Vertical transmission in Caenorhabditis nematodes of RNA molecules encoding a viral RNA-dependent RNA polymerase

International audienceHere, we report on the discovery in Caenorhabditis nematodes of multiple vertically transmitted RNAs coding for putative RNA-dependent RNA polymerases. Their sequences share similarity to distinct RNA viruses, including bunyaviruses, narnaviruses, and sobemoviruses. The sequences are present exclusively as RNA and are not found in DNA form. The RNAs persist in progeny after bleach treatment of adult animals, indicating vertical transmission of the RNAs. We tested one of the infected strains for transmission to an uninfected strain and found that mating of infected animals with uninfected animals resulted in infected progeny. By in situ hybridization, we detected several of these RNAs in the cytoplasm of the male and female germline of the nematode host. The Caenorhabditis hosts were found defective in degrading exogenous double-stranded RNAs, which may explain retention of viral-like RNAs. Strikingly, one strain, QG551, harbored three distinct virus-like RNA elements. Specific patterns of small RNAs complementary to the different viral-like RNAs were observed, suggesting that the different RNAs are differentially recognized by the RNA interference (RNAi) machinery. While vertical transmission of viruses in the family Narnaviridae, which are known as capsidless viruses, has been described in fungi, these observations provide evidence that multicellular animal cells harbor similar viruses

Comparative genomics of 10 new Caenorhabditis species

Abstract The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole‐genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model

Interaction of the chromatin remodeling protein hINO80 with DNA

The presence of a highly conserved DNA binding domain in INO80 subfamily predicted that INO80 directly interacts with DNA and we demonstrated its DNA binding activity in vitro. Here we report the consensus motif recognized by the DBINO domain identified by SELEX method and demonstrate the specific interaction of INO80 with the consensus motif. We show that INO80 significantly down regulates the reporter gene expression through its binding motif, and the repression is dependent on the presence of INO80 but not YY1 in the cell. The interaction is lost if specific residues within the consensus motif are altered. We identify a large number of potential target sites of INO80 in the human genome through in silico analysis that can grouped into three classes; sites that contain the recognition sequence for INO80 and YY1, only YY1 and only INO80. We demonstrate the binding of INO80 to a representative set of sites in HEK cells and the correlated repressive histone modifications around the binding motif. In the light of the role of INO80 in homeotic gene regulation in Drosophila as an Enhancer of trithorax and polycomb protein (ETP) that can modify the effect of both repressive complexes like polycomb as well as the activating complex like trithorax, it remains to be seen if INO80 can act as a recruiter of chromatin modifying complexes

The Ancestral Caenorhabditis elegans Cuticle Suppresses rol-1

Genetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancestral version of col-182 also modifies the phenotypes of four other classical cuticle mutant alleles, and the effects of natural genetic variation on worm shape and locomotion. These results underscore the importance of genetic background and the serendipity of Brenner’s choice of strain

<i>In vivo</i> interaction of INO80 on predicted gene targets.

<p>(A) A line diagram for the region 2Kb upstream of HOXC11 gene is shown as the example of the region analyzed by ChIP. The filled rectangle denotes the INO80 binding motif and the position of the primers (arrows) are marked. (B) ChIP-PCR results for the indicated genes on the human genome. The interaction of INO80 protein was examined in the upstream sequences of these genes using INO80 antibody in HEK293T cells. IgG antibody was used as the negative control for ChIP experiment. The negative (-ve) and positive (+ve) indicate the PCR controls. Input is 20% of sonicated chromatin. (C) Quantitative PCR for putative INO80 targets following ChIP assay in HEK293T cells. The Y axis shows the enrichment as percentage input observed. NAT2 and PSEN lack the INO80 binding motif. (*p value<0.05, **p value<0.001 Two tailed Student t-test)</p

Selective recognition of human telomeric G-quadruplex with designed peptide:Via hydrogen bonding followed by base stacking interactions

We described a novel synthetic peptide in which a glutamine residue binds through hydrogen bonding to a guanine-base and a trytophan residue intercalates with K(+) resulting in stabilization of a human telomeric G-quadruplex with high selectivity over its complementary c-rich strand and a double-stranded DNA and its complementary C-rich strand. This peptide offers great potential for cancer treatment by inhibiting the telomere extension by telomerase

Competitive EMSA with the mutant oligos.

<p>(A) List of mutant oligos used in the assays, (B) Results of competitive EMSA with mutant oligos at the indicated ratio, (C) Densitometric scan of gel shown in B. The intensity value of the band (shown by arrow) in the lanes shown in (B), normalized to band at the same position in lane 2, are plotted on the Y-axis. Three different ratios for each competing oligo were used as indicated in B and the mutant sequence used is mentioned below the histogram.</p

INO80 interaction with SELEX motif.

<p>(A) Interaction of GST-DBINO with DNA. (B) Optimization of molar ratio of oligonucleotide: nuclear extract from HEK293T cells for EMSA.</p

MEME-based prediction of INO80 binding motif.

<p>(A) Snapshot of MEME output for the sequences enriched after DBINO interaction, (B) Position weight matrix of the putative INO80 motif generated by MEME.</p