scholarly journals A developmental gene regulatory network for C. elegans anchor cell invasion

Development ◽  
2019 ◽  
Vol 147 (1) ◽  
pp. dev185850 ◽  
Author(s):  
Taylor N. Medwig-Kinney ◽  
Jayson J. Smith ◽  
Nicholas J. Palmisano ◽  
Sujata Tank ◽  
Wan Zhang ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Cell Invasion ◽  
Regulatory Network ◽  
Developmental Gene ◽  
C Elegans ◽  
Gene Regulatory ◽  
Anchor Cell

scholarly journals A developmental gene regulatory network for invasive differentiation of theC. elegansanchor cell

2019 ◽  
Author(s):  
Taylor N. Medwig-Kinney ◽  
Jayson J. Smith ◽  
Nicholas J. Palmisano ◽  
Sujata Tank ◽  
Wan Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Cell Fate ◽  
Regulatory Network ◽  
Cell Biology ◽  
Type I ◽  
Cell Specification ◽  
C Elegans ◽  
Gene Regulatory ◽  
Anchor Cell

ABSTRACTCellular invasion is a key part of development, immunity, and disease. Using thein vivomodel ofC. elegansanchor cell invasion, we characterize the gene regulatory network that promotes invasive differentiation. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conserved transcription factors,fos-1a(Fos),egl-43(EVI1/MEL),hlh-2(E/Daughterless) andnhr-67(NR2E1/TLX), that mediate anchor cell specification and/or invasive differentiation. Connections between these transcription factors and the underlying cell biology that they regulate is poorly understood. Here, using genome editing and RNA interference, we examine transcription factor interactions prior to and after anchor cell specification. During invasion we identify thategl-43,hlh-2, andnhr-67function together in a type I coherent feed-forward loop with positive feedback. Conversely, prior to specification, these transcription factors function independent of one another to regulate LIN-12 (Notch) activity. Together, these results demonstrate that, although the same transcription factors can function in fate specification and differentiated cell behavior, a gene regulatory network can be rapidly re-wired to reinforce a post-mitotic, pro-invasive state.SUMMARY STATEMENTBasement membrane invasion by theC. elegansanchor cell is coordinated by a dynamic gene regulatory network encompassing cell cycle dependent and independent sub-circuits.

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 Gene Regulatory Network inference in long-lived C. elegans reveals modular properties that are predictive of novel ageing genes

iScience ◽  
2021 ◽  
pp. 103663
Author(s):  
M. Suriyalaksh ◽  
C. Raimondi ◽  
A. Mains ◽  
A. Segonds-Pichon ◽  
S. Mukhtar ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Network Inference ◽  
Gene Regulatory Network Inference ◽  
C Elegans ◽  
Gene Regulatory

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
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