E-GEOD-39074 - Roles for Transcript Leaders in Translation and mRNA Decay Revealed by Transcript Leader Sequencing

Status
Released on 3 April 2013, last updated on 12 June 2013
Organism
Saccharomyces cerevisiae
Samples (11)
Protocols (6)
Description
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. TL-Seq (+/- pyrophosphatase), TATL-Seq (TL-Seq libraries from polysome gradient)
Experiment types
other, RNA-seq of coding RNA 
Contacts
Joshua A Arribere, Wendy V Gilbert
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-39074.idf.txt
Sample and data relationshipE-GEOD-39074.sdrf.txt
Processed data (1)E-GEOD-39074.processed.1.zip
Links