GEO DataSets

(Submitter supplied) The goal of this study was to position all transcripts extremities in two species of Cryptococcus using TSS-Seq and QuantSeq 3' mRNA-Seq when cells are grown under different conditions. We analysed also the level of expression of each genes in the same condition using the same cell sample. All these data have spiked in using a fixed quantity of S. cereviae cells added just before DNA and RNA extraction.

Organism:

Cryptococcus neoformans var. neoformans; Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26812 GPL19081

108 Samples

Download data: TXT, WIG

(Submitter supplied) We measured protein translation (by ribosome profiling) and RNA levels (by polyA-enriched RNA-seq) in Cryptococcus neoformans strain H99 and Cryptococcus neoformans strain JEC21. This is the first transcriptome-wide map of translation in this species complex.

Organism:

Cryptococcus neoformans; Cryptococcus neoformans var. neoformans

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26812 GPL19081

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs) in its >700 nt 5’-leader and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell-free extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4 in controlling translation. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

6 Samples

Download data: CSV, XLSX

(Submitter supplied) The translation pre-initiation complex (PIC) scans the mRNA for an AUG codon in favorable context. Previous findings suggest that the factor eIF1 discriminates against non-AUG start codons by impeding full accommodation of Met-tRNAi in the P site of the 40S ribosomal subunit, necessitating eIF1 dissociation for start codon selection. Consistent with this, yeast eIF1 substitutions that weaken its binding to the PIC increase initiation at UUG codons on a mutant his4 mRNA and particular synthetic mRNA reporters; and also at the AUG start codon of the mRNA for eIF1 itself owing to its poor Kozak context. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

4 Samples

Download data: WIG

(Submitter supplied) Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae. Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: WIG

(Submitter supplied) Most animal mRNAs contain upstream Open Reading Frames (uORFs). These uORFs represent an impediment to translation of the main ORF since ribosomes usually bind the mRNA cap at the 5’ end and then scan for ORFs in a 5’-to-3’ fashion. One way for ribosomes to bypass uORFs is via leaky scanning, whereby the ribosome disregards the uORF start codon. Hence leaky scanning is an important post-transcriptional mechanism affecting gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

16 Samples

Download data: XLSX

(Submitter supplied) Translation regulation occurs largely during initiation. Currently, translation initiation can be studied in vitro, but these systems lack features present in vivo and on endogenous mRNAs. Here we develop selective 40S footprinting for visualizing initiating 40S ribosomes on endogenous mRNAs in vivo. It pinpoints where on an mRNA initiation factors join the ribosome to act, and where they leave. We discover that in human cells most scanning ribosomes remain attached to the 5’ cap. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21697 GPL21626

60 Samples

Download data: XLSX

(Submitter supplied) Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of human genes, we identified 5 Hox gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

3 Samples

Download data: WIG

(Submitter supplied) We report the global profile of ribosome profilig to study the relationship between alternative translation initaiton sites and gene expression in tomato.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21762

6 Samples

Download data: TXT

(Submitter supplied) Genomic analyses in budding yeast have helped to define the foundational principles of eukaryotic gene expression, but have systematically excluded specific classes of potential coding regions, including those with non-AUG start codons. Without methods to define coding regions empirically, the prevalence of these non-canonical coding regions has been impossible to assess. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified a class of 149 genes that encode N-terminally extended alternate protein isoforms that result from translation initiation at non-AUG codons upstream of the annotated AUG start codon. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

11 Samples

Download data: CSV, FA, GTF, TXT