scholarly journals A genome-wide assessment of the ancestral neural crest gene regulatory network

2018 ◽  
Author(s):  
Dorit Hockman ◽  
Vanessa Chong-Morrison ◽  
Daria Gavriouchkina ◽  
Stephen Green ◽  
Chris T. Amemiya ◽  
...  
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Ancestral State ◽  
Enhancer Activity ◽  
Mesenchymal Transition ◽  
A Genome ◽  
Gene Regulatory ◽  
Insight Into

AbstractThe neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-α2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

scholarly journals A genome-wide assessment of the ancestral neural crest gene regulatory network

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Dorit Hockman ◽  
Vanessa Chong-Morrison ◽  
Stephen A. Green ◽  
Daria Gavriouchkina ◽  
Ivan Candido-Ferreira ◽  
...  
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Embryonic Cell ◽  
Ancestral State ◽  
Enhancer Activity ◽  
A Genome ◽  
Gene Regulatory ◽  
Insight Into

Abstract The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.

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 Modeling a gene regulatory network of EMT hybrid states for mouse embryonic skin cells

2019 ◽  
Author(s):  
Dan Ramirez ◽  
Vivek Kohar ◽  
Ataur Katebi ◽  
Mingyang Lu
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Epithelial Mesenchymal Transition ◽  
Expression Patterns ◽  
Mesenchymal Transition ◽  
Hybrid State ◽  
Regulatory Interactions ◽  
Skin Cells ◽  
Embryonic Skin ◽  
Gene Regulatory

AbstractEpithelial-mesenchymal transition (EMT) plays a crucial role in embryonic development and tumorigenesis. Although EMT has been extensively studied with both computational and experimental methods, the gene regulatory mechanisms governing the transition are not yet well understood. Recent investigations have begun to better characterize the complex phenotypic plasticity underlying EMT using a computational systems biology approach. Here, we analyzed recently published single-cell RNA sequencing data from E9.5 to E11.5 mouse embryonic skin cells and identified the gene expression patterns of both epithelial and mesenchymal phenotypes, as well as a clear hybrid state. By integrating the scRNA-seq data and gene regulatory interactions from the literature, we constructed a gene regulatory network model governing the decision-making of EMT in the context of the developing mouse embryo. We simulated the network using a recently developed mathematical modeling method, named RACIPE, and observed three distinct phenotypic states whose gene expression patterns can be associated with the epithelial, hybrid, and mesenchymal states in the scRNA-seq data. Additionally, the model is in agreement with published results on the composition of EMT phenotypes and regulatory networks. We identified Wnt signaling as a major pathway in inducing the EMT and its role in driving cellular state transitions during embryonic development. Our findings demonstrate a new method of identifying and incorporating tissue-specific regulatory interactions into gene regulatory network modeling.Author SummaryEpithelial-mesenchymal transition (EMT) is a cellular process wherein cells become disconnected from their surroundings and acquire the ability to migrate through the body. EMT has been observed in biological contexts including development, wound healing, and cancer, yet the regulatory mechanisms underlying it are not well understood. Of particular interest is a purported hybrid state, in which cells can retain some adhesion to their surroundings but also show mesenchymal traits. Here, we examine the prevalence and composition of the hybrid state in the context of the embryonic mouse, integrating gene regulatory interactions from published experimental results as well as from the specific single cell RNA sequencing dataset of interest. Using mathematical modeling, we simulated a regulatory network based on these sources and aligned the simulated phenotypes with those in the data. We identified a hybrid EMT phenotype and revealed the inducing effect of Wnt signaling on EMT in this context. Our regulatory network construction process can be applied beyond EMT to illuminate the behavior of any biological phenomenon occurring in a specific context, allowing better identification of therapeutic targets and further research directions.

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 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 Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 71
Author(s):  
Ammarin In-on ◽  
Roypim Thananusak ◽  
Marasri Ruengjitchatchawalya ◽  
Wanwipa Vongsangnak ◽  
Teeraphan Laomettachit
Keyword(s):  
Gene Regulatory Network ◽  
Secondary Metabolite ◽  
Regulatory Network ◽  
Cordyceps Militaris ◽  
Secondary Metabolite Production ◽  
Metabolite Production ◽  
A Genome ◽  
Gene Regulatory ◽  
Growth Development ◽  
Genome Scale

Cordyceps militaris is an edible fungus that produces many beneficial compounds, including cordycepin and carotenoid. In many fungi, growth, development and secondary metabolite production are controlled by crosstalk between light-signaling pathways and other regulatory cascades. However, little is known about the gene regulation upon light exposure in C. militaris. This study aims to construct a gene regulatory network (GRN) that responds to light in C. militaris. First, a genome-scale GRN was built based on transcription factor (TF)-target gene interactions predicted from the Regulatory Sequence Analysis Tools (RSAT). Then, a light-responsive GRN was extracted by integrating the transcriptomic data onto the genome-scale GRN. The light-responsive network contains 2689 genes and 6837 interactions. From the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified regulatory network and expression profiles from our analysis suggested how light may induce the growth and development of C. militaris into a sexual cycle. The light-mediated regulation also couples fungal development with cordycepin and carotenoid production. This study leads to an enhanced understanding of the light-responsive regulation of growth, development and secondary metabolite production in the fungi.

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