Cook KB et al. (2011) Nucleic Acids Res "RBPDB: a database of RNA-binding specificities."

Hughes TR, Cook KB, Kazan H, Zuberi K, Morris Q

[Nucleic Acids Res, 2011]

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo-bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/.

Nelson DW et al. (1989) Nucleic Acids Res "Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae."

Nelson DW, Honda BM

[Nucleic Acids Res, 1989]

The 5S RNA genes of Caenorhabditis briggsae consist of approximately 65 copies of a 1 kb repeat unit and 20 copies of a related 0.7 kb repeat unit, organized in separate tandem clusters. DNA sequence comparisons with the 1kb 5S DNA repeat from the closely related nematode C. elegans show that the 5S RNA coding region is perfectly conserved. Both C. briggsae 1 kb and 0.7 kb repeats are also efficiently transcribed in vitro,suggesting that both represent functional 5S RNA genes. Surprisingly, a second block of 118 bp is also perfectly conserved between the 1 kb repeats,and is less well conserved in the 0.7 kb repeat. In C. elegans, this DNA is transcribed to produce and abundant 100 nt transcript (SL RNA) which participates in a trans-splicing process (Krause and Hirsh, Cell 49:753, 1987). This SL RNA region of the C. briggsae 1 kb 5S DNA repeat also appears to be transcribed in vivo, while the corresponding region of the 0.7 kb repeat is not.

Gunther CV et al. (2004) J Biol Chem "Alternative polyadenylation results in a truncated daf-4 BMP receptor that antagonizes DAF-7-mediated development in Caenorhabditis elegans."

Gunther CV, Riddle DL

[J Biol Chem, 2004]

The DAF-4 receptor kinase, which promotes larval development, is encoded by a 2.9 kb mRNA transcribed from the only type II TGF-beta/BMP receptor gene in Caenorhabditis elegans. Here we report that alternative polyadenylation in intron 5 of daf-4 results in a 2.0 kb mRNA that encodes an open reading frame including only the N-terminal secretion signal and ligand-binding domains, and not the transmembrane or kinase domains, of DAF-4. Northern blots and real-time RT-PCR amplifications using RNA samples from developmentally staged animals show that expression levels of both the 2.9 kb and 2.0 kb transcripts are relatively constant, and their abundances similar, except for the transition between non-dauer and dauer stages. In dauer larvae, the steady-state level of the 2.0 kb mRNA increases more than 10-fold and exceeds the 2.9 kb transcript, coincident with an absence of signaling from DAF-4. Transgenic expression of a recombinant daf-4 transgene that encodes only the 2.0 kb mRNA enhances the Daf-c phenotype of a daf-4 hypomorph, whereas the same transgene with a nonsense mutation does not. These data suggest that a polypeptide encoded by the 2.0 kb transcript can function as an antagonist of full-length DAF-4 signaling. Alternative processing of type II receptor transcripts to generate an antagonist is a novel mechanism for negative regulation of a TGF-beta signaling pathway.

Okkema PG et al. (1991) EMBO J "Molecular analysis of tra-2, a sex determining gene in C.elegans."

Kimble JE, Okkema PG

[EMBO J, 1991]

We have cloned the Caenorhabditis elegans sex determining gene, tra-2, by transposon tagging. The tra-2 region is delineated by mapping Southern blot differences associated with 11 tra-2 mutations, mutant rescue, and analysis of tra-2 RNAs. The tra-2 gene encodes three transcripts. One transcript, a 1.8 kb RNA, is not detected in animals lacking a germ line, and therefore may be germline specific. Comparison of the two sexes shows that adult hermaphrodites have approximately 15-fold more tra-2 RNA than adult males. In addition, adult hermaphrodites contain 5 kb and 1.8 kb tra-2 RNAs whereas adult males possess 5 kb and 1.9 kb RNAs. A 1.9 kb tra-2 RNA is also found during hermaphrodite larval development, prior to sexual differentiation of the XX germ line. Surprisingly, analysis of tra-2 expression in selected sex determination mutants reveals that the sex specificity of tra-2 RNAs is not dictated by the pathway of sex determination that has been established by genetic experiments. This result can be interpreted in two ways. Either the sex specificity of the tra-2 RNAs is irrelevant to regulation of the sexual phenotype, which seems unlikely, or there is additional complexity within the hierarchy of sex determining genes, such as feedback regulation, which ensures that the tra-2 product corresponds to phenotypic sex.

Greenwald IS et al. (1987) Nucleic Acids Res "Correlation of the physical and genetic maps in the lin-12 region of Caenorhabditis elegans."

Greenwald IS, Sulston JE, Priess JR, Coulson AR

[Nucleic Acids Res, 1987]

We describe the assembly of a set of overlapping clones from the lin- 12 III chromosomal region that spans approximately 600 kb, and the identification of two restriction fragment length polymorphisms, eP6 and eP7, that flank the lin-12 locus. A comparison of the physical map and the genetic map yields approximate measurements of 930 kb/map unit for the eP6--lin-12 interval and 830 kb/map unit for the lin-12-- eP7 interval. We interpret these values as supporting the proposal that the apparent clustering of genes observed for C. elegans autosomes results from decreased recombination frequency in clusters and not from nonrandom distribution of genes on the

Nelson DW et al. (1985) Gene "Genes coding for 5S ribosomal RNA of the nematode Caenorhabditis elegans."

Nelson DW, Honda BM

[Gene, 1985]

We have identified a 1-kb genomic sequence that represents the major class of 5S rRNA genes in the nematode Caenorhabditis elegans. This 1- kb sequence is tandemly repeated 110 times in the haploid genome forming a single homogeneous gene family. Other nematode genomic sequences, distinct from the major 1-kb repeat class but homologous to it, may represent dispersed 5S rRNA genes or the ends of a gene cluster. One such fragment shows a restriction fragment length difference between two C. elegans strains. This should allow the genetic analysis of 5S rRNA-coding DNA (5S X rDNA) and its flanking regions in C. elegans.

Trent C et al. (1991) Mech Dev "Sex-specific transcriptional regulation of the C. elegans sex-determining gene her-1."

Wood WB, Trent C, Gavinski S, Chamblin C, Purnell B, Hageman JM

[Mech Dev, 1991]

Expression of the sex-determining gene her-1 is required in C. elegans for the normal male development of XO animals. Abnormal expression in XX animals, which normally develop as hermaphrodites, results in aberrant male development. We have isolated a molecular clone of the her-1 gene and have identified two transcripts that are present in XO animals at all stages of development: an abundant 0.8 kb transcript and a less abundant 1.2 kb transcript. In preparations of XX animals, the 0.8 kb transcript was observed only at very low levels in embryos or L1 larvae and the 1.2 kb transcript was not detected. Two gain-of-function her-1 mutations result in high levels of the 1.2 and 0.8 kb transcripts in XX animals. The levels of these transcripts are also elevated in XX animals carrying a loss-of-function mutation in either sdc-1 or sdc-2, consistent with the proposed roles of these genes as negative regulators of her-1. These results demonstrate that expression of the her-1 gene in males and hermaphrodites is controlled at the level of transcript synthesis or accumulation. This mode of regulation contrasts with that found for the Drosophila sex-determining genes, whose sex-specific expression is controlled by differential splicing in males and females.

L'Hernault SW et al. (1993) Genetics "Genetic and molecular characterization of the Caenorhabditis elegans spermatogenesis-defective gene spe-17."

Emmons RB, Benian GM, L'Hernault SW

[Genetics, 1993]

Two self-sterile mutations that define the spermatogenesis-defective gene spe-17 have been analyzed. These mutations affect unc-22 and fail to complement each other for both Unc-22 and spermatogenesis defects. Both of these mutations are deficiencies (hcDf1 and hDf13) that affect more than one transcription unit. Genomic DNA adjacent to and including the region deleted by the smaller deficiency (hcDf1) has been sequenced and four mRNAs (including unc-22) have been localized to this sequenced region. The three non unc-22 mRNAs are shown to be sex-specific: a 1.2-kb mRNA that can be detected in sperm-free hermaphrodites and 1.2- and 0.56-kb mRNAs found in males. hDf13 deletes at least 55 kb of chromosome IV, including all of unc-22, both male-specific mRNAs and at least part of the female-specific mRNA. hcDf1, which is approximately 15.6 kb, deletes only the 5' end of unc-22 and the gene that encodes the 0.56-kb male-specific mRNA. The common defect that apparently accounts for the defective sperm in hcDf1 and hDf13 homozygotes is deletion of the spe-17 gene, which encodes the 0.56-kb mRNA. Strains carrying two copies of either deletion are self-fertile when they are transgenic for any of four extrachromosomal array that include spe-17. We have sequenced two spe-17 cDNAs, and the deduced 142 amino acid protein sequence is highly charged and rich in serine and threonine, but shows no significant homology to any previously determined protein sequence.

Warren T et al. (1988) Nucleic Acids Res "A related moderately repetitive DNA family in the nematodes Ascaris lumbricoides and Panagrellus silusiae."

Pasternak JJ, Warren T

[Nucleic Acids Res, 1988]

Digestion of genomic DNA from the nematodes Panagrellus silusiae and Ascaris lumbricoides with restriction endonuclease BamH1 releases a 0.7 kilobase (kb) fragment. The 0.7 kb fragment from both nematodes was cloned onto E. coli plasmid pUC19. Using representative clones as DNA hybridization probes, it was found that (i) the BamH1 fragments cross-hybridize; (ii) a ladder-effect with multiples of 0.7 kb was evident in both species after hybridization to genomic DNA and (iii) the genomic copy number of BamH1 elements is 150 and 195 for P. silusiae and A. lumbricoides respectively. DNA sequence analysis of the inserts, AL700-1 and PS700-1, revealed nucleotide blocks with over 85% similarity. No open reading frames are present in either DNA fragment. Neither fragment hybridizes to genomic DNA from Caenorhabditis elegans. Northern blot hybridization indicated that the 0.7 kb element is transcribed into poly (A)- -RNA in P. silusiae; but it is not transcribed in adult Ascaris muscle. Thus, P. silusiae and A. lumbricoides share a homologous, tandemly arrayed, moderately repetitive DNA family.

Otsuka AJ et al. (1995) J Cell Biol "An ankyrin-related gene (unc-44) is necessary for proper axonal guidance in Caenorhabditis elegans."

Tang LZ, Otsuka AJ, Franco R, Jeyaprakash A, Shim KH, Wheaton VI, Hedgecock EM, Yang BJ

[J Cell Biol, 1995]

Caenorhabditis elegans unc-44 mutations result in aberrant axon guidance and fasciculation with inappropriate partners. The unc-44 gene was cloned by transposon tagging, and verified by genetic and molecular analyses of six transposon-induced alleles and their revertants. Nucleotide sequence analyses demonstrated that unc-44 encodes a series of putative ankyrin-related proteins, including AO49 ankyrin (1815 aa, 198.8 kD), AO66 ankyrin (1867 aa, 204 kD), and AO13 ankyrin (< or = 4700 aa, < or = 517 kD). In addition to the major set of approximately 6 kb alternatively spliced transcripts, minor transcripts were observed at approximately 3, 5, 7, and 14 kb. Evidence is provided that mutations in the approximately 14-kb AO13 ankyrin transcript are responsible for the neuronal defects. These molecular studies provide the first evidence that ankyrin-related molecules are required for axonal guidance.