Philippe Vaglio et al. (2001) International C. elegans Meeting "WorfDB: The C. elegans ORFeome database"

Marc Vidal, Jerome Reboul, Jean-Francois Rual, Philippe E Lamesch, David E Hill, Philippe Vaglio

[International C. elegans Meeting, 2001]

Kowalski T et al. (2015) PLoS One "Indexing Arbitrary-Length k-Mers in Sequencing Reads."

Grabowski S, Deorowicz S, Kowalski T

[PLoS One, 2015]

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.

Kaempfer, Philipp et al. (2015) International Worm Meeting "Improved C. briggsae genome assembly."

Dahl, Andreas, Schloissnig, Siegfried, Tinney, Mathew, Kaempfer, Philipp, Sarov, Mihail, Winkler, Sylke, Merret, Stephanie

[International Worm Meeting, 2015]

C. briggsae is and essential sister model to C. elegans for comparative genomics and evo-devo studies. Since the original genome was published in 2003 the genome assembly has been improved several times but it is still incomplete. We attempted to improve the quality of the C. briggsae genome assembly using the Pacific Bioscience sequencing platform and the more conventional approach of Illumina paired-end sequencing of total genomic DNA and an arrayed genomic fosmid library. We find that the PacBio data is sufficient for a very high quality assembly even in highly repetitive regions.The C. briggsae sequencing was our proof of principle experiment before we move on to other currently unsequenced or partially sequenced genomes that we need in order to study the evolutionary divergence of developmental programs. The meeting will be a good opportunity to compare our agenda with other similar initiatives to avoid duplication of effort and to optimise the use our resources.

Philippe Vaglio et al. (2002) West Coast Worm Meeting "THE C. ELEGANS ORFEOME CLONING PROJECT : VERSION 1.0"

Troy Moore, Jerome Reboul, Monica Martinez, Mike Brasch, Alban Chesneau, Marc Vidal, David E Hill, Jean-Francois Rual, Lynn Doucette-Stamm, Hongmei Lee, Philippe Vaglio, Nicolas Bertin, Laurent Jacotot, Philippe Lamesch, Jim Hartley, Christopher Armstrong

[West Coast Worm Meeting, 2002]

In addition to the draft of the human genome sequence, the genome sequences of an increasing number of model organisms are now available. This sequence information is expected to revolutionize the way biological questions can be addressed. Molecular mechanisms should now be approachable on a more global scale in the context of (nearly) complete sets of genes, rather than by analyzing genes individually. However most protein-encoding open reading frames (ORFs) predicted from these sequencing projects have remained completely uncharacterized at the functional level. For example, out of 19,000 ORFs predicted from the C. elegans genome sequence, the function of approximately 1,200 has been experimentally characterized during the last 30 years. Functional genomics and proteomics address this limitation through the simultaneous annotation of large numbers of predicted ORFs. Despite the urgent need for large-scale functional annotation projects, functional genomics approaches have remained relatively undeveloped in multicellular organisms, primarily because of the lack of suitable methods to clone large numbers of protein-encoding ORFs into many different expression vectors. Indeed, most strategies developed in these projects are based upon the expression of large numbers of proteins in exogenous settings and in fusion with relevant tags. In order to facilitate these different proteome-wide projects, a complete set of ORFs (or ?ORFeome?) will need to be cloned multiple times into many different expression vectors for each model organism of interest. To achieve this goal, one solution is to clone an ORFeome of interest once and for all in a "resource" vector allowing a convenient transfer to various expression vectors. To clone the C. elegans ORFeome into various expression vectors, we use a recombination cloning technique referred to as Gateway. This technique allows both the initial cloning of ORFs and their subsequent transfer into different expression vectors by site-specific recombination in vitro. We have now finished the first part of the C. elegans ORFeome project which was to attempt to clone the ~19,000 predicted ORFs. We will present the success rate in cloning of the ORFs and the overall quality of the ORFeome to date. We will also describe how the ORFeome was used as a new approach to construct a ~100% normalized yeast two-hybrid library. Finally we will show how we could transfer thousands of ORFs from the resource clones into a dozen different expression vectors for uses in large-scale functional genomic and proteomic projects such as gene inactivation by RNAi, protein interaction mapping by yeast two-hybrid, protein production for structural genomics etc.

J Connolly et al. (1999) International C. elegans Meeting "A C. elegans-based study of Huntington Disease-associated pathways"

M Chalfie, C Neri, S Holbert, I Denghien, C Philippe, J Connolly, S Moriniere

[International C. elegans Meeting, 1999]

Polyglutamine (polyQ) expansion in huntingtin (htt) underlies Huntington's disease (HD). The mechanisms which cause neuron dysfunction and degeneration in HD are unknown. To identify HD-associated pathways, we have undertaken a C. elegans-based study that relies on two approaches: screening for proteins able to interact with htt, and screening for genetic suppressors of mutated htt-dependent phenotypes in transgenic worms. We used the mec-3 promoter (mec-3p) to express GFP fusions which contain a short N-terminal fragment of htt with a normal (17 units) or expanded (84 units) polyQ tract. The mec-3 gene is expressed in 10 neurons including the six touch receptor neurons AVM, ALML, ALMR, PVM, PLML and PLMR. Worms expressing the long polyQ construct were less than 30% and 50% Mec at the tail at Day 1 and 7, respectively. Worms expressing the short polyQ construct or animals with GFP expression driven by mec-3p were less than 7% and 30% Mec at the tail over the same time-frame. Cell death was not observed in these experiments. There was an imperfect correlation between the perinuclear aggregation of GFP fusions in PLM cells and the Mec phenotypes observed. Our preliminary data suggest that N-terminal htt fragments with a long polyQ induce touch insensitivity when expressed in touch receptor neurons, and that transgenic worms expressing mutated htt might be useful for screening for genetic suppressors of behavioural phenotypes. We have screened a C. elegans cDNA library (R. Barstead, OMRC, OK) by using two-hybrid selection in yeast. The screening with a N-terminal htt fragment containing 15 Glns allowed the identification of a new Htt Interacting Protein (wHIP3). WHIP3 shows variation of interaction between normal and mutated htt, and is homologous with a human protein (hHIP3) encoded by a gene expressed in the brain. Additional studies are being performed in order to test whether hHIP3 might be involved in HD. We will present the results of experiments based on both approaches.

Dirksen, Philipp et al. (2011) International Worm Meeting "Natural ecology of C. elegans in Germany."

Petersen, Carola, Peters, Fabian, Chen, Wei, Dirksen, Philipp, Dierking, Katja, Schulenburg, Hinrich

[International Worm Meeting, 2011]

Taking a step outside the laboratory and exploring C. elegans in its natural habitat is part of our attempt to combine ecological, evolutionary, and molecular approaches to study host-microbe interactions under more realistic conditions. Here we report our recent findings on natural C. elegans populations from Germany. In 2010, we isolated nematodes from two different locations, Kiel at the Baltic Sea and Munster (Roxel) in northwest Germany. These samples are currently used to assess the diversity of associated microbial organisms, including pathogens as well as possible mutualists. We furthermore evaluate natural variation in ecologically relevant traits such as pathogen resistance, microbe-related choice behaviors and also mating incompatibilities. These analyses serve to identify the selective constraints that act on natural C. elegans populations and that are thus likely important determinants of nematode life-history characteristics as well as the underlying molecular signaling cascades.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

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.

Antika TR et al. (2023) J Biol Chem "Sequence-specific targeting of C. elegans C-Ala to the D-loop of tRNAAla."

Horng JC, Hsu HL, Nazilah KR, Wang CC, Wang TL, Wang SC, Antika TR, Chuang TH, Chrestella DJ, Wang SW, Tseng YK, Pan HC

[J Biol Chem, 2023]

Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Ala_c) robustly binds both ligands. How Ce-C-Ala_c targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Ala_c are responsible for DNA and tRNA binding, respectively. Ce-C-Ala_c specifically recognized the conserved invariant base G¹⁸ in the D-loop of tRNA^Ala through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala (Ce-C-Ala_m) robustly bound both tRNA^Ala and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNA^Ala.

Blumenthal TE et al. (1994) Worm Breeder's Gazette "C. elegans U2AF 65."

Zorio DAR, Lea K, Blumenthal TE

[Worm Breeder's Gazette, 1994]

C. elegans U2AF65