scholarly journals The transcription factor Zic4 acts as a transdifferentiation switch

2021 ◽  
Author(s):  
Matthias Christian Vogg ◽  
Jaroslav Ferenc ◽  
Wanda Christa Buzgariu ◽  
Chrystelle Perruchoud ◽  
Panagiotis Papasaikas ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Transcription Factor ◽  
Gene Regulatory Network ◽  
Cell Fate ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Model System ◽  
Cell Identity ◽  
Transcriptional Switch ◽  
Gene Regulatory

The molecular mechanisms that maintain cell identities and prevent transdifferentiation remain mysterious. Interestingly, both dedifferentiation and transdifferentiation are transiently reshuffled during regeneration. Therefore, organisms that regenerate readily offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4 silencing is sufficient to induce transdifferentiation of tentacle into foot cells. We identified a Wnt-controlled Gene Regulatory Network that controls a transcriptional switch of cell identity. Furthermore, we show that this switch also controls the re-entry into the cell cycle. Our data indicate that maintenance of cell fate by a Wnt-controlled GRN is a key mechanism during both homeostasis and regeneration.

scholarly journals Regulation of transcription reactivation dynamics exiting mitosis

2021 ◽  
Vol 17 (10) ◽  
pp. e1009354
Author(s):  
Sergio Sarnataro ◽  
Andrea Riba ◽  
Nacho Molina
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Control Cell ◽  
Core Gene ◽  
Regulation Of Transcription ◽  
Gene Regulatory

Proliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells. However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times. Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and predict a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could be relevant therapeutic targets to control cell proliferation.

scholarly journals Regulation of transcription reactivation dynamics exiting mitosis

2020 ◽  
Author(s):  
Sergio Sarnataro ◽  
Andrea Riba ◽  
Nacho Molina
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Control Cell ◽  
Core Gene ◽  
Regulation Of Transcription ◽  
Gene Regulatory

AbstractProliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells. However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times. Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and identify a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could represent relevant therapeutic targets to control cell proliferation.

Deciphering the transcription factor-microRNA-target gene regulatory network associated with graphene oxide cytotoxicity

2018 ◽  
Vol 12 (9) ◽  
pp. 1014-1026 ◽  
Author(s):  
Masoumeh Farahani ◽  
Mostafa Rezaei–Tavirani ◽  
Hakimeh Zali ◽  
Afsaneh Arefi Oskouie ◽  
Meisam Omidi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Graphene Oxide ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Target Gene ◽  
Microrna Target ◽  
Gene Regulatory

scholarly journals Shaping of Drosophila Neural Cell Lineages Through Coordination of Cell Proliferation and Cell Fate by the BTB-ZF Transcription Factor Tramtrack-69

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 773-788
Author(s):  
Françoise Simon ◽  
Anne Ramat ◽  
Sophie Louvet-Vallée ◽  
Jérôme Lacoste ◽  
Angélique Burg ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Transcription Factor ◽  
Cell Fate ◽  
Zinc Finger ◽  
Molecular Mechanisms ◽  
Neural Cell ◽  
Cell Cycle Exit ◽  
Cell Lineages ◽  
Accessory Cells

Cell diversity in multicellular organisms relies on coordination between cell proliferation and the acquisition of cell identity. The equilibrium between these two processes is essential to assure the correct number of determined cells at a given time at a given place. Using genetic approaches and correlative microscopy, we show that Tramtrack-69 (Ttk69, a Broad-complex, Tramtrack and Bric-à-brac - Zinc Finger (BTB-ZF) transcription factor ortholog of the human promyelocytic leukemia zinc finger factor) plays an essential role in controlling this balance. In the Drosophila bristle cell lineage, which produces the external sensory organs composed by a neuron and accessory cells, we show that ttk69 loss-of-function leads to supplementary neural-type cells at the expense of accessory cells. Our data indicate that Ttk69 (1) promotes cell cycle exit of newborn terminal cells by downregulating CycE, the principal cyclin involved in S-phase entry, and (2) regulates cell-fate acquisition and terminal differentiation, by downregulating the expression of hamlet and upregulating that of Suppressor of Hairless, two transcription factors involved in neural-fate acquisition and accessory cell differentiation, respectively. Thus, Ttk69 plays a central role in shaping neural cell lineages by integrating molecular mechanisms that regulate progenitor cell cycle exit and cell-fate commitment.

scholarly journals Tfap2a is a novel gatekeeper of differentiation in renal progenitors during kidney development

2018 ◽  
Author(s):  
Brooke E. Chambers ◽  
Gary F. Gerlach ◽  
Karen H. Chen ◽  
Eleanor G. Clark ◽  
Ignaty Leshchiner ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Genetic Control ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Kidney Development ◽  
Distal Segment ◽  
Distal Nephron ◽  
Nephron Segment ◽  
Gene Regulatory ◽  
First Time

AbstractRenal functional units known as nephrons undergo patterning events during development that create a segmental array of cellular populations with discrete physiological tasks. Knowledge about the terminal differentiation programs of each nephron segment has central importance for understanding kidney disease and to advance regenerative medicine, as mammalian nephrons grown in organoid cultures from pluripotent cells fail to terminally differentiate. Here, from a novel forward genetic screen using zebrafish we report the discovery that transcription factor AP-2 alpha (tfap2a) coordinates a gene regulatory network that controls the progression of nephron distal segment progenitors into the differentiated state. Overexpression of tfap2a rescued differentiation in mutants and caused ectopic expression of distal segment markers in wild-type nephrons, indicating tfap2a is sufficient to instigate the distal segment differentiation program. tfap2a/2b deficiency exacerbated distal nephron segment differentiation defects, revealing functional redundancy where tfap2a has a dominant role upstream of its family member. With further genetic studies, we assembled a blueprint of the tfap2a gene regulatory network during nephrogenesis. We demonstrate that tfap2a acts downstream of Iroquois homeobox 3b, a conserved distal lineage transcription factor. tfap2a controls a circuit consisting of irx1a, tfap2b, and genes encoding solute transporters that dictate the specialized metabolic functions of the distal nephron segments, and we show for the first time that this regulatory node is distinct from the pathway circuits controlling aspects such as apical-basal polarity and ciliogenesis during the differentiation process. Thus, our studies reveal new insights into the genetic control of differentiation, where tfap2a regulates the suite of segment transporter traits. These findings have relevance for understanding renal birth defects, as well as efforts to recapitulate nephrogenesis in vivo to make functional units that can facilitate organoid applications such as drug discovery and regenerative therapies.Summary StatementHere, we report for the first time that transcription factor AP-2 alpha (tfap2a) controls the progression from nephron progenitor into the fully differentiated state. This fundamentally deepens our knowledge about the genetic control of kidney development.

scholarly journals Evolution of Regulatory Complexity for Cell-Cycle Control

2021 ◽  
Author(s):  
Sam H. A. von der Dunk ◽  
Berend Snel ◽  
Paulien Hogeweg
Keyword(s):  
Cell Cycle ◽  
Gene Regulation ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Caulobacter Crescentus ◽  
Genome Structure ◽  
Cell Cycle Checkpoint ◽  
Evolutionary Strategies ◽  
Nutrient Levels ◽  
Gene Regulatory

How complexity arises is a fundamental evolutionary question. Complex gene regulation is thought to arise by the interplay between adaptive and non-adaptive forces at multiple organizational levels. Using a computational model, we investigate how complexity arises in cell-cycle regulation. Starting from the well-known Caulobacter crescentus network, we study how cells adapt their cell-cycle behaviour to a gradient of limited nutrient conditions using 10 replicate in silico evolution experiments. We find adaptive expansion of the gene regulatory network: improvement of cell-cycle behaviour allows cells to overcome the inherent cost of complexity. Replicates traverse different evolutionary trajectories leading to distinct eco-evolutionary strategies. In four replicates, cells evolve a generalist strategy to cope with a variety of nutrient levels; in two replicates, different specialist cells evolve for specific nutrient levels; in the remaining four replicates, an intermediate strategy evolves. The generalist and specialist strategies are contingent on the regulatory mechanisms that arise early in evolution, but they are not directly linked to network expansion and overall fitness. This study shows that functionality of cells depends on the combination of gene regulatory network topology and genome structure. For example, the positions of dosage-sensitive genes are exploited to signal to the regulatory network when replication is completed, forming a de novo evolved cell-cycle checkpoint. Complex gene regulation can arise adaptively both from expansion of the regulatory network and from the genomic organization of the elements in this network, demonstrating that to understand complex gene regulation and its evolution, it is necessary to integrate systems that are often studied separately.

scholarly journals Delilah, prospero, and D-Pax2 constitute a gene regulatory network essential for the development of functional proprioceptors

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Adel Avetisyan ◽  
Yael Glatt ◽  
Maya Cohen ◽  
Yael Timerman ◽  
Nitay Aspis ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Cell Fate ◽  
Binding Sites ◽  
Regulatory Network ◽  
Genetic Networks ◽  
Chordotonal Organ ◽  
Cell Fate Determination ◽  
Specific Expression ◽  
Gene Regulatory ◽  
Do So

Coordinated animal locomotion depends on the development of functional proprioceptors. While early cell-fate determination processes are well characterized, little is known about the terminal differentiation of cells within the proprioceptive lineage and the genetic networks that control them. In this work we describe a gene regulatory network consisting of three transcription factors–Prospero (Pros), D-Pax2, and Delilah (Dei)–that dictates two alternative differentiation programs within the proprioceptive lineage in Drosophila. We show that D-Pax2 and Pros control the differentiation of cap versus scolopale cells in the chordotonal organ lineage by, respectively, activating and repressing the transcription of dei. Normally, D-Pax2 activates the expression of dei in the cap cell but is unable to do so in the scolopale cell where Pros is co-expressed. We further show that D-Pax2 and Pros exert their effects on dei transcription via a 262 bp chordotonal-specific enhancer in which two D-Pax2- and three Pros-binding sites were identified experimentally. When this enhancer was removed from the fly genome, the cap- and ligament-specific expression of dei was lost, resulting in loss of chordotonal organ functionality and defective larval locomotion. Thus, coordinated larval locomotion depends on the activity of a dei enhancer that integrates both activating and repressive inputs for the generation of a functional proprioceptive organ.

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