scholarly journals Transcription Factors That Control Behavior—Lessons From C. elegans

2021 ◽  
Vol 15 ◽  
Author(s):  
Rasoul Godini ◽  
Ava Handley ◽  
Roger Pocock
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Behavioral Responses ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
C Elegans ◽  
Control Behavior ◽  
A Cell ◽  
Physical And Chemical ◽  
Chemical Response

Behavior encompasses the physical and chemical response to external and internal stimuli. Neurons, each with their own specific molecular identities, act in concert to perceive and relay these stimuli to drive behavior. Generating behavioral responses requires neurons that have the correct morphological, synaptic, and molecular identities. Transcription factors drive the specific gene expression patterns that define these identities, controlling almost every phenomenon in a cell from development to homeostasis. Therefore, transcription factors play an important role in generating and regulating behavior. Here, we describe the transcription factors, the pathways they regulate, and the neurons that drive chemosensation, mechanosensation, thermosensation, osmolarity sensing, complex, and sex-specific behaviors in the animal model Caenorhabditis elegans. We also discuss the current limitations in our knowledge, particularly our minimal understanding of how transcription factors contribute to the adaptive behavioral responses that are necessary for organismal survival.

scholarly journals Tissue-specific profiling reveals distinctive regulatory architectures for ubiquitous, germline and somatic genes

2020 ◽  
Author(s):  
Jacques Serizay ◽  
Yan Dong ◽  
Jürgen Jänes ◽  
Michael Chesney ◽  
Chiara Cerrato ◽  
...  
Keyword(s):  
Gene Expression ◽  
Core Promoter ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Somatic Tissue ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Detailed Knowledge ◽  
Tissue Specific ◽  
C Elegans

AbstractDespite increasingly detailed knowledge of gene expression patterns, the regulatory architectures that drive them are not well understood. To address this, we compared transcriptional and regulatory element activities across five adult tissues of C. elegans, covering ∼90% of cells, and defined regulatory grammars associated with ubiquitous, germline and somatic tissue-specific gene expression patterns. We find architectural features that distinguish two major promoter types. Germline-specific and ubiquitously-active promoters have well positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal. Somatic tissue-specific promoters lack these features, have wider nucleosome depleted regions, and are more enriched for core promoter elements, which surprisingly differ between tissues. A 10-bp periodic WW signal is also associated with +1 nucleosomes of ubiquitous promoters in fly and zebrafish but is not detected in mouse and human. Our results demonstrate fundamental differences in regulatory architectures of germline-active and somatic tissue-specific genes and provide a key resource for future studies.

scholarly journals Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes

2018 ◽  
Author(s):  
Annabel Ebbing ◽  
Abel Vertesy ◽  
Marco Betist ◽  
Bastiaan Spanjaard ◽  
Jan Philipp Junker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reproductive Tract ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Comprehensive Overview ◽  
Tissue Specific ◽  
C Elegans ◽  
Differential Gene ◽  
Fertility Genes

SummaryTo advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used RNA tomography to generate the first high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region and tissue-specific genes. Moreover, by combining pattern-based analysis with differential gene expression analysis, we have found extensive sex-specific gene expression differences in the germline and sperm. We have also identified genes that are specifically expressed in the male reproductive tract, including a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying novel tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, which opens up new possibilities for transcriptome-wide comparisons of gene expression patterns.

pha-4 is Ce-fkh-1, a fork head/HNF-3alpha, beta, gamma homolog that functions in organogenesis of the C. elegans pharynx

Development ◽  
1998 ◽  
Vol 125 (12) ◽  
pp. 2171-2180 ◽  
Author(s):  
J.M. Kalb ◽  
K.K. Lau ◽  
B. Goszczynski ◽  
T. Fukushige ◽  
D. Moons ◽  
...  
Keyword(s):  
Early Stage ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Specific Gene ◽  
Gata Factor ◽  
Enhancer Element ◽  
C Elegans ◽  
Fork Head ◽  
Organ Identity

The C. elegans Ce-fkh-1 gene has been cloned on the basis of its sequence similarity to the winged-helix DNA binding domain of the Drosophila fork head and mammalian HNF-3alpha, beta, gamma genes, and mutations in the zygotically active pha-4 gene have been shown to block formation of the pharynx (and rectum) at an early stage in embryogenesis. In the present paper, we show that Ce-fkh-1 and pha-4 are the same gene. We show that PHA-4 protein is present in nuclei of essentially all pharyngeal cells, of all five cell types. PHA-4 protein first appears close to the point at which a cell lineage will produce only pharyngeal cells, independently of cell type. We show that PHA-4 binds directly to a ‘pan-pharyngeal enhancer element’ previously identified in the promoter of the pharyngeal myosin myo-2 gene; in transgenic embryos, ectopic PHA-4 activates ectopic myo-2 expression. We also show that ectopic PHA-4 can activate ectopic expression of the ceh-22 gene, a pharyngeal-specific NK-2-type homeodomain protein previously shown to bind a muscle-specific enhancer near the PHA-4 binding site in the myo-2 promoter. We propose that it is the combination of pha-4 and regulatory molecules such as ceh-22 that produces the specific gene expression patterns during pharynx development. Overall, pha-4 can be described as an ‘organ identity factor’, completely necessary for organ formation, present in all cells of the organ from the earliest stages, capable of integrating upstream developmental pathways (in this case, the two distinct pathways that produce the anterior and posterior pharynx) and participating directly in the transcriptional regulation of organ specific genes. Finally, we note that the distribution of PHA-4 protein in C. elegans embryos is remarkably similar to the distribution of the fork head protein in Drosophila embryos: high levels in the foregut/pharynx and hindgut/rectum; low levels in the gut proper. Moreover, we show that pha-4 expression in the C. elegans gut is regulated by elt-2, a C. elegans gut-specific GATA-factor and possible homolog of the Drosophila gene serpent, which influences fork head expression in the fly gut. Overall, our results provide evidence for a highly conserved pathway regulating formation of the digestive tract in all (triploblastic) metazoa.

scholarly journals Regional and cell-specific gene expression patterns during petal development.

1992 ◽  
Vol 4 (11) ◽  
pp. 1383-1404 ◽  
Author(s):  
G N Drews ◽  
T P Beals ◽  
A Q Bui ◽  
R B Goldberg
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Petal Development

scholarly journals Microgenomic analysis reveals cell type-specific gene expression patterns between ray and fusiform initials within the cambial meristem ofPopulus

2008 ◽  
Vol 180 (1) ◽  
pp. 45-56 ◽  
Author(s):  
Nadia Goué ◽  
Marie-Claude Lesage-Descauses ◽  
Ewa J. Mellerowicz ◽  
Elisabeth Magel ◽  
Philippe Label ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Gene Expression ◽  
Fusiform Initials ◽  
Cell Type Specific

scholarly journals Plant-parasitic nematodes respond to root exudate signals with host-specific gene expression patterns

2019 ◽  
Vol 15 (2) ◽  
pp. e1007503 ◽  
Author(s):  
Christopher A. Bell ◽  
Catherine J. Lilley ◽  
James McCarthy ◽  
Howard J. Atkinson ◽  
P. E. Urwin
Keyword(s):  
Gene Expression ◽  
Root Exudate ◽  
Expression Patterns ◽  
Parasitic Nematodes ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Plant Parasitic Nematodes ◽  
Specific Gene Expression ◽  
Plant Parasitic

scholarly journals Analysis of region specific gene expression patterns in the heart and systemic responses after experimental myocardial ischemia

Oncotarget ◽  
2017 ◽  
Vol 8 (37) ◽  
pp. 60809-60825
Author(s):  
Matthias Zimmermann ◽  
Lucian Beer ◽  
Robert Ullrich ◽  
Dominika Lukovic ◽  
Elisabeth Simader ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Ischemia ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Experimental Myocardial Ischemia ◽  
Systemic Responses
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