Measurement of mRNA stability during transcriptional memory in mutants for RNA degradation
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE218400 | GEO | 2023/01/09
REPOSITORIES: GEO
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Project description:To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.
2023-07-27 | GSE235553 | GEO
Project description:Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
2019-08-21 | GSE90041 | GEO
Project description:Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
2019-08-21 | GSE129269 | GEO
Project description:Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
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Project description:The main cytoplasmic mRNA decay pathway in yeast uses the 5’-3’ exonuclease Xrn1 (Parker and Song, Nat Struct Mol Biol. 2004 ). This protein shuttles from the cytoplasm to the nucleus, where it has a role as transcription factor (Haimovich et al. Cell 2013). In this work, we find that most of the global phenotypes of an xrn1 mutant are partially complemented by a cytoplasmic version of the paralogous 5’-3’exonuclease Rat1 (cRat1) indicating that this 5’-3’-exonuclease has a similar enzymatic capacity as Xrn1. The lack of a cytoplasmatic 5’-3’-exoribonuclease is the cause of the physiological defects of an xrn1 mutant. The capacity of cRat1 to perform co-translational decay is, however, very limited. The comparison with the strain having a NLS1∆-NLS2∆-Xrn1 version shows that it is slightly deficient in 5’→3’-co-translational decay but much more efficient than cRat1. In both strains, cRat1 and -Xrn1-NLS1&2, the lack of nuclear Xrn1 has a very minor influence on cell growth.
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Project description:The main decay pathway of yeast mRNAs in the cytoplasm uses the 5’-3’ exonuclease Xrn1. This protein shuttles from the cytoplasm to the nucleus, where it has a role as transcription factor. We have recently demonstrated that importing depends on two nuclear localization sequences (NLS 1 & NLS2) and that exporting depends on its binding (presumably co-transcriptional) to mRNAs. It is also known that Xrn1 is able to degrade decapped mRNAs that are still being translated by ribosomes. In this work, we analyze the pleiotropic functions of Xrn1 by comparing the phenotypes of yeast strains lacking Xrn1 or its capacity to be imported into the nucleus with those of the substitution of Xrn1 by a cytoplasmic version of the paralogous 5’-3’ exonuclease Rat1 (cRat1). We find that most of the global phenotypes of an xrn1 mutant are partially complemented by cRat1 indicating that this 5’-3’ exonuclease has a similar enzymatic capacity as Xrn1 and that the lack of a cytoplasmic 5’-3’-exoribonuclease is the cause of the physiological defects of an xrn1 mutant. The capacity of cRat1 to perform co-translational decay is, however, very limited. The comparison with the strain carrying Xrn1 with non-functional NLSs (Xrn1ΔNLS1/2) shows that it is slightly deficient in 5’→3’-co-translational decay but much more efficient than cRat1. In both strains, cRat1 and Xrn1ΔNLS1/2, the lack of nuclear Xrn1 has a very minor influence on cell growth experiment in wild type and xrn1 mutant strains.
2024-06-01 | GSE198240 | GEO
Project description:mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5’ to 3’ exonuclease Xrn1 - a major mRNA synthesis and decay factor. Here we show that nucleocytoplasmic shuttling of several mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromise transcription and, unexpectedly, also the cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both the “classical” and the novel pathways, the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper adaptation to environmental changes, in particular to ever changing environmental fluctuations.
2022-09-19 | PXD036414 | Pride
Project description:Ribosomal RNAs (rRNAs) biogenesis are multistep processes requiring the activity of several nuclear and cytoplasmic exonucleases. The exact processing steps for mammalian 5.8S rRNA remains obscure. Here, using loss-of-function approaches in mouse embryonic stem cells and deep sequencing of rRNA intermediates, we investigate at nucleotide resolution the requirements of exonucleases known to be involved in 5.8S maturation, and explore the role of the Perlman syndrome-associated 3’-5’ exonuclease Dis3l2 in rRNA processing. We expand the repertoire of Dis3l2 targets to three 5.8S, 5S, and 28S rRNAs. We uncover a novel cytoplasmic intermediate that we name ‘7SB’ rRNA that is generated through sequential processing by distinct exosome complexes. 7SB rRNA can be oligouridylated by TUT4/7 and subsequently processed by Dis3l2 and Eri1. Moreover, exosome depletion triggers Dis3l2-mediated decay (DMD) as a surveillance pathway for rRNAs. Our data identify previously unknown 5.8S rRNA processing steps and provide nucleotide level insight into the exonuclease requirements for mammalian rRNA processing.
2019-04-13 | GSE129734 | GEO
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci). Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.
2015-04-13 | E-GEOD-57936 | biostudies-arrayexpress
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). Compared with Col-0, 4394 genes exhibited differential expression in ein5-1 ski2-3, much more than those in the ein5-1 (1138 genes) or ski2-3 (1040 genes) single mutant (2-fold cutoff, p < 0.01, FDR < 0.05), suggesting a largely disturbed transcriptome in the absence of both EIN5 and SKI2. While a small overlap was found between the differentially expressed genes in e/C and s/C comparisons, the gene lists from es/C, es/e and es/s comparisons (2-fold cutoff, p < 0.01, FDR < 0.05) largely overlapped with each other, indicating a collaborative function of EIN5 and SKI2 on a transcriptome-wide scale. The 1670 genes overlapped in the es/C, es/e and es/s comparisons included 1306 upregulated genes and 360 downregulated genes with only 4 genes as exception. 994 of the 1306 upregulated genes (76.1%) and 273 of the 360 downregulated genes (75.8%) were differentially expressed in the es/res comparison like that in es/C, es/e and es/s, indicating a substantial supression of the redundant function of EIN5 and SKI2 by RDR6. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways. Examination of transcriptomes in 6 genotypes.
2015-04-13 | E-GEOD-52407 | biostudies-arrayexpress