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Survey of cryptic unstable transcripts in yeast

ABSTRACT: Survey of cryptic unstable transcripts in yeast

OTHER RELATED OMICS DATASETS IN: GSE74028

PROVIDER: PRJNA298766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2649930.fastq.gz	Fastqsanger.gz
	SRR2649940.fastq.gz	Fastqsanger.gz
	SRR2649931.fastq.gz	Fastqsanger.gz
	SRR2649941.fastq.gz	Fastqsanger.gz
	SRR2649932.fastq.gz	Fastqsanger.gz

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Survey of cryptic unstable transcripts in yeast

Project description:We sequenced both the stable (WT) and unstable (rrp6delta) transcriptomes of three S.cerevisiae strains: S288c, Σ1278b, JAY291 and the S.paradoxus strain N17 for de novo annotation of cryptic unstable transcripts (CUTs). Doing so we have greatly expanded on previous CUTs which were limited to the S.cerevisiae strain S288c and have provided the first assessment of CUT expression conservation in yeast

2016-05-23 | GSE74028 | GEO

Detection of cryptic unstable transcripts associated with ribosomes in yeast

Project description:Detection of cryptic unstable transcripts associated with ribosomes in yeast

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Detection of cryptic unstable transcripts associated with ribosomes in yeast

Project description: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. We performed 5PSeq after glucose depletion to increase the number of ribosomes stop at the 5’UTR and start codon.

2019-10-01 | GSE119134 | GEO

[E-MTAB-75] Cryptic unstable transcripts in yeast

Project description: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

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Survey of cryptic unstable transcripts in yeast.

Project description:BackgroundCryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. We sought to ascertain the extent of conserved CUT expression across a variety of Saccharomyces yeast strains to further understand and characterize the nature of CUT expression.ResultsWe sequenced the WT and rrp6Δ transcriptomes of three S.cerevisiae strains: S288c, Σ1278b, JAY291 and the S.paradoxus strain N17 and utilized a hidden Markov model to annotate CUTs in these four strains. Utilizing a four-way genomic alignment we identified a large population of CUTs with conserved syntenic expression across all four strains. By identifying configurations of gene-CUT pairs, where CUT expression originates from the gene 5' or 3' nucleosome free region, we observed distinct gene expression trends specific to these configurations which were most prevalent in the presence of conserved CUT expression. Divergent pairs correlate with higher expression of genes, and convergent pairs correlate with reduced gene expression.ConclusionsOur RNA-seq based method has greatly expanded upon previous CUT annotations in S.cerevisiae underscoring the extensive and pervasive nature of unstable transcription. Furthermore we provide the first assessment of conserved CUT expression in yeast and globally demonstrate possible modes of CUT-based regulation of gene expression.

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Transcription profiling of wild type yeast grown with ethanol, glucose and galactose and the deletion mutant of Rrp6 to identify transcription start and end positions

Project description:To obtain a comprehensive survey of the structure and expression level of transcripts across the yeast genome, we used tiling arrays to profile wild-type transcriptomes in ethanol (YPE), glucose (YPD, SDC), and galactose (YPGal), which together encompass the main laboratory growth conditions of yeast. Transcript start and end positions were mapped to the genome by a segmentation algorithm and subsequent manual curation. To identify Cryptic Unstable Transcripts (CUTs), profiles were also measured for a deletion mutant of Rrp6, an important component of the nuclear exosome, which is involved in the degradation of CUTs. Expression profiles are provided in a searchable web-database (http://steinmetzlab.embl.de/NFRsharing).

2008-11-26 | E-TABM-590 | biostudies-arrayexpress

Chromatin-dependent cryptic promoters encode alternative protein isoforms in yeast

Project description: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. We define the 5’ and 3’ boundaries of cryptic transcripts and show that, contrary to RNA degradation-dependent ones , they often overlap with the end of the gene thereby using the canonical polyadenylation site and associate to polyribosomes. In fact, we show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Our work suggests that a significant fraction of chromatin-dependent internal cryptic promoters are in fact alternative truncated mRNA isoforms. The expression of these chromatin-dependent isoforms is conserved from yeast to human expanding the functional consequences of cryptic transcription and proteome complexity.

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Sense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype.

2012-07-25 | GSE37102 | GEO

Antisense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype.

2012-07-25 | GSE37042 | GEO

Saccharomyces cerevisiae

Project description:[E-MTAB-75] Cryptic unstable transcripts in yeast

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