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Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

ABSTRACT: 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.

SUBMITTER: Nelson DW

PROVIDER: S-EPMC335034 | biostudies-other | 1989 Nov

REPOSITORIES: biostudies-other

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Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

Nelson D W DW Honda B M BM

Nucleic acids research 19891101 21

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 se ...[more]

PMID: 2587214

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Project description:Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a robust program called OrthoCluster, and an online database OrthoClusterDB. In this work, we have demonstrated the application of OrthoCluster in identifying synteny blocks between the genomes of Caenorhabditis elegans and Caenorhabditis briggsae, two closely related hermaphrodite nematodes.Initial identification and analysis of synteny blocks using OrthoCluster enabled us to systematically improve the genome annotation of C. elegans and C. briggsae, identifying 52 potential novel genes in C. elegans, 582 in C. briggsae, and 949 novel orthologous relationships between these two species. Using the improved annotation, we have detected 3,058 perfect synteny blocks that contain no mismatches between C. elegans and C. briggsae. Among these synteny blocks, the majority are mapped to homologous chromosomes, as previously reported. The largest perfect synteny block contains 42 genes, which spans 201.2 kb in Chromosome V of C. elegans. On average, perfect synteny blocks span 18.8 kb in length. When some mismatches (interruptions) are allowed, synteny blocks ("imperfect synteny blocks") that are much larger in size are identified. We have shown that the majority (80%) of the C. elegans and C. briggsae genomes are covered by imperfect synteny blocks. The largest imperfect synteny block spans 6.14 Mb in Chromosome X of C. elegans and there are 11 synteny blocks that are larger than 1 Mb in size. On average, imperfect synteny blocks span 63.6 kb in length, larger than previously reported.We have demonstrated that OrthoCluster can be used to accurately identify synteny blocks and have found that synteny blocks between C. elegans and C. briggsae are almost three-folds larger than previously identified.

Project description:BackgroundAn organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans.ResultsWe have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance.ConclusionOur data set provides a catalog for future functional investigations and indicates novel insight into evolutionary mechanisms. We discuss the limited conservation of core developmental and transcriptional programs as a common aspect of animal evolution.

Dataset Information

Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

Publications

Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

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