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Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals [ncRNA-Seq]

ABSTRACT: Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE57448 | GEO | 2015/02/16

SECONDARY ACCESSION(S): PRJNA246475

REPOSITORIES: GEO

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Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. WT, rnt1 delta and rrp6 delta strains where grown independently and analyzed by Affymetrix yeast tiling microarray analysis

2015-02-16 | E-GEOD-57390 | biostudies-arrayexpress

Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. Total RNA from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then enriched for small RNA.

2015-02-16 | E-GEOD-57448 | biostudies-arrayexpress

Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals [Expression 1]

2015-02-16 | GSE57390 | GEO

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. Total RNA and whole cell extract from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then treated with recombinant Xrn1p.

2015-02-16 | E-GEOD-57447 | biostudies-arrayexpress

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals [Expression 2]

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

2015-02-16 | GSE57447 | GEO

Yeast RNase III triggers polyadenylation independent transcription termination

Project description:Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p dependent 5’-3’ exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast orthologue of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes and the deletion of RNT1 resulted in transcription read-through. Inactivation of Rat1p impaired Rnt1p dependent termination and resulted in the accumulation of 3’ end cleavage products. These results support a new model for transcription termination in which co-transcriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

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Project description:In Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B. In vitro and in vivo experiments indicated that snR39 is normally processed from the lariat of RPL7A, suggesting that the expressions of RPL7A and snR39 are linked. In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously. The results presented here reveal a new role of yeast RNase III in the processing of intron-encoded snoRNAs that permits independent regulation of the host mRNA and its associated snoRNA. RNA from wild type, rnt1d and rnt1ts grown at 26 C and 37 C on rich media

2015-01-21 | E-GEOD-65111 | biostudies-arrayexpress

Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals

2015-01-21 | GSE65111 | GEO

Massively parallel reporter assay of 3’UTR sequences identifies in vivo rules for mRNA degradation

Project description:The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here, we introduce UTR-Seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens-of-thousands of 3’UTR sequences during early zebrafish embryogenesis. UTR-Seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation. Three signals regulated early-onset rates: stabilizing poly-U and UUAG sequences, and destabilizing GC-rich signals. Three signals explained late-onset degradation: miR-430 seeds, AU-rich sequences and Pumilio recognition sites. Sequence based regression models translated 3’UTRs into their unique decay patterns, and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial 3’UTRs that conferred specific mRNA dynamics. UTR-Seq provides a general strategy to uncover the rules of RNA cis-regulation.

2017-12-12 | GSE106677 | GEO

Pombe_polyA_mapping_NGS_v3

Project description:Regulatory elements in the 3M-^R untranslated regions (UTRs) of eukaryotic mRNAs influence mRNA localization, translation, and stability. The length of these regions is determined by the location at which mRNAs are cleaved and polyadenylated. The use of alternative polyadenylation sites is common, and can be regulated in different situations. I present here a new method to identify cleavage and polyadenylation sites (CSs) at the genome-wide level. The approach is strand-specific, avoids RNA enzymatic modification steps that can introduce sequence-specific biases, and uses molecular barcodes to ensure that every identified CS originates from an individual RNA molecule. I applied to create the first comprehensive genome-wide map of polyadenylation sites in the fission yeast Schizosaccharomyces pombe, comprising the analysis of over two million individual mRNAs that defined 10,422 major CSs. CSs were identified for 90% of coding genes and 15% of non-coding RNAs. Alternative polyadenylation was prevalent in both groups, with 61% and 49% of all detected genes, respectively, displaying more than one CS. The specificity of the cleavage reaction was gene-specific, resulting in highly variable levels of heterogeneity in the length of the 3' UTRs. Finally, I show that for both coding and non-coding genes the most common regulatory motif associated with CSs in fission yeast is the canonical human AAUAAA sequence.

2013-11-19 | E-MTAB-1642 | biostudies-arrayexpress

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