Hope IA (1991) Development "'Promoter trapping' in Caenorhabditis elegans."

Hope IA

[Development, 1991]

A screen of gene expression patterns has been developed for the nematode Caenorhabditis elegans. Promoter-reporter gene fusions were constructed in vitro by ligating C. elegans genomic DNA fragments upstream of a lacZ gene. Patterns of beta-galactosidase expression were examined by histochemical staining of C. elegans lines transformed with the constructs. beta-galactosidase expression depended on translational fusion, so constructs were assayed in large pools to expedite detection of the low proportion that were active. Expression in a variety of cell types and temporal patterns was observed with different construct pools. The most striking expression patterns were obtained when the beta-galactosidase activity was localized to subcellular structures by the C. elegans portion of the fusion protein. The active constructs of three selected pools were identified subsequently by an efficient combinatorial procedure. The genomic locations of the DNA fragments from the active constructs were determined and appear to define previously uncharacterized genetic loci.

Hope IA et al. (2003) Gene "The forkhead gene family of Caenorhabditis elegans."

Mounsey A, Aslam S, Bauer P, Hope IA

[Gene, 2003]

The forkhead genes encode a family of transcriptional regulators with important roles in the control of animal development. The genomic sequence has revealed Caenorhabditis elegans has 15 forkhead genes of which six had been experimentally characterised previously. The remaining nine have now been investigated by RNAi and reporter gene expression pattern analysis. Two (B0286.5 and F26B1.7) have key developmental roles, four (F26D12.1, K03C7.2, F40H3.4 and C25A1.2) are expressed in, and may function in, the nervous system and three (C29F7.4, C29F7.5 and F26A1.2), which are closely related to each other, do not appear to be essential. Conservation with forkhead genes in the closely related nematode Caenorhabditis briggsae does not appear to correspond completely with demonstrated functionality in C. elegans. Comparisons of expression patterns and RNAi/mutant phenotypes for all 15 C. elegans forkhead genes reveal the potential complexity of functional interactions for this gene family.

Hope IA et al. (1998) Mol Gen Genet "Promoter trapping identifies real genes in C. elegans."

Arnold JM, McCarroll D, Herbert R, Jun G, Hope IA, Krupa AP

[Mol Gen Genet, 1998]

Promoter trapping involved screening uncharacterized fragments of C. elegans genomic DNA for C. elegans promoter activity. By sequencing the ends of these DNA fragments and locating their genomic origin using the available genome sequence data, promoter trapping has now been shown to identify real promoters of real genes, exactly as anticipated. Developmental expression patterns have thereby been linked to gene sequence, allowing further inferences on gene function to be drawn. Some expression patterns generated by promoter trapping include subcellular details. Localization to the surface of particular cells or even particular aspects of the cell surface was found to be consistent with the genes, now associated with these patterns, encoding membrane-spanning proteins. Data on gene expression patterns are easier to generate and characterize than mutant phenotypes and may provide the best means of interpreting the large quantity of sequence data currently being generated in genome projects.

Hope IA et al. (1996) Trends Genet "The C. elegans expression pattern database: a beginning."

Albertson DG, Martinelli SD, Hope IA, Sonnhammer ELL, Durbin RM, Lynch AS

[Trends Genet, 1996]

Several different biological aspects of the nematode worm, Caenorhabditis elegans, have been thoroughly described. Embryonic and postembryonic development have been described precisely at the cellular level with unique names for each somatic cell (959 in the hermaphrodite and 1031 in the male) created during an individual's lifetime. There is an ordered set of DNA clones covering almost the entire genome and soon the whole genome will have been sequenced. There will then be complete descriptions of this species at both a light microscope level and a molecular genetic level. However, if we are to understand how the one-dimensional genetic information directs the four-dimensional development of the living animal, these two levels of description need to be interconnected. One form of connection is through the genetic map; gene function within the organism is inferred from mutant phenotype. Another more direct connection is through descriptions of when and

Hope IA (1994) Development "PES-1 is expressed during early embryogenesis in Caenorhabditis elegans and has homology to the fork head family of transcription factors."

Hope IA

[Development, 1994]

Promoter trapping has identified a gene, pes-1, which is expressed during C . elegans embryogenesis. The beta-galactosidase expression pattern, directed by the pes-1/lacZ fusion through which this gene was cloned, has been determined precisely in terms of the embryonic cell lineage and has three components. One component is in a subset of cells of the AB founder cell lineage during early embryogenesis, suggesting pes-1 may be regulated both by cell autonomous determinants and by intercellular signals. Analysis of cDNA suggests pes-1 has two sites for initiation of transcription and the two transcripts would encode related but distinct proteins. The predicted PES-1 proteins have homology to the fork head family of transcription factors and therefore may have important regulatory roles in early embryogenesis.

Hope IA et al. (2004) Genome Res "Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system."

Hayes J, Vidal M, Brasch MA, Hope IA, Stevens J, Garner A, Cheo DL

[Genome Res, 2004]

The understanding of gene function increasingly requires the characterization of DNA segments containing promoters and their associated regulatory sequences. We describe a novel approach for linking multiple DNA segments, here applied to the generation of promoter::reporter fusions. Promoters from Caenorhabditis elegans genes were cloned using the MultiSite Gateway cloning technology. The capacity for using this system for efficient construction of chimeric genes was explored by constructing promoter::reporter gene fusions with a gfp reporter. The promoters were found to provide appropriate expression of GFP upon introduction into C. elegans, demonstrating that the short Gateway recombination site between the promoter and the reporter did not interfere with transcription or translation. The recombinational cloning involved in the Gateway system, which permits the highly efficient and precise transfer of DNA segments between plasmid vectors, makes this technology ideal for genomics research programs.

Chalfie M (1997) Biol Bull "A molecular model for mechanosensation in Caenorhabditis elegans."

Chalfie M

[Biol Bull, 1997]

Sensory signaling by chemicals and light are fairly well understood in molecular terms, but the molecules needed for molecular signaling, which underlies the senses of touch, hearing, and balance, are not known. By analyzing the genes needed for mechanosensation in the nematode Caenorhabditis elegans, we hope to gain this molecular

Crook M et al. (2022) MicroPubl Biol "Modelling the Caenorhabditis elegans gonad over developmental time using the Distal Tip Cell marker lag-2p::gfp"

Davis P, Page RB, Crook M, Carvajal T, Tennyson E, Ferdush J

[MicroPubl Biol, 2022]

Development is a process that occurs over time, but defects are often scored at the end point of the process being studied. We are interested in understanding the molecular basis of gonad development in Caenorhabditis elegans and have used the Distal Tip Cell marker lag-2p::gfp to develop a larval size model of gonad growth. We found that gonad length demonstrates two distinct phases relative to larval length, with a breakpoint in mid-L3 stage. We hope that this model will help determine at what point in gonad development our genes of interest act.

Zeng XS et al. (2018) ASN Neuro "Neurotoxin-Induced Animal Models of Parkinson Disease: Pathogenic Mechanism and Assessment."

Jia JJ, Geng WS, Zeng XS

[ASN Neuro, 2018]

Parkinson disease (PD) is the second most common neurodegenerative movement disorder. Pharmacological animal models are invaluable tools to study the pathological mechanisms of PD. Currently, invertebrate and vertebrate animal models have been developed by using several main neurotoxins, such as 6-hydroxydopamine, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, paraquat, and rotenone. These models achieve to some extent to reproduce the key features of PD, including motor defects, progressive loss of dopaminergic neurons in substantia nigra pars compacta, and the formation of Lewy bodies. In this review, we will highlight the pathogenic mechanisms of those neurotoxins and summarize different neurotoxic animal models with the hope to help researchers choose among them accurately and to promote the development of modeling PD.

Bell AD et al. (2024) MicroPubl Biol "A web application for gene-based queries of CaeNDR RNA-seq data."

Bell AD, Paaby AB

[MicroPubl Biol, 2024]

Variation in gene expression is a feature of all living systems and has recently been characterized extensively among wild strains of the model organism <i>Caenorhabditis elegans.</i> To enable researchers to query gene expression and gene expression variation at any gene of interest, we have created a user-friendly web application that shares RNA-seq transcription data for 208 wild <i>C. elegans</i> strains generated by the <i>Caenorhabditis</i> Natural Diversity Resource (CaeNDR). Here, we describe the features of the web application and the details of the data and data processing underlying it. We hope that this website, wildworm.biosci.gatech.edu/cendrexp/ , will help <i>C. elegans</i> researchers better understand their favorite genes and strains.