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| Status |
Public on Apr 03, 2013 |
| Title |
Roles for Transcript Leaders in Translation and mRNA Decay Revealed by Transcript Leader Sequencing |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| Summary |
Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-Sequencing (TL-Seq), a technique combining enzymatic capture of m7G-capped mRNA 5'-ends with high-throughput sequencing. TL-Seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Transcription initiation sites occur in at least 5% of protein-coding regions and are concentrated near the 5'ends of ORFs. These truncated mRNAs are translated, based on ribosome density analysis. Translation Associated TL-Seq (TATL-Seq), which combines TL-Seq with polysome fractionation, revealed substantial differences in translation of alternative TL isoforms. Globally, while some TL features are associated with poor translation and nonsense-mediated mRNA decay (uAUGs, very short length), others (secondary structure, long length) have much less impact than predicted from analyses of individual genes. TL-Seq and TATL-Seq can be applied to any eukaryote to investigate TL-mediated regulation of gene expression.
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| Overall design |
TL-Seq (+/- pyrophosphatase), TATL-Seq (TL-Seq libraries from polysome gradient)
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| Contributor(s) |
Arribere JA, Gilbert WV |
| Citation(s) |
23580730 |
| Submission date |
Jul 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua A Arribere |
| E-mail(s) |
arribere@mit.edu
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| Phone |
6172533707
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| Organization name |
MIT
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| Department |
Biology
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| Lab |
Gilbert
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| Street address |
31 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
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| Platforms (2) |
| GPL9377 |
Illumina Genome Analyzer II (Saccharomyces cerevisiae) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA169917 |
| SRA |
SRP014003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39074_RAW.tar |
10.2 Mb |
(http)(custom) |
TAR (of TXT, WIG) |
| GSE39074_TATL-SeqCombined.wig.gz |
3.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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