E-SMDB-1388 - Transcription profiling of C. elegans operons

Status
Released on 13 July 2005, last updated on 27 March 2012
Organism
Caenorhabditis elegans
Samples (0)
Arrays (2)
Description
Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons1. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP2, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal3. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters4. To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships.
Experiment types
transcription profiling by array, unknown experiment type
Contacts
Citation
A global analysis of Caenorhabditis elegans operons. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-SMDB-1388.idf.txt
Sample and data relationshipE-SMDB-1388.sdrf.txt
Raw data (1)E-SMDB-1388.raw.1.zip
Processed data (1)E-SMDB-1388.processed.1.zip
Array designsA-SMDB-354.adf.txt, A-SMDB-378.adf.txt
Links