scholarly journals Inference of the gene regulatory network acting downstream of CROWN ROOTLESS  1 in rice reveals a regulatory cascade linking genes involved in auxin signaling, crown root initiation, and root meristem specification and maintenance

2019 ◽  
Vol 100 (5) ◽  
pp. 954-968 ◽  
Author(s):  
Jérémy Lavarenne ◽  
Mathieu Gonin ◽  
Soazig Guyomarc'h ◽  
Jacques Rouster ◽  
Antony Champion ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Root Meristem ◽  
Auxin Signaling ◽  
Root Initiation ◽  
Crown Root ◽  
Regulatory Cascade ◽  
Gene Regulatory

scholarly journals Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi

2018 ◽  
Author(s):  
Ming-Yueh Wu ◽  
Matthew E. Mead ◽  
Mi-Kyung Lee ◽  
Sun-Chang Kim ◽  
Antonis Rokas ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Filamentous Fungi ◽  
Regulatory Network ◽  
Morphological Differentiation ◽  
Human Infection ◽  
Global Regulators ◽  
Asexual Sporulation ◽  
Regulatory Cascade ◽  
Gene Regulatory ◽  
Species Specific

AbstractAsexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. InAspergillus, the production of asexual spores is primarily governed by the BrlA→AbaA→WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and not only governs the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genusAspergillus, the structure and degree of conservation of thewetAgene regulatory network (GRN) remains largely unknown. We carried out comparative transcriptome analyses betweenwetAnull mutant and wild type asexual spores in three representative species spanning the diversity of the genusAspergillus:A. nidulans, A. flavus, andA. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascade’s first step. Furthermore, ChIP-seq experiments inA. nidulansasexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA→AbaA→WetA cascade’s regulatory role in cellular and chemical asexual spore development is functionally conserved, but that thewetA-associated GRN has diverged duringAspergillusevolution.

scholarly journals Segmentation and patterning of the vertebrate hindbrain

Development ◽  
2021 ◽  
Vol 148 (15) ◽  
Author(s):  
Robb Krumlauf ◽  
David G. Wilkinson
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Dynamic Regulation ◽  
Regulatory Cascade ◽  
Gene Regulatory ◽  
Key Aspects ◽  
Cell Segregation ◽  
A Site

ABSTRACT During early development, the hindbrain is sub-divided into rhombomeres that underlie the organisation of neurons and adjacent craniofacial tissues. A gene regulatory network of signals and transcription factors establish and pattern segments with a distinct anteroposterior identity. Initially, the borders of segmental gene expression are imprecise, but then become sharply defined, and specialised boundary cells form. In this Review, we summarise key aspects of the conserved regulatory cascade that underlies the formation of hindbrain segments. We describe how the pattern is sharpened and stabilised through the dynamic regulation of cell identity, acting in parallel with cell segregation. Finally, we discuss evidence that boundary cells have roles in local patterning, and act as a site of neurogenesis within the hindbrain.

scholarly journals Study on the Relationship between the miRNA-centered ceRNA Regulatory Network and Fatigue

2021 ◽  
Author(s):  
Xingzhe Yang ◽  
Feng Li ◽  
Jie Ma ◽  
Yan Liu ◽  
Xuejiao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Hot Spot ◽  
Genetic Research ◽  
Noncoding Rnas ◽  
Messenger Rnas ◽  
Effective Prevention ◽  
Gene Regulatory ◽  
The Relationship

AbstractIn recent years, the incidence of fatigue has been increasing, and the effective prevention and treatment of fatigue has become an urgent problem. As a result, the genetic research of fatigue has become a hot spot. Transcriptome-level regulation is the key link in the gene regulatory network. The transcriptome includes messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). MRNAs are common research targets in gene expression profiling. Noncoding RNAs, including miRNAs, lncRNAs, circRNAs and so on, have been developed rapidly. Studies have shown that miRNAs are closely related to the occurrence and development of fatigue. MiRNAs can regulate the immune inflammatory reaction in the central nervous system (CNS), regulate the transmission of nerve impulses and gene expression, regulate brain development and brain function, and participate in the occurrence and development of fatigue by regulating mitochondrial function and energy metabolism. LncRNAs can regulate dopaminergic neurons to participate in the occurrence and development of fatigue. This has certain value in the diagnosis of chronic fatigue syndrome (CFS). CircRNAs can participate in the occurrence and development of fatigue by regulating the NF-κB pathway, TNF-α and IL-1β. The ceRNA hypothesis posits that in addition to the function of miRNAs in unidirectional regulation, mRNAs, lncRNAs and circRNAs can regulate gene expression by competitive binding with miRNAs, forming a ceRNA regulatory network with miRNAs. Therefore, we suggest that the miRNA-centered ceRNA regulatory network is closely related to fatigue. At present, there are few studies on fatigue-related ncRNA genes, and most of these limited studies are on miRNAs in ncRNAs. However, there are a few studies on the relationship between lncRNAs, cirRNAs and fatigue. Less research is available on the pathogenesis of fatigue based on the ceRNA regulatory network. Therefore, exploring the complex mechanism of fatigue based on the ceRNA regulatory network is of great significance. In this review, we summarize the relationship between miRNAs, lncRNAs and circRNAs in ncRNAs and fatigue, and focus on exploring the regulatory role of the miRNA-centered ceRNA regulatory network in the occurrence and development of fatigue, in order to gain a comprehensive, in-depth and new understanding of the essence of the fatigue gene regulatory network.

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