Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710

Opperman CH et al. (1992) Parasitol Today "Nematode acetylcholinesterases--molecular forms and their potential role in nematode behavior."

Chang S-H, Opperman CH

[Parasitol Today, 1992]

Nematode movement is reliant upon the somatic musculature that runs longitudinally along the body wall. Neuromuscular synapses occur in the ventral and dorsal cords and employ the excitatory neurotransmitter, acetylcholine (ACh), for modulation of muscle activity. Acetylcholine activity is terminated by hydrolysis by acetylcholinesterase (AChE). Here, Charles Opperman and Stella Chang discuss the molecular forms and potential role of this enzyme.

Sterling P et al. (2023) Anim Cogn "Why an animal needs a brain."

Sterling P, Laughlin S

[Anim Cogn, 2023]

In Principles of Neural Design (2015, MIT Press), inspired by Charles Darwin, Sterling and Laughlin undertook the unfashionable task of distilling principles from facts in the technique-driven, data-saturated domain of neuroscience. Their starting point for deriving the organizing principles of brains are two brainless single-celled organisms, Escherichia coli and Paramecium, and the 302-neuron brain of the nematode Caenorhabditis elegans. The book is an exemplar in how to connect the dots between simpler and (much) more complex organisms in a particular area. Here, they have generously agreed to republish an abridged version of Chapter 2 (Why an Animal Needs a Brain), in which many of their principles are first described.

Mangone, Marco et al. (2009) International Worm Meeting "The UTRome project: A resource to study 3'UTR biology in C.elegans."

Salehi-Ashtiani, Kourosh, Vidal, Marc, Attie, Oliver, Mis, Emily, Zegar, Charles, Piano, Fabio, Mangone, Marco, MacMenamin, Philip, Gunsalus, Kris

[International Worm Meeting, 2009]

Three-prime untranslated regions (3''UTRs) are widely recognized as important post-transcriptional regulatory portions of mRNAs. RNA-binding proteins and small non-coding RNAs such as microRNAs (miRNAs) bind to functional elements within 3''UTRs to influence mRNA stability, translation and localization. To characterize and clone C.elegans 3''UTRs, we have developed a high throughput 3''RACE strategy and have characterized an initial target set of 7,014 genes. For each gene, we use a transcript-specific forward primer and a universal polydT(23) anchored reverse primer. The primers are designed to generate products compatible with the Promoterome and ORFeome resource. We cloned the 3''UTRs into an entry vector ready to be used for the third position in the multi-site Gateway system suitable for downstream functional analysis. In our first cycle, we cloned 3''UTRs of ~ 6,000 genes and sequence verified these as mixed bacterial transformants (or "minipools"). For half of these genes, the analysis of their 3''ends identified new 3''UTRs compared to data present in Wormbase WS190 (http://wormbase.org). We subsequently separated these minipools into ~56,000 isolated colonies and re-sequenced our library by deep sequencing (Illumina/Solexa and 454/Roche). We obtained unique cloned 3''UTR isoforms for over 90% of our target set, and observed multiple 3''UTR isoforms for over half. Most of the alternative isoforms are produced by differential PAS site usage. Our data and annotations are being deposited into the modENCODE website (http://www.modencode.org), and are also viewable in our 3''UTR-centric website (http://www.utrome.org). We will present the status of this project and its applications to study 3''UTR biology in C.elegans.

Fradin, Helene et al. (2017) International Worm Meeting "Genome architecture and evolution of the unichromosomal asexual nematode, Diploscapter coronatus."

Piano, Fabio, Corcoran, David, Gunsalus, Kristin, Kovtun, Mikhail, Gutwein, Michelle, Zegar, Charles, Fradin, Helene, Baugh, Ryan, Lucas, Jessica, Fitch, David, Kiontke, Karin

[International Worm Meeting, 2017]

Long-lived clades of animals that reproduce exclusively asexually are rare, presumably because lack of variation in such species results in high extinction rates. Longevity of asexual clades appears to be correlated with the maintenance of heterozygosity across generations. To understand how successful asexual lineages evolve while maintaining heterozygosity, we investigated the reproductive biology and genome sequence of the nematode Diploscapter coronatus. D. coronatus is a species that belongs to the Protorhabditis group, the sister group to Caenorhabditis. We confirmed the existence of a long-lived (approx. 18 million years) asexual clade within Protorhabditis and resolved its phylogeny. We found that all asexual species in the clade have an unusual karyotype: a single pair of chromosomes. This karyotype evolved once from an ancestor with six chromosome pairs. This drastic drop in the number of chromosomes coincides with the transition from sexual to asexual reproduction. We determined the D. coronatus genome structure and sequence, and find evidence in the genome assembly that the single chromosome resulted from the fusion of ancestral chromosomes. This fusion is associated with extensive rearrangement among neighboring regions, which we used to infer a partial spatial order in which ancestral chromosomes fused. The genome can be organized into two divergent homologous haplotypes, confirming that heterozygosity is maintained in this species despite the asexual reproduction. Interestingly, two adjacent fused regions, corresponding to ancestral chromosomal domains I and X, show lower levels of heterozygosity than the other domains. These data are consistent with a scenario in which an initial X-I fusion became a neo-X chromosome in a sexual ancestor. This neo-X would have had a reduced effective population size and thus reduced heterozygosity and increased linkage disequilibrium relative to the autosomes. Consistent with chromosomal fusions, we find no evidence of typical nematode telomeres in the D. coronatus genome. Parthenogenesis likely evolved after chromosomal fusion. Cytological observations indicate that D. coronatus reproduces with a modified meiosis that skips Meiosis I, synapsis and recombination and results in a diploid embryo without fertilization. Consistent with this model, certain key conserved genes with roles in homologous pairing and recombination were not found in the D. coronatus genome. Also, oogenesis without Meiosis I is one way in which parthenogenetic organisms can maintain heterozygosity. As a prelude to functional studies, we also show that D. coronatus is amenable to experimental manipulation by RNAi.

Wyatt TD (2017) Curr Biol "Pheromones."

Wyatt TD

[Curr Biol, 2017]

The reality of invisible chemical signals, pheromones, between members of the same species was recognized long before they could be identified. Charles Darwin proposed that the breeding season sexual smells of male crocodiles, goats and other animals, too, could have evolved by sexual selection of the smelliest males through female choice. But it's not just sex. We now know that pheromones are used by species all across the animal kingdom, in every habitat, and in a wide range of biological contexts, from trail, alarm, and queen pheromones in social insects to the mammary pheromone produced by mother rabbits. Pheromones have provided fascinating examples of signal evolution. In some model organisms, such as moths, Drosophila, Caenorhabditis elegans, and Mus musculus, a complete signaling system can be genetically dissected, from the enzymes producing pheromones, perception by chemosensory receptors, through to the neural circuits processing the signals.

Choi, Myung-kyu et al. (2013) International Worm Meeting "Elucidation of a neuronal mechanism of nictation, a dispersal behavior, in C. elegans."

Choi, Myung-kyu, Park, Dongjun, Lee, Harksun, Lee, Junho, Lee, Daehan

[International Worm Meeting, 2013]

Charles Darwin described that invertebrates can be dispersed by hitch-hiking on other animals. However, a neuronal and molecular mechanism of such dispersal behaviors is not studied well. As a means to dispersal, C. elegans exhibits dauer-specific behavior called nictation: standing and waving at the tip of three-dimensional objects. We have shown that nictation is carried out to facilitate relocation to a favorable environment. We also demonstrated that acetylcholine in IL2 ciliated neurons is important for nictation. According to the observation that dauers only nictate in three-dimensional objects such as micro-dirt chips, we have speculated that mechanical stimuli rather than chemical ones provide initial clues to nictation. Now we are searching for external signals that can activate IL2 neurons. For searching better habitats, individuals must make a decision between exploration and exploitation. Nictation is a decision making behavior because nictation is the outcome of the decision of dauers on whether they ambush or cruise. It is known that a neuromodulatory system can offer flexibility to the output of neural circuits. So, we have also established mutant screening about genes involved in neuromodulation. The results will show that stage-specific alteration in neural substrate can affect stage-specific, dispersal behavior.

Mangone, Marco et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "The landscape of C. elegans 3'UTRs."

Sugano, Sumio, Suzuki, Yukata, Salehi-Ashtiani, Kourosh, Gunsalus, Kris C, Rajewsky, Nikolaus, Harkins, Tim, Prasad Manoharan, Arun, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Mis, Emily, Mackowiak, Sebastian, Han, Ting, Khivansara, Vishal, Kim, John, Piano, Fabio, Zegar, Charles, Gutwein, Michelle, Mangone, Marco, Kohara, Yuji, Buffard, Pascal

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

Three-prime untranslated regions (3UTRs) of metazoan mRNAs contain numerous regulatory elements, yet the structure and developmental impact of 3UTRs remain largely uncharacterized. By integrating data from all Caenorhabditis elegans (C. elegans) developmental stages obtained by polyA capture, 3RACE, full-length cDNAs, and RNAseq, we define ~26,000 distinct mRNA 3 UTRs for ~85% of the 18,328 experimentally supported protein coding genes and refine the annotation of ~30% of gene models. Alternative 3UTR isoforms display widespread differential expression during development. Surprisingly, no canonical or variant polyadenylation signal (PAS) sequence is detec ted for 13% of polyA sites, most frequently among shorter alternative isoforms. Comparing trans-spliced and non trans-spliced genes reveals a strong correlation between the processing of transcript 5 and 3 ends: trans-spliced mRNAs possess longer 3UTRs and a higher frequency of no PAS or variant PAS motifs. We also predict conserved isoform-specific microRNA (miRNA) binding sites and identify additional evolutionarily constrained sequence blocks that may mediate 3UTR regulation. Thus, our data reveal a rich complexity of 3UTRs genome-wide and throughout development in C. elegans.

Boom J et al. (1991) International C. elegans Meeting "OPSIN-FAMILY GENES OF CAENORHABDITIS ELEGANS."

Burr AHJ, Boom J, Hayes M

[International C. elegans Meeting, 1991]

Hoping to find a gene for the visual pigment responsible for the light sensitivity of C. elegans (Burr, 1985), we have cloned 5 unique genomic fragments which hybridize with cDNA probes derived from the Drosophila ninaE opsin gene CThis is one of four opsin genes expressed in Drosophila eyes). A 1.6 kb cDNA probe provided by Charles Zuker was used to screen a C. elegans genomic library in Lambda Charon 4 phage ( made by Terry Snutch) at moderate stringency (62 C; 1 x SSPE). Thirteen positive phage were grouped into 5 unique classes (designated s401-s405) based on the restriction patterns produced by combined digestion with EcoRI and HindIII. The digests were labelled by either of the two PstI fragments of the coding region of the probe. The 5 classes mapped to widely separated cosmids of the C. elegans genome ( courtesy of Alan Coulson and John Sulston). Since hybridization occurred at moderate stringency levels, there appears to be a greater sequence homology between the ninaE and C. elegans opsin genes than between ninaE and many visual pigment opsin genes for which lower stringency levels are necessary for cross-hybridization. It is also possible that the genes we have isolated could be genes of other members of the family of opsin-like receptor proteins. These include hormone, neurotransmitter and pheromone sensors. However, in investigations of vertebrates these others do not cross-hybridize with opsin genes. We plan to identify the function of the five genes by obtaining their sequence and studying their expression and hope to have some sequence to report by meeting time.

Mangone, Marco et al. (2009) International Worm Meeting "The landscape of C.elegans 3'UTRs."

Thierry-Mieg, Danielle, Piano, Fabio, Prasad Manoharan, Arun, Rajewsky, Nikolaus, Thierry-Mieg, Jean, Chen, Kevin, MacMenamin, Philip, Kim, John, Zegar, Charles, Ting, Han, Chen, Wei, Mis, Emily, Mangone, Marco, Kohara, Yuji, Vidal, Marc, Attie, Oliver, Khivansara, Vishal, Salehi-Ashtiani, Kourosh, Gunsalus, Kristin

[International Worm Meeting, 2009]

Three-prime untranslated regions (3''UTRs) contain sequence elements used by RNA-binding proteins and regulatory RNAs such as microRNAs (miRNAs) to influence mRNA stability, translation and localization. However, the annotation of these regions within transcripts is generally incomplete. In C.elegans, which has a well annotated genome, about half of the ~20,000 curated genes in WS190 are not annotated with any 3''UTR and less than 10% are annotated with multiple or alternative 3''UTR isoforms. As part of the modENCODE project, we have developed a pipeline targeting ~7,000 genes using 3'' RACE and found at least one 3''UTR for around 90% of this targeted set. To analyze these data we have used different sequencing technologies that resulted in the identification of multiple distinct 3''UTR isoforms for over half of the targeted genes. In addition to 3''RACE, we have developed a technique to capture polyA ends followed by deep sequencing. This polyA-capture approach has resulted in over 2,000,000 polyA tags that map to ~12,000 genes across all major developmental stages and males, with the majority of these sequences mapping to full-length 3''UTRs. The depth of these data shows the remarkable complexity in the distribution of polyadenylation events in vivo. We have also manually curated 3''UTR boundaries using all available cDNAs, derived mostly from the 200,000 staged ESTs, and obtained 3''UTRs boundaries for ~11,500 genes. For about half of these (~5,000 genes), the data connect 3''UTRs to specific transcripts with known trans-spliced leader sequences at the 5'' end. Combining the results of these analyses has increased our knowledge of 3''UTR structures significantly, identifying novel 3''UTR isoforms for about half of all C.elegans protein-coding genes.