Turner, C. et al. (2019) International Worm Meeting "Loss of O-GlcNacyation Supresses the Activity of a skn-1 Gain-of-Fucnction Mutant."

Curran, S., Turner, C., Pratt, M.

[International Worm Meeting, 2019]

Recently SKN-1 activity was shown to be dependent on the post translational modification O-linked-N-Acetylglucosamine. Here we seek to determine the capacity of this known regulator to influence the activity of a constitutively activated variant of SKN-1. Using genetic nulls of the O-GlcNAc cycling enzymes ogt-1and oga-1, we find that a loss of ogt-1results in an attenuation of SKN-1 gain-of-function phenotypes. Using transcriptomic analysis we find a reduced expression of oxidative stress response genes, while Oil-Red-O lipid staining reveals an attenuation of soma to germline lipid reallocation in late life. These findings demonstrate that this gain-of-function variant of SKN-1 can still be influenced by known regulatory pathways.

Turner LM et al. (1987) International C. elegans Meeting "gamma-irradiation in C elegans."

Turner LM, Baillie DL, Rosenbluth RE

[International C. elegans Meeting, 1987]

Clovis, Y.M. et al. (2017) International Worm Meeting "Rapid phenotypic assessment for mutations involved in human diseases: Uncovering a novel model for cardiac arrhythmia in the nematode C. elegans."

Turner, C, Clovis, Y.M., Webb, A, McCormick, K, Lockery, S

[International Worm Meeting, 2017]

Humans have over 70 potassium channel genes, but only some of these have been linked to disease. In this respect, the KCNQ family of potassium channels is exceptional: mutations in four out of five KCNQ genes underlie a range of diseases including cardiac arrhythmias, deafness, and epilepsy. For example, mutations in KCNQ1 are associated with heart arrhythmias such as long-QT syndrome (LQTS), in which the cardiac action potential is prolonged. Mutations in KCNQ2 and KCNQ3 are associated with benign neonatal epilepsy. Homologs of KCNQ genes are found in a wide range of model organisms, including flies and mice, where they often have functions analogous to those in humans, but less is known about the functions of these potassium channels in the nematode C. elegans. We investigated the effect of mutations in C. elegans KCNQ-like genes on the electrical excitability of the pharynx, a rhythmic muscular pump involved in feeding. One such gene, kqt-1, is orthologous to the subfamily of human KCNQ genes that comprises KCNQ2 to KCNQ5, and is mainly expressed in the muscles of the pharynx. kqt-3 is orthologous to the human gene KCNQ1. Although not expressed in the pharynx, kqt-3 is present in mechanosensory and chemosensory neurons, which can regulate feeding behavior. We hypothesized that mutations in kqt-1 and kqt-3 induce abnormalities in pharyngeal pumping that are reminiscent of cardiac arrhythmias. Taking advantage of a new microfluidic system for C. elegans electrophysiology (NemaMetrix ScreenChip(TM)), we tested this hypothesis by measuring the duration of pharyngeal action potentials and related parameters of pharyngeal pumping. We present evidence that kqt-1 and kqt-3 are necessary for normal pharyngeal pumping, consistent with the well-known role of KCNQ potassium channel mutations in generating cardiac arrhythmias in humans and model organisms. Both genes are required for normal pumping frequency and pump duration, whereas kqt-1 is also required for normal inter-pump intervals. We propose that the strains tested, as well as the recording methodology used, could be the basis of future studies to identify pharmacological agents that mitigate certain arrhythmias.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Siddiqui SS (2000) East Coast Worm Meeting "Kinesin motors moving chromosomal cargo"

Siddiqui SS

[East Coast Worm Meeting, 2000]

Kinesins form a large family of microtubule based motors, which mediate intracellular transport including vesicle delivery, ciliary growth, and chromosomal movement during cell cycle. We have brought to light genes encoding for all known kinesin subfamilies found in mammals in the nematode C. elegans (viz. klp-1-klp-20), by a combination of genetic and molecular approaches. The simple nematode provides an excellent model to elucidate the relationship between structure and function for all kinesin motors within a simple model animal. Our results suggest that the nematode kinesins perform highly specialized cellular functions in ciliary and axonal growth, neurotransmitter vesicle transport, and chromosomal movement during meiosis and mitosis. Most of these in vivo functions are conserved in species as divergent as the nematode and humans. Elucidating kinesin motor function during cell division will unravel how the spindle precisely segregates chromosomes, and may offer insights into the molecular basis of disease states that arise from abnormal spindle dynamics. For example, chromosome non-disjunction during meiosis causes defects as Klinefelter, Down, and Turner Syndromes. Chromosome non-disjunction during mitosis is critical for tumor progression. Chromosome specific kinesin motors provide novel targets for intervention into cell division cycle, and strategies that allow specific blockage of motor function during mitosis may have powerful chemotherapeutic potential.

Oomura, S. et al. (2019) International Worm Meeting "Early embryogenesis of C. inopinata, a sibling species of C.elegans."

Matsumura, Y., Haruta, N., Hoshi, Y., Sugimoto, A., Oomura, S.

[International Worm Meeting, 2019]

C. inopinata is a newly discovered sibling species of C. elegans. Despite their phylogenetic closeness, they have many differences in morphology and ecology. For example, while C. elegans is hermaphroditic, C. inopinata is gonochoristic; C. inopinata is nearly twice as long as C. elegans. A comparative analysis of C. elegans and C. inopinata enables us to study how genomic changes cause these phenotypic differences. In this study, we focused on early embryogenesis of C. inopinata. First, by the microparticle bombardment method we made a C. inopinata line that express GFP::histone in whole body, and compared the early embryogenesis with C. elegans by DIC and fluorescent live imaging. We found that the position of pronuclei and polar bodies were different between these two species. In C. elegans, the female and male pronuclei first become visible in anterior and posterior sides, respectively, then they meet at the center of embryo. On the other hand, the initial position of pronuclei were more closely located in C. inopinata. Also, the polar bodies usually appear in the anterior side of embryo in C. elegans, but they appeared at random positions in C. inopinata. Therefore, we infer that C. inopinata may have a different polarity formation mechanism from that in C. elegans. We are also analyzing temperature dependency of embryogenesis in C. inopinata, whose optimal temperature is ~7 degree higher than that in C. elegans.

Karin Kiontke et al. (2008) Development & Evolution Meeting "New Phylogeny Of Caenorhabditis Including Recently Discovered Species"

David Fitch, Karin Kiontke, Marie-Anne FELIX

[Development & Evolution Meeting, 2008]

Recently, seven new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to 17, 10 of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10, 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Whereas none of them is likely to be the sister species of C. elegans, we now know of two close relatives of C. briggsae-C. sp. 5 and C. sp. 9. C. sp. 9 can hybridize with C. briggsae in the laboratory [see abstract by Woodruff et al.]. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. This species is easier to cultivate than C. japonica and may be a better candidate for comparative experimental work. Two of the new species branch off before C. japonica as sister species of C. sp. 3 and C. drosophilae+C. sp. 2, respectively. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and five from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last two years. There is no indication that we are even close to knowing all species in this genus.

Schartner, Caitlin M. et al. (2015) International Worm Meeting "X-chromosome evolution: divergence of X-sequence motifs that drive dosage compensation across Caenorhabditis species."

Meyer, Barbara J., Lo, Te-Wen, Schartner, Caitlin M.

[International Worm Meeting, 2015]

Dosage compensation (DC) across Caenorhabditis species exemplifies an essential process that has undergone rapid co-evolution of protein-DNA interactions central to its mechanism. In C. elegans, recruitment elements on X (rex sites) recruit a condensin-like DC complex (DCC) to hermaphrodite X chromosomes to balance gene expression between the sexes. Recruitment assays in vivo showed that C. elegans rex sites do not recruit the DCC of C. briggsae, and vice versa. To understand how DC complexes and X chromosomes evolved to use different X targeting sequences, we compared DCC subunits and binding sites in C. elegans to those in three species of the C. briggsae clade (15-30 MYR diverged): C. briggsae, its close relative C. nigoni (C. sp. 9), and C. tropicalis (C. sp. 11). By raising antibodies and introducing endogenous tags with TALENs or CRISPR/Cas9, we showed that homologs of both SDC-2, the pivotal X targeting factor, and DPY-27, a DCC-specific condensin subunit, bind X chromosomes of XX animals. Although the DCC shares key components across these four species, the binding sites differ. First, ChIP-seq studies in C. briggsae and C. nigoni identified DCC binding sites that are homologous across these close relatives but differ from C. elegans sites in sequence and location. Second, C. elegans sites use motifs enriched on X (MEX and MEXII) to drive DCC binding, but these motifs are not in C. briggsae or C. nigoni DCC sites and are not X-enriched. Third, we found an X-enriched motif at DCC binding sites of C. briggsae and C. nigoni that is not X-enriched in C. elegans. An oligo with the C. briggsae motif recruits the DCC in C. briggsae, but a similar oligo lacking the motif fails to recruit, establishing the importance of the motif. Fourth, another motif was found in C. briggsae and C. nigoni that shares a few nucleotides with MEX, but its functional divergence was shown by C. elegans recruitment assays. Fifth, two endogenous C. briggsae X-chromosome regions with strong C. elegans MEX motifs fail to recruit the C. briggsae DCC, as assayed by ChIP-seq and recruitment assays. None of these DCC motifs is enriched on the C. tropicalis draft X sequence, supporting further binding site divergence within the C. briggsae clade. Ongoing ChIP-seq studies in C. tropicalis will help determine how C. elegans and C. briggsae clade motifs are evolutionarily related. Comparison of DCC targeting mechanisms across these four species allows us to characterize a rarely captured event: the recent co-evolution of a protein complex and its rapidly diverged target sequences across an entire X chromosome.

Yang, Bing et al. (2015) International Worm Meeting "Identifying genes involved in H3K9me2 regulation in C. elegans."

Xu, Xia, Maine, Eleanor, Yang, Bing

[International Worm Meeting, 2015]

Histones can receive many different modifications, and the presence/absence of certain modifications is implicated in transcriptional control and chromosomal events. One modification, H3K9me2, has been found to be associated with unpaired chromatin during meiosis in different organisms, including C. elegans [1-3]. For example, in the male C. elelgans germline, the single X chromosome is unpaired during pachytene and is detected as a single strong focus of H3K9me2 by immuno-labeling. This interesting phenomenon led to the question of how H3K9me2 marks are specifically targeted to their genomic sites.In order to address this question, we are identifying H3K9me2 methyltransferase (MET-2) co-factors. To do so, we generated antibody against MET-2 and epitope-tagged met-2 transgenes. Using these reagents, we performed immunoprecipitation and tandem MS sequencing to recover potential co-factors. Currently, we are testing a list of potential interactors by two different approaches. First, we utilize RNAi to knock down or a mutation to knock out the candidate gene product and then examine the H3K9me2 distribution pattern in the male germline. Second, we perform reverse co-immunoprecipitation by using antibody against the candidate gene product or epitope-tagged transgene product generated either by Mos1-mediated single copy insertion [4] or CRISPR-Cas9 [5] methods. Among the list of candidate genes that have been tested so far, we have identified several genes whose activity impacts H3K9me2 deposition.References: 1. Shiu, P.K., et al., Cell, 2001. 107(7): 905-16. 2. Kelly, W.G., et al., Development, 2002. 129(2): 479-92. 3. Turner, J.M., et al., Nat Genet, 2005. 37(1): 41-7. 4. Frokjaer-Jensen, C., et al., Nat Meth, 2014. 11(5): 529-534. 5. Ran, F.A., et al., Cell. 154(6): p. 1380-1389.

Kiontke, Karin C. et al. (2009) International Worm Meeting "New Caenorhabditis species: phylogeny and evolution."

Fitch, David H. A., Felix, Marie-Anne, Kiontke, Karin C.

[International Worm Meeting, 2009]

Recently, nine new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to nineteen, eleven of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10 and 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Although none of them is the sister species of C. elegans, C. sp. 5 and C. sp. 9 are close relatives of C. briggsae. C. sp. 9 can hybridize with C. briggsae in the laboratory. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. Three of these species, C. sp. 7, C. sp. 9 and C. sp. 11 have been chosen for genome sequencing. Four further new species branch off before C. japonica within a monophyletic clade which also comprises C. sp. 3 and C. drosophilae. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and seven from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. Other characters, like the shape of the stoma and the male tail, introns, susceptibility to RNAi and genome size are being evaluated in the context of the phylogeny. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last few years. There is no indication that we are even close to knowing all species in this genus.