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[
European Worm Meeting,
2008]
Transposable elements (TE) are widely acknowledged as drivers of genome. evolution. To analyze the potential mutagenicity of TE excision, we. investigated the nature of the modifications that the C. elegans genome. undergoes during the repair of a DNA double-strand break (DSB) triggered by. TE mobilization.. Mos1 is a Drosophila transposon which can be experimentally mobilized. in C. elegans. We took advantage of this system to trigger single DSBs at. defined loci and study their repair. We demonstrated that DSB are repaired. by pathways relying on both end-joining and homologous recombination.. Specifically, detailed analysis of germ line repair events showed that most. of the Mos1-induced DSB are repaired by recombination using the homologous. chromosome as a repair template and that these events can be associated. with crossovers. Recombination at homologous ectopic sites was also. observed at a low but significant frequency. In addition, end-joining. events and intrachromosomal recombination were also detected. Together,. these results demonstrate that TE can induce heritable gross chromosomal. rearrangements as well as point mutations and small deletions or insertions. when they transpose in the germ line of wild-type C. elegans.. These data were used to develop MosTIC (which stands for "Mos1 induced. transgene instructed gene conversion"), a technique based on homologous. recombination that enables genomic engineering in C. elegans. This. technique will be presented in details.
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Cerrato, C., Dong, Y., Dernburg, A.F., Ahringer, J., Janes, J., Carelli, F.N., Appert, A.
[
International Worm Meeting,
2019]
Transposable elements (TEs) are DNA sequences capable of inserting into new genomic locations. Although new TE integrations are usually neutral or deleterious for the host, TE amplification can disperse protein binding sites in the genome, and thus generate new regulatory elements. Distinct classes of TEs have been shown to be enriched at promoters or enhancers active in specific tissues or cell types. TE expansion has, therefore, the potential to drive the evolution of gene regulatory networks. To date, nonetheless, these observations have been mostly limited to correlation analyses or tested in cell lines. Here we provide evidence that two classes of DNA transposons have been co-opted as new regulatory elements in C. elegans. We found that a pair of DNA motifs, strongly enriched in germline-specific promoters, are part of the inverted repeat sequences of CERP2 and CELE2, two inactive DNA transposons. Through reporter assays, we validated the activity of the two motifs, confirming their role in driving germline-specific regulatory elements in vivo. Comparative analyses revealed that CERP2-associated motifs are found across the whole Caenorhabditis clade but not in other nematodes, whereas the CELE2-expanded motifs are C. elegans-specific. By annotating regulatory elements in the sister species C. briggsae, we confirmed that C. elegans-specific repeat expansions led to the emergence of a number of germline promoters which could not be identified at the orthologous locations in C. briggsae. Finally, using chromatin immunoprecipitation assays, we found that two fast evolving proteins important for germ line function have binding associated with the CERP2/CELE2 motifs. Overall, our work provides strongly suggests that distinct waves of TE expansion have shaped the germline regulatory network in the Caenorhabditis genus.
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[
International Worm Meeting,
2021]
Breeding systems determine the way genes are transmitted to the next generation, consequently driving genetic variation and genome evolution. Breeding systems may also play a role in the activity and prevalence of transposable elements. Selfing should increase the selection efficacy against TEs as a result of high homozygosity, with the majority of TEs present having reached fixation through genetic drift. Conversely, outcrossing should facilitate the spread of TE insertions throughout populations, and result in a higher number of moderately deleterious mutations. In the Caenorhabditis group Elegans, there doesn't appear to be a clear pattern of TE dynamics across partially-selfing species and obligately outcrossing species. Most species in the Elegans group, appear to have chromosomal heterogeneity in repeat density, with chromosome arms being more repeat rich, and gene poor, than the centers. This association is not always consistent, as is the case for the outcrossing species C. inopinata and C. bovis, where some, but not all, repeat types have a more uniform distribution across the chromosome, with little divergence between copies, which may indicate recent TE activity. It is currently unknown whether these observations are also found across species from the obligately outcrossing Caenorhabditis group Japonica. Here we present the first chromosome-scale assembly for a species belonging to the Japonica group, Caenorhabditis becei. This high-quality assembly was generated from PacBio long read data, Hi-C data, and a genetic map of an advanced intercross panel. The gene annotation for this genome was generated using Iso-Seq data and RNA-seq data from C. becei, as well as orthologous protein-coding and protein sequences from other Caenorhabditis species. We then characterized features such as synteny to other Caenorhabditis species, genome size, recombination rate domain structure, gene content, orthology, and distribution. We created a classified library of repetitive elements identified through de novo approaches. We generated TE annotations for the C. becei genome, and we reveal the patterns of repeat density, prevalence, distribution, and divergence.
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[
International Worm Meeting,
2009]
The C. elegans genome is around 100 Mb long, and about 12% of it is derived from transposable elements (TEs). There has been a recent growing interest in the possible role of mobile elements in genome regulation and evolutionary plasticity; however, there has been no comprehensive, detailed analysis of the overall C. elegans TE distribution and their possible functional roles. In this study, we analyzed the intra and inter-chromosomal distribution pattern of all 156 TE families known in C. elegans. We found that more than 12% of these families are over-represented on the X chromosome. The many unique features of the X chromosome, such as dosage compensation, inactivation in the germline and low gene density make it an interesting case study for possible biological relevance of the skewed distribution of these families. Cele45, for example, is a family of Short Interspersed Elements (SINEs) which has 3 times more insertions on the X chromosome than expected. Conversely, we found that 10% of the TE families are completely absent in this chromosome, despite their high copy number (more than 500 copies) in the autosomes. Cele4, a DNA transposon, has 831 copies in the C. elegans genome and none of those are found on the X chromosome. It has been previously shown that the distribution pattern of DNA transposons is positively correlated with high recombination rates, which usually occur in the chromosomal arms. In the X chromosome, however, recombination rates are uniform across its length. Intriguingly, we found that the distribution pattern of most of the families (51%) of both DNA and RNA transposons does not correlate with recombination rate on the X chromosome. Thus, other factors must account for the preferential accumulation of these TEs on the arms of the X chromosome.
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[
International Worm Meeting,
2021]
Transposable elements (TEs) are powerful agents of evolution that can rewire transcriptional programs by mobilizing and distributing transcription factor (TF) DNA-binding motifs throughout genomes. To investigate the extent that TEs provide TF-binding motifs in C. elegans, we determined the genomic positions of DNA-binding motifs for over 200 different TFs (1). Surprisingly, we found that almost all of the examined TFs have binding motifs that reside within TEs, and all types of TEs have at least one instance of a TF motif, demonstrating that TEs provide previously unappreciated numbers of TF-binding motifs to the C. elegans genome. After determining the occurrence of TF motifs in TEs relative to the rest of the genome, we identified numerous TF-binding motifs that are highly enriched within TEs compared to what would be expected by chance. Consistent with potential functional roles for these TE-enriched TF-binding sequences, we found that significantly more TEs with TF motifs display evidence for selection compared to those lacking motifs through the use of publicly available genome variation data (2). We also compared the locations of TE-residing TF motifs to published ATAC-seq (3) and ChIP-seq (4) data, which identify regions of open chromatin associated with TF DNA binding and regions bound by TFs of interest, respectively. Strikingly, we found that all of the TF motif types that occur in TEs have instances of residing within accessible chromatin, and the overwhelming majority of TF-binding motifs located within TEs associate with their cognate TFs, suggesting extensive binding of TFs to sequences within TEs. Additionally, TEs with accessible or TF-bound motifs reside in the putative promoter regions of ~14% of all protein-coding genes, providing widespread possibilities for influencing gene expression. Taken together, our work shows that TE-provided TF-binding sites are ubiquitous in C. elegans and have broad potential to rewire gene expression. 1. Weirauch et al. (2014) Cell 158:1431-1443. 2. Cook et al. (2016) Nucleic Acids Research 45:D650-D657. 3. Daugherty et al. (2017) Genome Research 27:2096-2107. 4. Kudron et al. (2018) Genetics 208:937-949.
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[
International Worm Meeting,
2013]
The nematode Caenorhabditis elegans has emerged as an important tool in pharmacology and toxicology because of its invariant and fully described developmental program, well-characterized genome, ease of maintenance and genetic manipulation, short and prolific life cycle, and small body size. This model has shown to be useful in the evaluation of the biological activity and the mechanisms of action of new synthetic compounds such as organoselenium and organotellurium compounds. Most of these compounds depict antioxidant potential in other models, however little is known regarding their mechanisms. Antioxidant response can be modulated by intracellular signaling, such as FOXO pathway, which is DAF-16 pathway in worms. This work was based on the hypothesis that depending on the chemical structure of the compounds, they would modulate the insulin-like pathway DAF-16 and consequently depict higher antioxidant potential against pro-oxidants. N2, TJ356 and CF1553 strains were handled and maintained at 20 deg C on E. coli OP50/ NGM plates. The lethal dose 50% (LD50) of the compounds was determined with doses ranging from 0.1 to 2250 mM. Synchronized L1 worms were treated with the compounds for 30 min. For stress- resistance assays, worms were pre-treated for 30 min with compounds and then exposed for 30 min to the prooxidant paraquat. We determined the LD50 using a sigmoidal dose-reponse curve and for the resistance assays we used one-way ANOVA to compare groups. Our results showed that xylofuranosides and some quinolines containing Se or Te have very low toxicity. We have found that Te-containing compounds can modulate DAF-16 pathway at lower concentrations, with consequent increase in SOD-3::GFP expression. Consequently, these compounds presented higher antioxidant potential at sublethal concentrations in wild type worms, as observed by protection against paraquat. We also observed that quinolines with a donator group have higher antioxidant activity. Furthermore, these studies show that C. elegans can be contribute to the rational drug synthesis field.
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[
International Worm Meeting,
2007]
To confer resistance against the root gall nematode Meloidogyne incognita, a study was performed to introduce Bacillus thuringiensis (Bt) crystal protein toxin genes into tomato plant (Lycopersicon esculentum var. Rutgers select) hairy roots. Crystal toxin gene sequences were altered to allow plant expression and in some cases also included unique intron sequences to aid in protein expression. Genes were inserted into the pBluscript in concert with a double 35S plant promoter and kanamycin resistance. The vector was used to transform the plant pathogenic bacterium Agrobacterium rhizogenes. The transformed Agrobacterium was used to induce the toxin genes into plants by co-cultivation with tomato cotyledons. Hairy root lines were selected via kanamycin resistance and once established, root extracts were tested for relative expression of crystal toxin by western blot analysis using a polyclonal detection sera specific for each toxin. Induced resistance against the root gall nematode was examined by hairy root challenge against a load of J2 stage parasitic nematodes. Subsequent enumeration of total egg masses (EM), total sites of infection (INF) and total calculated eggs (TE) per root plate were used to determine resistance against nematode infections. Results of these studies will be discussed. Data suggests that some Bt crystal proteins have excellent potential to control plant parasitic nematode (PPN) infections in transgenic plants.
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[
C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany,
2010]
Immunoglobulin superfamily Cell Adhesion Molecules (IgCAMs) are key regulators of nervous system development. The contactin subgroup of IgCAMs consists of GPI-anchored glycoproteins implicated in axon outgrowth, guidance, fasciculation and neuronal differentiation. The intracellular mechanism by which contactins facilitate neuronal development is not understood. To gain insight into the function of contactins, we characterized RIG-6, the sole contactin of C. elegans. Here, we show that RIG-6 affects longitudinal axon outgrowth of mechanosensory neurons in a cell autonomous manner. Furthermore RIG-6 is implicated in axon guidance along the circumferential axis. We find that RIG-6 facilitates accurate nervous system patterning by prohibiting commissural dendri te convergence and branching, as well as axon cross-over at the ventral nerve cord. RIG-6 expression levels are critical for nervous system architecture. Upregulation of this contactin causes several behavioral deficits such as abnormal locomotion, egg laying and defecation. In addition to its neuronal function, RIG-6 is also involved in non-neuronal cell migration and morphogenesis. Our data suggest that RIG-6 and the cytoplasmic protein UNC-53 synergize to direct axon guidance and branching along both the anterior-posterior and dorso-ventral direction. This implies that UNC-53/NAV2 proteins may contribute to relay signaling via contactins.
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[
Aging, Metabolism, Stress, Pathogenesis, and Small RNAs, Madison, WI,
2010]
DAF-16, a forkhead-type transcription factor, function in downstream of an insulin/insulin-like growth factor-1 (Ins/IGF-1) signaling pathway, and is related to regulation of aging and oxidative stress resistance in the nematode Caenorhabditis elegans (C. elegans). In the latest report, we described that a consensus DAF-16 binding element (DBE), which binds the DAF-16 transcription factor, was discovered in the promoter region of
sod-5 gene encoding a Cu/Zn superoxide dismutase (SOD) in C. elegans. The DBE position was 192 base pairs (bp) upstream of the first exon of
sod-5 gene from the C. elegans genomic database. In a
daf-16 gene null mutant,
daf-16(mgDf50) strain, the
sod-5 gene expression as well as
sod-3 gene was obviously suppressed compared with it in wild-type N2. The phenotype of lifespan in
daf-16(mgDf50) animals was reduced when compared with N2. Therefore, it is suggested that
sod-5 gene expression is necessary to maintain the lifespan in wild-type with
sod-3 gene during normal aging. In addition, we could not find a functional compensation by
sod-1 gene in the
sod-5 deletion mutant such as the compensatory expression of
sod-5 gene via the Ins/IGF-1 signaling pathway in the
sod-1 deletion mutants (1).
sod-1 gene might have considerable capacity in the expression during the C. elegans normal aging. Thus, it is assumed that the Ins/IGF-1 signaling pathway plays more important role to epigenetic regulation of the target genes under aging and stressful conditions. Reference 1. Yanase S, Onodera A, Tedesco P, Johnson TE, Ishii N (2009) SOD-1 deletions in Caenorhabditis elegans alter localization of intracellular reactive oxygen species and show molecular compensation. J Geront 64A: 530-539.