scholarly journals The MITF paralog tfec is required in neural crest development for fate specification of the iridophore lineage from a multipotent pigment cell progenitor

2019 ◽  
Author(s):  
K. Petratou ◽  
S. A. Spencer ◽  
R. N. Kelsh ◽  
J. A. Lister
Keyword(s):  
Neural Crest ◽  
Regulatory Network ◽  
Pigment Cell ◽  
Cell Types ◽  
Cellular Mechanisms ◽  
Cell Fates ◽  
Master Regulator ◽  
Fate Specification ◽  
Multipotent Progenitors ◽  
Gene Regulatory

Understanding how fate specification of distinct cell-types from multipotent progenitors occurs is a fundamental question in embryology. Neural crest stem cells (NCSCs) generate extraordinarily diverse derivatives, including multiple neural, skeletogenic and pigment cell fates. Key transcription factors and extracellular signals specifying NCSC lineages remain to be identified, and we have only a little idea of how and when they function together to control fate. Zebrafish have three neural crest-derived pigment cell types, black melanocytes, light-reflecting iridophores and yellow xanthophores, which offer a powerful model for studying the molecular and cellular mechanisms of fate segregation. Mitfa has been identified as the master regulator of melanocyte fate. Here, we show that an Mitf-related transcription factor, Tfec, functions as master regulator of the iridophore fate. Surprisingly, our phenotypic analysis of tfec mutants demonstrates that Tfec also functions in the initial specification of all three pigment cell-types, although the melanocyte and xanthophore lineages recover later. We show that Mitfa represses tfec expression, revealing a likely mechanism contributing to the decision between melanocyte and iridophore fate. Our data is consistent with the long-standing proposal of a tripotent progenitor restricted to pigment cell fates. Moreover, we investigate activation, maintenance and function of tfec in multipotent NCSCs, demonstrating for the first time its role in the gene regulatory network forming and maintaining early neural crest cells. In summary, we build on our previous work to characterise the gene regulatory network governing iridophore development, establishing Tfec as the master regulator driving iridophore specification from multipotent progenitors, while shedding light on possible cellular mechanisms of progressive fate restriction.

scholarly journals The MITF paralog tfec is required in neural crest development for fate specification of the iridophore lineage from a multipotent pigment cell progenitor

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244794 ◽  
Author(s):  
Kleio Petratou ◽  
Samantha A. Spencer ◽  
Robert N. Kelsh ◽  
James A. Lister
Keyword(s):  
Neural Crest ◽  
Regulatory Network ◽  
Pigment Cell ◽  
Cell Types ◽  
Cellular Mechanisms ◽  
Cell Fates ◽  
Master Regulator ◽  
Fate Specification ◽  
Multipotent Progenitors ◽  
Gene Regulatory

Understanding how fate specification of distinct cell-types from multipotent progenitors occurs is a fundamental question in embryology. Neural crest stem cells (NCSCs) generate extraordinarily diverse derivatives, including multiple neural, skeletogenic and pigment cell fates. Key transcription factors and extracellular signals specifying NCSC lineages remain to be identified, and we have only a little idea of how and when they function together to control fate. Zebrafish have three neural crest-derived pigment cell types, black melanocytes, light-reflecting iridophores and yellow xanthophores, which offer a powerful model for studying the molecular and cellular mechanisms of fate segregation. Mitfa has been identified as the master regulator of melanocyte fate. Here, we show that an Mitf-related transcription factor, Tfec, functions as master regulator of the iridophore fate. Surprisingly, our phenotypic analysis of tfec mutants demonstrates that Tfec also functions in the initial specification of all three pigment cell-types, although the melanocyte and xanthophore lineages recover later. We show that Mitfa represses tfec expression, revealing a likely mechanism contributing to the decision between melanocyte and iridophore fate. Our data are consistent with the long-standing proposal of a tripotent progenitor restricted to pigment cell fates. Moreover, we investigate activation, maintenance and function of tfec in multipotent NCSCs, demonstrating for the first time its role in the gene regulatory network forming and maintaining early neural crest cells. In summary, we build on our previous work to characterise the gene regulatory network governing iridophore development, establishing Tfec as the master regulator driving iridophore specification from multipotent progenitors, while shedding light on possible cellular mechanisms of progressive fate restriction.

scholarly journals Insights Into the Early Gene Regulatory Network Controlling Neural Crest and Placode Fate Choices at the Neural Border

2020 ◽  
Vol 11 ◽  
Author(s):  
Subham Seal ◽  
Anne H. Monsoro-Burq
Keyword(s):  
Neural Crest ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cell Types ◽  
Model Systems ◽  
Early Gene ◽  
Secretory Cells ◽  
Peripheral Neurons ◽  
Gene Regulatory

The neural crest (NC) cells and cranial placodes are two ectoderm-derived innovations in vertebrates that led to the acquisition of a complex head structure required for a predatory lifestyle. They both originate from the neural border (NB), a portion of the ectoderm located between the neural plate (NP), and the lateral non-neural ectoderm. The NC gives rise to a vast array of tissues and cell types such as peripheral neurons and glial cells, melanocytes, secretory cells, and cranial skeletal and connective cells. Together with cells derived from the cranial placodes, which contribute to sensory organs in the head, the NC also forms the cranial sensory ganglia. Multiple in vivo studies in different model systems have uncovered the signaling pathways and genetic factors that govern the positioning, development, and differentiation of these tissues. In this literature review, we give an overview of NC and placode development, focusing on the early gene regulatory network that controls the formation of the NB during early embryonic stages, and later dictates the choice between the NC and placode progenitor fates.

scholarly journals Brachyury controls Ciona notochord fate as part of a feedforward network and not as a unitary master regulator

2020 ◽  
Author(s):  
Wendy M. Reeves ◽  
Kotaro Shimai ◽  
Konner M. Winkley ◽  
Michael T. Veeman
Keyword(s):  
Transcription Factor ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cell Types ◽  
Binding Motif ◽  
Fgf Signaling ◽  
Feedforward Network ◽  
Master Regulator ◽  
Gene Regulatory ◽  
Direct Activator

AbstractThe notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically-defined master regulator.

scholarly journals Brachyury controls Ciona notochord fate as part of a feedforward network

Development ◽  
2021 ◽  
pp. dev.195230
Author(s):  
Wendy M. Reeves ◽  
Kotaro Shimai ◽  
Konner M. Winkley ◽  
Michael T. Veeman
Keyword(s):  
Transcription Factor ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cell Types ◽  
Binding Motif ◽  
Fgf Signaling ◽  
Feedforward Network ◽  
Master Regulator ◽  
Gene Regulatory ◽  
Direct Activator

The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a, and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically-defined master regulator.

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 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

Prenet: Predictive network from ATAC-SEQ data

2020 ◽  
Vol 18 (01) ◽  
pp. 2040003 ◽  
Author(s):  
Nazmus Salehin ◽  
Patrick P. L. Tam ◽  
Pierre Osteil
Keyword(s):  
Regulatory Network ◽  
State Of The Art ◽  
Cell Types ◽  
Cell Type ◽  
Regulatory Pathways ◽  
Novel Approach ◽  
Multiple Cell ◽  
Bona Fide ◽  
Gene Regulatory ◽  
Accessible Chromatin

Assays for transposase-accessible chromatin sequencing (ATAC-seq) provides an innovative approach to study chromatin status in multiple cell types. Moreover, it is also possible to efficiently extract differentially accessible chromatin (DACs) regions by using state-of-the-art algorithms (e.g. DESeq2) to predict gene activity in specific samples. Furthermore, it has recently been shown that small dips in sequencing peaks can be attributed to the binding of transcription factors. These dips, also known as footprints, can be used to identify trans-regulating interactions leading to gene expression. Current protocols used to identify footprints (e.g. pyDNAse and HINT-ATAC) have shown limitations resulting in the discovery of many false positive footprints. We generated a novel approach to identify genuine footprints within any given ATAC-seq dataset. Herein, we developed a new pipeline embedding DACs together with bona fide footprints resulting in the generation of a Predictive gene regulatory Network (PreNet) simply from ATAC-seq data. We further demonstrated that PreNet can be used to unveil meaningful molecular regulatory pathways in a given cell type.

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
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