Unknown,Transcriptomics,Genomics,Proteomics

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Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

ABSTRACT: In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the recruitment of THO complex subunit upon Rho activation, which revealed that Tho2 was over-recruited in opposition to its counterparts. We then tracked the recruitment of Rrp6 upon Rho induction in WT strain and in strains lacking either Mft1 or Tho2, showing the implication of Tho2 in Rrp6 recruitment over Rho induction. Finally, we measured the recruitment of Rrp6 upon partial deletion of Tho2 C-terminal domain responsible for its RNA interaction ability, proving that Tho2 presence on the chromatin is required for the Rho-induced Rrp6 recruitment..

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Valentin Beauvais

PROVIDER: E-MTAB-12378 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Mitochondrial DNA-depleted human skin fibroblasts (HSF rho0) with suppressed oxidative phosphorylation were characterized by significant changes in the expression of 2100 nuclear genes, encoding numerous protein classes, in NF-kappaB and STAT3 signaling pathways and by decreased activity of the mitochondrial death pathway, compared to the parent rho+ HSF. In contrast, the extrinsic TRAIL/TRAIL-Receptor-mediated death pathway remained highly active, and exogenous TRAIL induced higher levels of apoptosis in rho0 cells compared to rho+ HSF. Global gene expression analysis using microarray and quantitative RT-PCR demonstrated that expression levels of many growth factors and their adaptor proteins (FGF13, HGF, IGFBP4, IGFBP6, IGFL2), cytokines (IL6, IL17B, IL18, IL19, IL28B) and cytokine receptors (IL1R1, IL21R, IL31RA) were substantially decreased after mitochondrial depletion. Some of these genes were targets of NF-kappaB and STAT3, and their protein products could regulate the STAT3 signaling pathway. Alpha-irradiation induced expression of several NF-kappaB/STAT3 target genes, including IL1A, IL1B, IL6, PTGS2/COX2 and MMP12, in rho+ HSF, but this response was substantially decreased in rho0 HSF. Suppression of the IKK-NF-kappaB pathway by the small molecular inhibitor BMS-345541 and of the JAK2-STAT3 pathway by AG490 dramatically increased TRAIL-induced apoptosis in the control and irradiated rho+ HSF. Inhibitory antibodies against IL6, the main activator of JAK2-STAT3 pathway, added into the cell media, also increased TRAIL-induced apoptosis in rho+ HSF. However, NF-kappaB activation was partially lost in mitochondrial DNA-depleted HSF resulting in downregulation of the basal or radiation-induced expression of numerous NF-kappaB targets, further suppressing IL6-JAK2-STAT3, that in concert with NF-kappaB, regulated protection against TRAIL-induced apoptosis. There are 12 total samples, 3 biological replicates each of HSF rho+ and rho0 cells that were not irradiated (control=C) or irradiated (alpha=A). Cells were harvested at 4 hours after treatment.

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Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

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