Genomes and Genes
Summary: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
- Ciosk R, DePalma M, Priess J. Translational regulators maintain totipotency in the Caenorhabditis elegans germline. Science. 2006;311:851-3 pubmed
- Lee R, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001;294:862-4 pubmed..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse. ..
- Zemann A, op de Bekke A, Kiefmann M, BROSIUS J, Schmitz J. Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 2006;34:2676-85 pubmed..Some target sites modified by snoRNAs were changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs. ..
- Mango S. Stop making nonSense: the C. elegans smg genes. Trends Genet. 2001;17:646-53 pubmed..Here I describe what is known about the smg genes and their potential functions in these two mRNA degradation pathways. ..
- Zipperlen P, Fraser A, Kamath R, Martinez Campos M, Ahringer J. Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy. EMBO J. 2001;20:3984-92 pubmed
- Winston W, Sutherlin M, Wright A, Feinberg E, Hunter C. Caenorhabditis elegans SID-2 is required for environmental RNA interference. Proc Natl Acad Sci U S A. 2007;104:10565-70 pubmed..elegans. SID-2, when expressed in the environmental RNAi defective species Caenorhabditis briggsae, confers environmental RNAi. ..
- Gauci C, Lightowlers M. Alternative splicing and sequence diversity of transcripts from the oncosphere stage of Taenia solium with homology to the 45W antigen of Taenia ovis. Mol Biochem Parasitol. 2001;112:173-81 pubmed..In this respect, the generation of sequence diversity and hence potential antigenic diversity through alternative splicing of TSO45 genes may have implications for the use of these proteins in vaccines against T. solium cysticercosis. ..
- GONCZY P, Echeverri C, Oegema K, Coulson A, Jones S, Copley R, et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature. 2000;408:331-6 pubmed
- Longman D, Johnstone I, Caceres J. Functional characterization of SR and SR-related genes in Caenorhabditis elegans. EMBO J. 2000;19:1625-37 pubmed..RNAi with CeSRPK, an SR protein kinase, resulted in early embryonic lethality, suggesting an essential role for SR protein phosphorylation during development. ..
- Wachi M, Ogawa T, Yokoyama K, Hokii Y, Shimoyama M, Muto A, et al. Isolation of eight novel Caenorhabditis elegans small RNAs. Gene. 2004;335:47-56 pubmed..The results of our study suggest that there are more as-yet-unidentified small ncRNAs of which genes are located in the intron regions of protein-coding genes in C. elegans. ..
- Williams D, Sayed A, Bernier J, Birkeland S, Cipriano M, Papa A, et al. Profiling Schistosoma mansoni development using serial analysis of gene expression (SAGE). Exp Parasitol. 2007;117:246-58 pubmed..A number of novel, differentially expressed genes have been identified, both within and between the different developmental stages found in the mammalian and snail hosts. ..
- Ruby J, Jan C, Bartel D. Intronic microRNA precursors that bypass Drosha processing. Nature. 2007;448:83-6 pubmed..This suggests that other lineages with many similarly sized introns probably also have mirtrons, and that the mirtron pathway could have provided an early avenue for the emergence of miRNAs before the advent of Drosha. ..
- Geldhof P, Murray L, Couthier A, Gilleard J, McLauchlan G, Knox D, et al. Testing the efficacy of RNA interference in Haemonchus contortus. Int J Parasitol. 2006;36:801-10 pubmed..elegans and other nematodes have limited efficacy in H. contortus. This may reflect differences between nematode species in dsRNA uptake and transport into cells and between cells. ..
- Pinkston Gosse J, Kenyon C. DAF-16/FOXO targets genes that regulate tumor growth in Caenorhabditis elegans. Nat Genet. 2007;39:1403-9 pubmed
- Copeland C, Marz M, Rose D, Hertel J, Brindley P, Santana C, et al. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics. 2009;10:464 pubmed publisher..This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large. ..
- Jasmer D, Mitreva M, McCarter J. mRNA sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity compared with other adult mammalian parasitic nematodes. Mol Biochem Parasitol. 2004;137:297-305 pubmed..contortus. Therefore, adaptations related to nutrient acquisition may vary markedly among these parasitic nematodes. ..
- Mitreva M, McCarter J, Martin J, Dante M, Wylie T, Chiapelli B, et al. Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res. 2004;14:209-20 pubmed..We also provide functional classifications of S. stercoralis clusters...
- Jedrusik M, Schulze E. A single histone H1 isoform (H1.1) is essential for chromatin silencing and germline development in Caenorhabditis elegans. Development. 2001;128:1069-80 pubmed..Our observations therefore support this interpretation of the mes phenotype and they identify a single histone H1 isoform (H1.1) as a new component specifically involved in chromatin silencing in the germline of C. elegans. ..
- Skelly P, Da dara A, Harn D. Suppression of cathepsin B expression in Schistosoma mansoni by RNA interference. Int J Parasitol. 2003;33:363-9 pubmed..This ability to manipulate gene expression represents a powerful new tool for investigating gene function in these debilitating human parasites. ..
- Lim L, Lau N, Weinstein E, Abdelhakim A, Yekta S, Rhoades M, et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 2003;17:991-1008 pubmed..Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species. ..
- Pothof J, van Haaften G, Thijssen K, Kamath R, Fraser A, Ahringer J, et al. Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev. 2003;17:443-8 pubmed..Because known mutator genes are causally involved in many hereditary and sporadic human cancers, it is likely that some of these new mutators are equally relevant in cancer etiology. ..
- Leiers B, Kampkotter A, Grevelding C, Link C, Johnson T, Henkle Dührsen K. A stress-responsive glutathione S-transferase confers resistance to oxidative stress in Caenorhabditis elegans. Free Radic Biol Med. 2003;34:1405-15 pubmed..The Ce-GST-p24 was also localized in BL1 C. elegans by confocal laser-scanning microscopy, revealing a wide-spread distribution profile. ..
- Kamath R, Fraser A, Dong Y, Poulin G, Durbin R, Gotta M, et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003;421:231-7 pubmed..Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans. ..
- Cheung I, Schertzer M, Rose A, Lansdorp P. Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA. Nat Genet. 2002;31:405-9 pubmed..We propose that DOG-1 is required to resolve the secondary structures of guanine-rich DNA that occasionally form during lagging-strand DNA synthesis. ..
- Lau N, Lim L, Weinstein E, Bartel D. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 2001;294:858-62 pubmed..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals. ..
- Murphy C, McCarroll S, Bargmann C, Fraser A, Kamath R, Ahringer J, et al. Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature. 2003;424:277-83 pubmed
- Chirgwin S, Coleman S, Klei T. Brugia pahangi: in vivo tissue migration of early L3 alters gene expression. Exp Parasitol. 2008;118:89-95 pubmed..These data suggest that migratory activity, exposure to potentially different host environments and/or host location may be important external factors in influencing larval gene expression...
- Domeier M, Morse D, Knight S, Portereiko M, Bass B, Mango S. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. Science. 2000;289:1928-31 pubmed..The levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes. ..
- Viney M, Thompson F. Two hypotheses to explain why RNA interference does not work in animal parasitic nematodes. Int J Parasitol. 2008;38:43-7 pubmed
- Yigit E, Batista P, Bei Y, Pang K, Chen C, Tolia N, et al. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell. 2006;127:747-57 pubmed..Interestingly, these AGO proteins lack key residues required for mRNA cleavage. Our findings support a two-step model for RNAi, in which functionally and structurally distinct AGOs act sequentially to direct gene silencing. ..
- Gobert G, Moertel L, Brindley P, McManus D. Developmental gene expression profiles of the human pathogen Schistosoma japonicum. BMC Genomics. 2009;10:128 pubmed publisher..Advanced analyses including ANOVA, principal component analysis, and hierarchal clustering provided a global synopsis of gene expression relationships among the different developmental stages of the schistosome parasite...
- Ranjit N, Jones M, Stenzel D, Gasser R, Loukas A. A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy. Int J Parasitol. 2006;36:701-10 pubmed..Expressed sequence tags corresponding to known and potential recombinant vaccines were identified and these included homologues of proteases, anti-clotting factors, defensins and integral membrane proteins involved in cell adhesion...
- Slack F, Basson M, Liu Z, Ambros V, Horvitz H, Ruvkun G. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell. 2000;5:659-69 pubmed..We suggest that late larval activation of let-7 RNA expression downregulates LIN-41 to relieve inhibition of lin-29. ..
- Sakurai M, Ohtsuki T, Watanabe K. Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm. Nucleic Acids Res. 2005;33:1653-61 pubmed..Thus, m1A9 is indispensable for the structure and function of T-armless tRNAs of nematode mitochondrial origin. ..
- Fitzpatrick J, Johansen M, Johnston D, Dunne D, Hoffmann K. Gender-associated gene expression in two related strains of Schistosoma japonicum. Mol Biochem Parasitol. 2004;136:191-209 pubmed..japonicum gender-associated gene transcripts that may be considered targets for improved intervention strategies. ..
- Reinhart B, Slack F, Basson M, Pasquinelli A, Bettinger J, Rougvie A, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000;403:901-6 pubmed..We propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory RNAs triggers transitions in the complement of heterochronic regulatory proteins to coordinate developmental timing. ..
- Xue X, Sun J, Zhang Q, Wang Z, Huang Y, Pan W. Identification and characterization of novel microRNAs from Schistosoma japonicum. PLoS ONE. 2008;3:e4034 pubmed publisher..Although a large number of miRNAs have been identified from plants to mammals, it remains no experimental proof whether schistosome exist miRNAs...
- Ambros V. Control of developmental timing in Caenorhabditis elegans. Curr Opin Genet Dev. 2000;10:428-33 pubmed..These regulators interact with each other to elaborate stage-specific regulatory switches and act through downstream effectors to control the timing of cell-type-specific developmental events. ..
- He H, Wang J, Liu T, Liu X, Li T, Wang Y, et al. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res. 2007;17:1471-7 pubmed..After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed. ..
- Hao L, Cai P, Jiang N, Wang H, Chen Q. Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum. BMC Genomics. 2010;11:55 pubmed publisher..Both miRNA and siRNAs are potentially important regulators in the development of schistosomal parasites. ..
- Suga K, Welch D, Tanaka Y, Sakakura Y, Hagiwara A. Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PLoS ONE. 2007;2:e671 pubmed..However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking...
- Hanazawa M, Mochii M, Ueno N, Kohara Y, Iino Y. Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2001;98:8686-91 pubmed..These results demonstrate the efficacy of the screening strategy using the EST library combined with the RNAi technique in C. elegans. ..
- Verjovski Almeida S, Venancio T, Oliveira K, Almeida G, DeMarco R. Use of a 44k oligoarray to explore the transcriptome of Schistosoma mansoni adult worms. Exp Parasitol. 2007;117:236-45 pubmed..Moreover, detection of bi-directional transcription for 7% of the active "no match" genes in adults leads us to hypothesize a widespread production of antisense RNA in S. mansoni, with possible regulatory roles. ..
- Knight S, Bass B. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science. 2001;293:2269-71 pubmed..Mutant animals have germ line defects that lead to sterility, suggesting that cleavage of dsRNA to short pieces is a requisite event in normal development. ..
- Ruby J, Jan C, Player C, Axtell M, Lee W, Nusbaum C, et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell. 2006;127:1193-207 pubmed..The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs). ..
- Alkharouf N, Klink V, Matthews B. Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes. Exp Parasitol. 2007;115:247-58 pubmed..Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing...
- Visser A, Geldhof P, De Maere V, Knox D, Vercruysse J, Claerebout E. Efficacy and specificity of RNA interference in larval life-stages of Ostertagia ostertagi. Parasitology. 2006;133:777-83 pubmed..In conclusion, the results indicate that the RNAi pathway is probably present in O. ostertagi but that the current RNAi techniques can not be used as a reliable screening method...
- Winston W, Molodowitch C, Hunter C. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science. 2002;295:2456-9 pubmed..One of these loci, sid-1, encodes a conserved protein with predicted transmembrane domains. SID-1 is expressed in cells sensitive to RNAi, is localized to the cell periphery, and is required cell-autonomously for systemic RNAi. ..
- Pettitt J, Crombie C, Schumperli D, Muller B. The Caenorhabditis elegans histone hairpin-binding protein is required for core histone gene expression and is essential for embryonic and postembryonic cell division. J Cell Sci. 2002;115:857-66 pubmed..In addition, we have observed defects in the specification of vulval cell fate in animals depleted for histone H3 and H4, which indicates that histone proteins are required for cell fate regulation during vulval development. ..
- Pasquinelli A, Reinhart B, Slack F, Martindale M, Kuroda M, Maller B, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature. 2000;408:86-9 pubmed..elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny. ..
- Anders K, Grimson A, Anderson P. SMG-5, required for C.elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2A. EMBO J. 2003;22:641-50 pubmed..Our results suggest that PP2A is the SMG-2 phosphatase, and the role of SMG-5 is to direct PP2A to its SMG-2 substrate. We discuss cycles of SMG-2 phosphorylation and their roles in NMD. ..