The rDNA of<i>C. elegans</i>: sequence and structure

Ellis, Ronald; Sulston, John; Coulson, Alan

doi:10.1093/nar/14.5.2345

Cited by 226 publications

(119 citation statements)

References 56 publications

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“…The secondary structure models proposed by others are not entirely applicable to every eukaryotic srRNA molecule. Our model comes closest to that proposed by Ellis and co-workers [3] [5,6,8,10] adopt a similar topology for the secondary structure of eukaryotic and prokaryotic srRNAs in this area. Others [l-3,7,9] advocate a eukaryote-specific topology for this region.…”

Section: Resultssupporting

confidence: 83%

“…The reason is that in the partial secondary structure model for this E21 area This extra sequence can be folded into a hairpin was proposed by Nelles and co-workers [2]. structure bearing the number E43-1, which is abRecently, other authors [3,7,10,1 l] advocated sent in the remaining known 18 S rRNAs.…”

Section: Resultsmentioning

confidence: 99%

“…The Metazoa are represented in this collection by eight different species, of which there are six vertebrates and only two invertebrates, viz. Arfemia sulina (phylum Arthropoda, class Crustacea) [2] and Caenorhabditis elegans (phylum Nemathelminthes, class Nematoda) [3]. Here, we report the primary structure of the srRNA from another Arthropod, Tenebrio molitor (class Insecta).…”

Section: Introductionmentioning

confidence: 99%

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Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

et al. 1988

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The sequence of the 18 S rRNA of Tenebrio molitor is reported. A detailed secondary structure model for eukaryotic small subunit rRNAs is proposed. The model comprises 48 universal helices that eukaryotic and prokaryotie small subunit rRNAs have in common, plus a number of helices in areas of variable secondary structure. For the central area of the model, an alternative structure is possible, applicable only to eukaryotic small subunit rRNAs. Possibly, small subunit rRNA switched to this alternative conformation after the eukaryotic branch had been established in evolution. Another possibility is that the two conformers represent a dynamic structural switch functioning during the translational activity of the eukaryotic ribosome.small ribosomal subunit RNA; 18 S rRNA; Nucleotide sequence; Secondary structure; (Tenebrio molitor)

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Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

et al. 1988

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“…www.genome.org a default BLAT analysis of the 312,492 pyrosequencing reads versus the 5S rDNA (Ce5SSL1) (chromosome V: ∼110 copes, 982 bp) (Nelson and Honda 1985;Krause and Hirsh 1987) and 18/26S rDNA genes (chromosome I: ∼55 copies, 7203 bp) (Files and Hirsh 1981;Ellis et al 1986). A total of 786 of 312,492 total sequencing runs corresponded to the Ce5SSL1 repeat (0.25%).…”

Section: Genome Research 1509mentioning

confidence: 99%

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

Johnson¹,

Tan²,

McCullough³

et al. 2006

Genome Res.

178

158

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Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.

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“…The second internal transcribed spacer region (ITS-2) of the ribosomal RNA gene of the six species of Elaphostrongylus (E. cervi L1, E. rangiferi adult, E. alces L3) and Parelaphostrongylus (P. tenuis L1, P. andersoni adult, P. odocoilei adult) was amplified by PCR using conserved 20-mer oligonucleotide primers NC1-forward: (5Ј-ACGTCTGGTTCAGGGT TGTT-3Ј) and NC2-reverse: (5Ј-TTAGTTTCT TTTCCTCCGCT-3Ј) derived from the free-living nematode, Caenorhabditis elegans (Ellis et al, 1986). The amplified products were electrophoresed on a 1.5% agarose gel and the band of ITS-2 excised and purified with a GeneClean II kit (Bio/Can Scientific, Vista, California, USA) according to the manufacturer's instructions.…”

Section: Pcr Primers and Conditionsmentioning

confidence: 99%

DIFFERENTIATION OF DORSAL-SPINED ELAPHOSTRONGYLINE LARVAE BY POLYMERASE CHAIN REACTION AMPLIFICATION OF ITS-2 of rDNA

Gajadhar

Steeves-Gurnsey

Kendall

et al. 2000

Journal of Wildlife Diseases

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Molecular genetics was used to devise the first reliable diagnostic tool for differentiating morphologically indistinguishable dorsal-spined, first-stage larvae (L1's) and other stages of the nematode protostrongylid subfamily Elaphostrongylinae. A polymerase chain reaction (PCR) assay employing specifically designed primers was developed to selectively amplify DNA of the ITS-2 region of the ribosomal gene. Amplification of the entire ITS-2 region differentiated between larvae of the genera Elaphostrongylus and Parelaphostrongylus, based on the lengths of fragments produced. Three sets of primers were designed and used successfully to distinguish larvae at the species level. Although it was demonstrated that one primer set in a single PCR assay was capable of distinguishing each of the three Parelaphostrongylus spp., a second primer set would be required for confirmation in routine diagnostic use. Two of the three primer sets were capable of amplifying DNA from all six elaphostrongyline species and of identifying Elaphostrongylus alces and Parelaphostrongylus odocoilei. Although two separate fragments were produced from each Elaphostrongylus cervi and Elaphostrongylus rangiferi, it was not possible to distinguish these two parasites from each other based on the fragment size. The use of various nematodes, hosts, and fecal controls demonstrated the reliability of the primers for all developmental stages including L1's, third-stage larvae, and adult worms. These primers also have potential for identifying other lungworms as was shown by the amplification of Umingmakstrongylus pallikuukensis, the muskox protostrongylid, and Dictyocaulus sp. from white-tailed deer. Although this assay may benefit from further refinement, its present design provides researchers, wildlife managers, clinicians, and animal health regulators with a practical tool for the control, management, and study of meningeal and tissue worms and their close relatives.

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The rDNA ofC. elegans: sequence and structure

Cited by 226 publications

References 56 publications

Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

DIFFERENTIATION OF DORSAL-SPINED ELAPHOSTRONGYLINE LARVAE BY POLYMERASE CHAIN REACTION AMPLIFICATION OF ITS-2 of rDNA

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