scholarly journals Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes

2021 ◽  
Author(s):  
Martin Kinisu ◽  
Yong Jin Choi ◽  
Claudia Cattoglio ◽  
Ke Liu ◽  
Hector Roux de Bezieux ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Endogenous Retroviruses ◽  
Preimplantation Embryos ◽  
Cell State ◽  
Upstream Regulator ◽  
Evolutionarily Conserved ◽  
A Cell ◽  
Dual Activation ◽  
Transcription Program

SummaryEarly blastomeres of mouse preimplantation embryos exhibit bi-potential cell fate, capable of generating both embryonic and extra-embryonic lineages in blastocysts. Here, we identified three major 2 cell (2C) specific endogenous retroviruses (ERVs) as the molecular hallmark of the bi-potential plasticity. Using the LTRs of all three 2C-ERVs, we identified Klf5 as their major upstream regulator. Klf5 is essential for bi-potential cell fate: a single Klf5-overexpressing ESC generated terminally differentiated embryonic and extra-embryonic lineages in chimeric embryos, and Klf5 directly induces both ICM and TE specification genes. Intriguingly, Klf5 and Klf4 act redundantly during ICM specification, whereas Klf5 deficiency alone impairs TE specification. Klf5 is regulated by multiple 2C-specific transcription factors, particularly Dux, and the Dux/Klf5 axis is evolutionarily conserved. Altogether, the 2C-specific transcription program converges on Klf5 to establish bi-potential cell fate, enabling a cell state with dual activation of ICM and TE genes.

Spalt modifies EGFR-mediated induction of chordotonal precursors in the embryonic PNS of Drosophila promoting the development of oenocytes

Development ◽  
2001 ◽  
Vol 128 (5) ◽  
pp. 711-722 ◽  
Author(s):  
T.E. Rusten ◽  
R. Cantera ◽  
J. Urban ◽  
G. Technau ◽  
F.C. Kafatos ◽  
...  
Keyword(s):  
Nervous System ◽  
Cell Fate ◽  
System Development ◽  
Cell Types ◽  
Nervous System Development ◽  
Dual Function ◽  
Evolutionarily Conserved ◽  
A Cell ◽  
And Migration

Genes of the spalt family encode nuclear zinc finger proteins. In Drosophila melanogaster, they are necessary for the establishment of head/trunk identity, correct tracheal migration and patterning of the wing imaginal disc. Spalt proteins display a predominant pattern of expression in the nervous system, not only in Drosophila but also in species of fish, mouse, frog and human, suggesting an evolutionarily conserved role for these proteins in nervous system development. Here we show that Spalt works as a cell fate switch between two EGFR-induced cell types, the oenocytes and the precursors of the pentascolopodial organ in the embryonic peripheral nervous system. We show that removal of spalt increases the number of scolopodia, as a result of extra secondary recruitment of precursor cells at the expense of the oenocytes. In addition, the absence of spalt causes defects in the normal migration of the pentascolopodial organ. The dual function of spalt in the development of this organ, recruitment of precursors and migration, is reminiscent of its role in tracheal formation and of the role of a spalt homologue, sem-4, in the Caenorhabditis elegans nervous system.

scholarly journals The SOXE transcription factors—SOX8, SOX9 and SOX10—share a bi-partite transactivation mechanism

2019 ◽  
Vol 47 (13) ◽  
pp. 6917-6931 ◽  
Author(s):  
Abdul Haseeb ◽  
Véronique Lefebvre
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Binding Pocket ◽  
Molecular Networks ◽  
Transactivation Domain ◽  
Campomelic Dysplasia ◽  
Incomplete Knowledge ◽  
Evolutionarily Conserved ◽  
Sox Proteins ◽  
Disease Understanding

Abstract SOX8, SOX9 and SOX10 compose the SOXE transcription factor group. They govern cell fate and differentiation in many lineages, and mutations impairing their activity cause severe diseases, including campomelic dysplasia (SOX9), sex determination disorders (SOX8 and SOX9) and Waardenburg-Shah syndrome (SOX10). However, incomplete knowledge of their modes of action limits disease understanding. We here uncover that the proteins share a bipartite transactivation mechanism, whereby a transactivation domain in the middle of the proteins (TAM) synergizes with a C-terminal one (TAC). TAM comprises amphipathic α-helices predicted to form a protein-binding pocket and overlapping with minimal transactivation motifs (9-aa-TAD) described in many transcription factors. One 9-aa-TAD sequence includes an evolutionarily conserved and functionally required EΦ[D/E]QYΦ motif. SOXF proteins (SOX7, SOX17 and SOX18) contain an identical motif, suggesting evolution from a common ancestor already harboring this motif, whereas TAC and other transactivating SOX proteins feature only remotely related motifs. Missense variants in this SOXE/SOXF-specific motif are rare in control individuals, but have been detected in cancers, supporting its importance in development and physiology. By deepening understanding of mechanisms underlying the central transactivation function of SOXE proteins, these findings should help further decipher molecular networks essential for development and health and dysregulated in diseases.

scholarly journals RBP-Jκ-Dependent Notch Signaling Is Dispensable for Mouse Early Embryonic Development

2006 ◽  
Vol 26 (13) ◽  
pp. 4769-4774 ◽  
Author(s):  
Céline Souilhol ◽  
Sarah Cormier ◽  
Kenji Tanigaki ◽  
Charles Babinet ◽  
Michel Cohen-Tannoudji
Keyword(s):  
Embryonic Development ◽  
Notch Signaling ◽  
Signaling Pathway ◽  
Cell Fate ◽  
Notch Pathway ◽  
Notch Signaling Pathway ◽  
Preimplantation Embryos ◽  
Cell Fate Specification ◽  
Fate Specification ◽  
Evolutionarily Conserved

ABSTRACT The Notch signaling pathway is an evolutionarily conserved signaling system which has been shown to be essential in cell fate specification and in numerous aspects of embryonic development in all metazoans thus far studied. We recently demonstrated that several components of the Notch signaling pathway, including the four Notch receptors and their five ligands known in mammals, are expressed in mouse oocytes, in mouse preimplantation embryos, or both. This suggested a possible implication of the Notch pathway in the first cell fate specification of the dividing mouse embryo, which results in the formation of the blastocyst. To address this issue directly, we generated zygotes in which both the maternal and the zygotic expression of Rbpsuh, a key element of the core Notch signaling pathway, were abrogated. We find that such zygotes give rise to blastocysts which implant and develop normally. Nevertheless, after gastrulation, these embryos die around midgestation, similarly to Rbpsuh-null mutants. This demonstrates that the RBP-Jκ-dependent pathway, otherwise called the canonical Notch pathway, is dispensable for blastocyst morphogenesis and the establishment of the three germ layers, ectoderm, endoderm, and mesoderm. These results are discussed in the light of recent observations which have challenged this conclusion.

scholarly journals Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Wu ◽  
Jiaqi Wu ◽  
Minghua Deng ◽  
Yihan Lin
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Stress Response ◽  
Cell Fate ◽  
Functional Redundancy ◽  
Yeast Cells ◽  
Fate Control ◽  
A Cell ◽  
Temporal Redundancy ◽  
Cell Fate Control

AbstractRecent single-cell studies have revealed that yeast stress response involves transcription factors that are activated in pulses. However, it remains unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. We find that individual pulses of Msn2 and Msn4 are largely redundant, and cells can enhance the expression of their shared targets by increasing their temporal divergence. Thus, functional redundancy between these two paralogs is modulated in a dynamic manner to confer fitness advantages for yeast cells, which might feed back to promote the preservation of their redundancy. This evolutionary implication is supported by evidence from Msn2/Msn4 orthologs and analyses of other transcription factor paralogs. Together, we show a cell fate control mechanism through temporal redundancy modulation in yeast, which may represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.

scholarly journals Mapping Vector Field of Single Cells

2019 ◽  
Author(s):  
Xiaojie Qiu ◽  
Yan Zhang ◽  
Dian Yang ◽  
Shayan Hosseinzadeh ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vector Field ◽  
Cell Fate ◽  
Single Cells ◽  
Mathematical Framework ◽  
Cell State ◽  
Global Mapping ◽  
A Cell ◽  
Short Time

AbstractUnderstanding how gene expression in single cells progress over time is vital for revealing the mechanisms governing cell fate transitions. RNA velocity, which infers immediate changes in gene expression by comparing levels of new (unspliced) versus mature (spliced) transcripts (La Manno et al. 2018), represents an important advance to these efforts. A key question remaining is whether it is possible to predict the most probable cell state backward or forward over arbitrary time-scales. To this end, we introduce an inclusive model (termed Dynamo) capable of predicting cell states over extended time periods, that incorporates promoter state switching, transcription, splicing, translation and RNA/protein degradation by taking advantage of scRNA-seq and the co-assay of transcriptome and proteome. We also implement scSLAM-seq by extending SLAM-seq to plate-based scRNA-seq (Hendriks et al. 2018; Erhard et al. 2019; Cao, Zhou, et al. 2019) and augment the model by explicitly incorporating the metabolic labelling of nascent RNA. We show that through careful design of labelling experiments and an efficient mathematical framework, the entire kinetic behavior of a cell from this model can be robustly and accurately inferred. Aided by the improved framework, we show that it is possible to reconstruct the transcriptomic vector field from sparse and noisy vector samples generated by single cell experiments. The reconstructed vector field further enables global mapping of potential landscapes that reflects the relative stability of a given cell state, and the minimal transition time and most probable paths between any cell states in the state space. This work thus foreshadows the possibility of predicting long-term trajectories of cells during a dynamic process instead of short time velocity estimates. Our methods are implemented as an open source tool, dynamo (https://github.com/aristoteleo/dynamo-release).

scholarly journals GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate

2020 ◽  
Author(s):  
Mengyi Song ◽  
Xuefei Yuan ◽  
Claudia Racioppi ◽  
Meaghan Leslie ◽  
Anastasiia Aleksandrova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Heart Development ◽  
Gene Expression Analysis ◽  
Cell Fate Decisions ◽  
Evolutionarily Conserved ◽  
Cell Gene Expression ◽  
Cell Gene ◽  
Cardiac Mesoderm ◽  
Invertebrate Chordate

AbstractGATA4/5/6 transcription factors play essential, conserved roles in heart development. How these factors mediate the transition from multipotent mesoderm progenitors to a committed cardiac fate is unclear. To understand how GATA4/5/6 modulate cell fate decisions we labelled, isolated, and performed single-cell gene expression analysis on cells that express gata5 at pre-cardiac time points spanning gastrulation to somitogenesis. We found that most mesendoderm-derived lineages had dynamic gata5/6 expression. In the absence of Gata5/6, the population structure of mesendoderm-derived cells was dramatically altered. In addition to the expected absence of cardiac mesoderm, we observed a concomitant expansion of cranial-pharyngeal mesoderm. Functional genetic analyses in zebrafish and the invertebrate chordate Ciona, which possess a single GATA4/5/6 homolog, revealed an essential and cell-autonomous role for GATA4/5/6 in promoting cardiac and inhibiting pharyngeal mesoderm identity. Overall, the maintenance and repression of GATA4/5/6 activity plays a critical, evolutionarily conserved role in early development.

scholarly journals The Role of Caspase-2 in Regulating Cell Fate

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1259
Author(s):  
Vasanthy Vigneswara ◽  
Zubair Ahmed
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Apoptotic Cell ◽  
Comprehensive Overview ◽  
Cellular Processes ◽  
Evolutionarily Conserved ◽  
Caspase Family ◽  
A Cell ◽  
Caspase 2 ◽  
Cycle Regulation

Caspase-2 is the most evolutionarily conserved member of the mammalian caspase family and has been implicated in both apoptotic and non-apoptotic signaling pathways, including tumor suppression, cell cycle regulation, and DNA repair. A myriad of signaling molecules is associated with the tight regulation of caspase-2 to mediate multiple cellular processes far beyond apoptotic cell death. This review provides a comprehensive overview of the literature pertaining to possible sophisticated molecular mechanisms underlying the multifaceted process of caspase-2 activation and to highlight its interplay between factors that promote or suppress apoptosis in a complicated regulatory network that determines the fate of a cell from its birth and throughout its life.

scholarly journals A Molecular Framework for Plant Regeneration

Science ◽  
2006 ◽  
Vol 311 (5759) ◽  
pp. 385-388 ◽  
Author(s):  
Jian Xu ◽  
Hugo Hofhuis ◽  
Renze Heidstra ◽  
Michael Sauer ◽  
Jiří Friml ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Auxin Transport ◽  
Root Tips ◽  
Root Stem Cell ◽  
Regeneration Response ◽  
A Cell ◽  
Molecular Framework

Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin—a cell-fate–instructive plant hormone—in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux–facilitating membrane proteins to reconstitute auxin transport in renewed root tips.Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.

scholarly journals Development in the Mammalian Auditory System Depends on Transcription Factors

2021 ◽  
Vol 22 (8) ◽  
pp. 4189
Author(s):  
Karen L. Elliott ◽  
Gabriela Pavlínková ◽  
Victor V. Chizhikov ◽  
Ebenezer N. Yamoah ◽  
Bernd Fritzsch
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Auditory System ◽  
Hair Cells ◽  
System Development ◽  
Neuronal Cell ◽  
Spiral Ganglion Neuron ◽  
Cochlear Hair Cells ◽  
Cochlear Nuclei ◽  
Bhlh Genes

We review the molecular basis of several transcription factors (Eya1, Sox2), including the three related genes coding basic helix–loop–helix (bHLH; see abbreviations) proteins (Neurog1, Neurod1, Atoh1) during the development of spiral ganglia, cochlear nuclei, and cochlear hair cells. Neuronal development requires Neurog1, followed by its downstream target Neurod1, to cross-regulate Atoh1 expression. In contrast, hair cells and cochlear nuclei critically depend on Atoh1 and require Neurod1 expression for interactions with Atoh1. Upregulation of Atoh1 following Neurod1 loss changes some vestibular neurons’ fate into “hair cells”, highlighting the significant interplay between the bHLH genes. Further work showed that replacing Atoh1 by Neurog1 rescues some hair cells from complete absence observed in Atoh1 null mutants, suggesting that bHLH genes can partially replace one another. The inhibition of Atoh1 by Neurod1 is essential for proper neuronal cell fate, and in the absence of Neurod1, Atoh1 is upregulated, resulting in the formation of “intraganglionic” HCs. Additional genes, such as Eya1/Six1, Sox2, Pax2, Gata3, Fgfr2b, Foxg1, and Lmx1a/b, play a role in the auditory system. Finally, both Lmx1a and Lmx1b genes are essential for the cochlear organ of Corti, spiral ganglion neuron, and cochlear nuclei formation. We integrate the mammalian auditory system development to provide comprehensive insights beyond the limited perception driven by singular investigations of cochlear neurons, cochlear hair cells, and cochlear nuclei. A detailed analysis of gene expression is needed to understand better how upstream regulators facilitate gene interactions and mammalian auditory system development.

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