TL-seq and TATL-seq study of 5' UTRs

Arribere_2013_PMID_23580730.README
Created: 2013-01-18
Last modified: 2014-05-01

Arribere JA and Gilbert WV (2013) Roles for transcript leaders in
translation and mRNA decay revealed by transcript leader
sequencing. Genome Res 23(6):977-87
PMID:23580730

Description of data: Arribere et al. used a genome-wide approach to
5'RACE, TL-seq, to annotated TSSs in a high-throughput manner for the
yeast genome. Their annotations are consistent with known features of
TSSs. They identify two classes of TLs that impact translation of the
downstream ORF: extremely short TLs (<12nts) that lead to inefficient
start codon recognition and initiation at downstream AUGs, and
AUG-containing TLs where ribosomes tend to initiation at an AUG in the
TL and thus decrease initiation at the downstream AUG. Because both
types of TLs lead to translation termination at the 5'end of a
transcript, they lead to mRNA decay via the Nonsense-Mediated mRNA
Decay pathway. TL-seq also identifies >6% of yeast genes as having
well-separated alternative TL isoforms. By applying TL-seq to
fractions of a polysome gradient, which sediments mRNAs by the number
of bound ribosomes, they show that a majority of these TL variants
lead to distinct translation activities, thus implicating TL isoform
diversity as an important contributor to translational regulation.

Experiment type: RNA-seq 
Platform: Illumina GA II| Illumina HiSeq
Strain_background: Sigma 1278b| BY4742 
Genotype: MAT a ura3 leu2 trp1 his3| Mat α his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0
Growth conditions: YPAD
Phase: mid-log
Analysis software: Bowtie
Reference Genome: R64-1-1

GEO Accessions: 
GSE39074
GSM955198
GSM955199
GSM955200
GSM955201
GSM955202
GSM955203
GSM955204
GSM955205
GSM955206

Data Files: 
Arribere_2013_GSE39074_TATL-SeqCombined.bw
Arribere_2013_GSM955198_TL-SeqPlusTAP.bw
Arribere_2013_GSM955199_TL-SeqMinusTAP.bw

Original GEO Files: 
GSE39074_TATL-SeqCombined.wig
GSM955198_TL-SeqPlusTAP.wig
GSM955199_TL-SeqMinusTAP.wig
GSM955200_TATL-SeqFraction1.wig
GSM955201_TATL-SeqFraction2.wig
GSM955202_TATL-SeqFraction3.wig
GSM955203_TATL-SeqFraction4.wig
GSM955204_TATL-SeqFraction5.wig
GSM955205_TATL-SeqFraction6.wig
GSM955206_TATL-SeqFraction7.wig