A global analysis of Caenorhabditis elegans operons

@article{Blumenthal2002AGA,
  title={A global analysis of Caenorhabditis elegans operons},
  author={T. Blumenthal and Donald Evans and C. Link and A. Guffanti and D. Lawson and J. Thierry-Mieg and D. Thierry-Mieg and W. Chiu and K. Duke and M. Kiraly and Stuart K. Kim},
  journal={Nature},
  year={2002},
  volume={417},
  pages={851-854}
}
The nematode worm Caenorhabditis elegans and its relatives are unique among animals in having operons. Operons are regulated multigene transcription units, in which polycistronic pre-messenger RNA (pre-mRNA coding for multiple peptides) is processed to monocistronic mRNAs. This occurs by 3′ end formation and trans-splicing using the specialized SL2 small nuclear ribonucleoprotein particle for downstream mRNAs. Previously, the correlation between downstream location in an operon and SL2 trans… Expand
The frataxin-encoding operon of Caenorhabditis elegans shows complex structure and regulation.
TLDR
The heterogeneity of the genes, and their complex expression patterns, suggests that the clustering of CEOP2232 is not due to a need for synchronized expression of genes involved in the same physiological pathway, and could be due to the presence of internal promoters and regulatory sequences in the operon. Expand
Germline Expression Influences Operon Organization in the Caenorhabditis elegans Genome
TLDR
It is demonstrated that mechanisms governing germline gene expression influence operon origination and/or maintenance in Caenorhabditis elegans, and gene expression in a specific tissue can have profound effects on the evolution of genome organization. Expand
Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes.
TLDR
The relationship between gene location and expression in Caenorhabditis elegans is analyzed and evidence for at least three different processes resulting in local expression similarity is found, suggesting that such genes may share regulatory elements or be regulated at the level of chromatin structure. Expand
Identification and analysis of internal promoters in Caenorhabditis elegans operons.
TLDR
Hybrid operons are common in the C. elegans genome and that internal promoters influence not only gene organization and expression but also operon evolution, suggesting their necessity in gene regulation and survival. Expand
In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs
TLDR
The study has demonstrated that the three upstream motifs UM1-3 have promoter activity, and showed that upstream motif 1 (UM1) can drive the expression of green fluorescent protein (GFP), and utilized this for detailed analysis of temporal and spatial expression patterns of 5 SL2 RNAs. Expand
The Evolutionary Dynamics of Operon Distributions in Eukaryote Genomes
TLDR
It is found that birth–death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, nonoperon genes that likely participate in the birth– death process. Expand
Genome Mapping and Genomics of Caenorhabditis elegans
The nematode Caenorhabditis elegans is one of the most extensively studied and utilized model organisms, owing to experimental advantages such as its ease of culture and rapid growth, facileExpand
On the Paucity of Duplicated Genes in Caenorhabditis elegans Operons
TLDR
Analysis of the frequency of duplication of operonic genes in C. elegans confirmed that they are duplicated less often in the genome than monocistronic genes, which might place a large constraint on the plasticity of the genome. Expand
Caenorhabditis elegans Operons Contain a Higher Proportion of Genes with Multiple Transcripts and Use 3′ Splice Sites Differentially
TLDR
The analyses suggest that C. elegans operons enhance expression complexity by increasing the proportion of genes that express multiple transcript isoforms and maintain splicing efficiency by differential use of common 3′ splice sites. Expand
Regulation of transcription termination in the nematode Caenorhabditis elegans
TLDR
It is found that pol II generally transcribes up to 1 kb past the poly(A) sites into the 3′ flanking regions of the nematode genes before it terminates, and cis-splicing of the first intron located in downstream positioned genes in these polycistronic pre-mRNAs is critical for their expression and may play a role in preventing premature pol II transcription termination. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 19 REFERENCES
Operons as a common form of chromosomal organization in C. elegans
TLDR
Identifying gene clusters using the extensive data generated by the genome project and testing seven genes for trans-splicing specificity indicate that the pre-mRNAs of about 70% of C. elegans genes are trans-split and as many as a quarter are transcribed in operons. Expand
Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis.
TLDR
It appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family Rhabditidae, and may be more widespread than is currently appreciated. Expand
Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans.
TLDR
These full-genome DNA microarrays are used to show the relative levels of gene expression for nearly every gene during development, from eggs through adulthood, and identify many genes likely to be involved in sex-specific differentiation and behavior. Expand
Two functionally dependent acetylcholine subunits are encoded in a single Caenorhabditis elegans operon.
TLDR
It is shown that des-2, a gene in which mutations suppress deg-3(u662), is the upstream gene in that operon, which appears to regulate the coordinate expression of two channel subunits. Expand
The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans
TLDR
The Intronerator is a set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans that includes a display of cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes and a database of introns. Expand
A second trans-spliced RNA leader sequence in the nematode Caenorhabditis elegans.
  • X. Y. Huang, D. Hirsh
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1989
TLDR
In the nematode Caenorhabditis elegans, a trans-spliced leader whose sequence differs from that of the original spliced leader, although both are 22 nucleotides long is identified. Expand
Operons in C. elegans: Polycistronic mRNA precursors are processed by trans-splicing of SL2 to downstream coding regions
TLDR
Evidence is presented that the genes in these clusters are cotranscribed and downstream mRNAs are formed by cleavage at the polyadenylation site and trans-splicing, suggesting that polycistronic RNAs can be processed by trans- Splicing. Expand
SL1 trans Splicing and 3′-End Formation in a Novel Class of Caenorhabditis elegansOperon
  • Carol Williams, Lei Xu, T. Blumenthal
  • Biology, Medicine
  • Molecular and Cellular Biology
  • 1999
TLDR
An exceptionally long polypyrimidine tract found in the 3′ untranslated regions of the three known SL1-type operons is shown to be required for the accumulation of both upstream and downstream mRNAs. Expand
The Caenorhabditis elegans locus lin-15, a negative regulator of a tyrosine kinase signaling pathway, encodes two different proteins.
TLDR
The Caenorhabditis elegans locus lin-15 negatively regulates an intercellular signaling process that induces formation of the hermaphrodite vulva and contains deletions and insertions that affect the lin- 15 genomic region. Expand
Cyclophilin and protein disulfide isomerase genes are co-transcribed in a functionally related manner in Caenorhabditis elegans.
  • A. P. Page
  • Biology, Medicine
  • DNA and cell biology
  • 1997
TLDR
Reporter gene analysis provides strong evidence that both genes are controlled by a single upstream regulatory element, which directs expression of both enzymes in the hypodermal cells that synthesize the cuticle. Expand
...
1
2
...