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| Status |
Public on Sep 07, 2007 |
| Title |
Mapping the C. elegans non-coding transcriptome with a whole genome tiling microarray |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by genome tiling array
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| Summary |
The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein coding transcriptome remains unknown. Expression profiling on whole genome tiling microarrays applied to a mixed stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11 %) of the polyadenylated transcription is non-annotated, and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this 70% overlap the boundaries of protein coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 98% of all annotated small ncRNAs, and suggested that the transcriptome contains about 1,200 small (<500 nt) unannoted non-coding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed.
Keywords: RNA fractions
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| Overall design |
RNA was extracted from mixed stage wild-type N2 strain worms cultivated at 20oC according to the Trizol (Invitrogen) protocol. Small RNAs (< 500nt, SNPA sample) were isolated using a Qiagen tip (Qiagen), and the Poly(A) Purist MAG (Ambion) and MicrobExpress kits (Ambion) were adapted to remove remaining mRNAs and rRNAs (Deng et al. 2006). The enriched ncRNA pool was cloned using an adaptor-mediated library construction protocol. RNAs were dephosphorylated with calf intestine alkaline phosphatase (Fermentas), then ligated to the 3’-adaptor (3AD) oligonucleotide by T4 RNA ligase (Fermentas) (He et al. 2006). Polyadenylated RNA (PA sample) was isolated from total RNA using the Poly(A) Purist MAG kit (above). Non-polyadenylated RNA (NPA sample) was prepared by removing polyadenylated RNA using the Poly(A) Purist MAG kit and rRNA using the MicrobExpress kit.
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| Contributor(s) |
He H, Wang J, Liu T, Skogerbø G, Chen R |
| Citation(s) |
17785534 |
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| Submission date |
Jul 20, 2007 |
| Last update date |
Jul 24, 2013 |
| Contact name |
Tao Liu |
| E-mail(s) |
tao.liu@roswellpark.org
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| Phone |
7168451300
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| Organization name |
Roswell Park Comprehensive Cancer Institute
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| Department |
Biostatistics and Bioinformatics
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| Street address |
Elm and Carlton St
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platforms (1) |
| GPL5634 |
[Ce25b_MR] Affymetrix C. elegans Tiling 1.0R Array |
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| Samples (3) |
| GSM212071 |
mixed stage polyadenylated RNA, two replicates |
| GSM212072 |
mixed stage small non-polyadenylated RNA, two replicates |
| GSM212073 |
mixed stage non-polyadenylated RNA (fishout of polyadenylated RNA), three replicates |
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| Relations |
| BioProject |
PRJNA101685 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8543_RAW.tar |
435.5 Mb |
(http)(custom) |
TAR (of BAR, CEL, TXT) |
| Processed data provided as supplementary file |
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