GEO DataSets

(Submitter supplied) We investigated cryptic transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. We show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and have the potential to produce truncated polypeptides by using downs-stream, in-frame start codons. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

4 Samples

Download data: BEDGRAPH

(Submitter supplied) We investigated cryptic transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. Here we assay the effect of Cycloheximide treatment (CHX) in the co-translational degradation profile of using strains where cryptic transcription is enhanced. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Application of TIF-Seq to mutants of the molecular components involved in transcription process.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

2 Samples

Download data: TXT

(Submitter supplied) We investigated the association of cryptic unstable transcripts (CUTs) to ribosomes in Saccharomyces cerevisiae. We used 5’cap-sequence followed by sucrose gradient fractionation of polyribosome fractions after ultracentrifugation to assess the relative association of transcripts to the ribosomes. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL19756

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We show that transcription start sites of chromatin-dependent internal cryptic transcripts resemble those of protein coding genes in terms of DNA sequence, directionality and chromatin accessibility. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

16 Samples

Download data: BEDGRAPH

(Submitter supplied) Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, hence preventing the emergence of cryptic transcript from spurious promoter sequences. How these transcripts are regulated and processed by cells remains poorly characterized. Notably, very little is known about the termination of cryptic transcription. Here we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

12 Samples

Download data: BW

(Submitter supplied) Poly(A) and CUT RNA fractions are compared using 3 'Long-SAGE deep-sequencing. ArrayExpress Release Date: 2008-12-19 Publication Title: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast Publication Author List: Helen Neil, Christophe Malabat, Yves d'Aubenton-Carafa, Zhenyu Xu, Lars M. Steinmetz and Alain Jacquier Person Roles: submitter Person Last Name: Malabat Person First Name: Christophe Person Mid Initials: Person Email: christophe.malabat@pasteur.fr Person Phone: Person Address: Unité de Génétique des Interactions Macromoléculaires; CNRS, URA2171,F-75015, Paris, France Person Affiliation: Institut Pasteur

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11160

2 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) Microarray analysis was used to identify all cryptic promoters in the S. cerevisiae genome that are activated in spt6 and spt16 mutants. These experiments showed that cryptic initiation is widespread, occurring in approximately 1,000 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7078

6 Samples

Download data: GPR

(Submitter supplied) We performed a fluorescent reporter based screen to identify factors determining transcriptional directionality from bidirectional promoters that give rise to a coding and a non-coding transcript. Promoters like these are most frequent in many organisms and non-coding transcription from this origin represents a large fraction of total long non-coding transcripts. We applied NET-seq to compare nascent transcription in yeast wild-type and mutations in the three members of the CAF-I complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL21656

49 Samples

Download data: BIGWIG

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. We have identified that the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21656

7 Samples

Download data: BIGWIG

(Submitter supplied) Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

18 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

8 Samples

Download data: BEDPE

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21656 GPL17342 GPL19756

288 Samples

Download data: BED, BEDPE, BW

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

36 Samples

Download data: BED, BW

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

81 Samples

Download data: BW

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

82 Samples

Download data: BW

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

81 Samples

Download data: BW

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18330

40 Samples

Download data: BED, WIG