that may explain observed variations in some characteristics of mammalian PSCs. We further revealed that positively selected genes could be associated with species’ unique adaptive characteristics that were 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.

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