The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage
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ABSTRACT:
PROVIDER: PRJNA1080508 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28093300.fastq.gz | Fastqsanger.gz | |||
| SRR28093301.fastq.gz | Fastqsanger.gz | |||
| SRR28093302.fastq.gz | Fastqsanger.gz | |||
| SRR28093303.fastq.gz | Fastqsanger.gz | |||
| SRR28093216.fastq.gz | Fastqsanger.gz |
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Project description:In Saccharomyces cerevisiae, the kinase Rio1 regulates rDNA transcription and segregation, pre-rRNA cleavage, and 40S ribosomal subunit maturation. Other roles are unknown. Human orthologue RIOK1; which is frequently overexpressed in malignancies, drives tumor growth and metastasis. Again, also RIOK1 biology is poorly understood. In this study, we charted the global activity of Rio1 in budding yeast. By producing and systems-integrating its protein-interaction, gene-transcription, and chromatin-binding maps we generated Rio1's multi-layered activity network, which controls protein synthesis and turnover, metabolism, growth, proliferation, and genetic stability. Rio1 regulates itself at the transcriptional level, and manages its network both directly and indirectly, via a battery of regulators and transcription factors, including Gcn4. We experimentally confirmed the network and show that Rio1 commands its downstream circuit depending on the growth conditions encountered. We also find that Rio1 and RIOK1 activities are functionally equivalent. Our data suggest that pathological RIOK1 expression may deregulate its network and fuel promiscuous transcription and ribosome production, uncontrolled metabolism, growth, proliferation, and chromosomal instability; well-known contributors to cancer initiation, maintenance and metastasis.
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Project description:The conserved Saccharomyces cerevisiae kinase/ATPase Rio1 downregulates rDNA transcription to promote rDNA stability and segregation. To uncover additional roles in transcriptional regulation beyond the rDNA locus we defined the global Rio1 transcriptiome. By NGS we identify 818 differentially expressed genes that are under the transcriptional control of Rio1.
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Project description:In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. Here we surveyed the position of ribosome collisions, caused by ribosome pausing, at a genome-wide level using the modified ribosome profiling in human and zebrafish. The collided ribosomes, i.e. disome, emerge at various sites; the proline-proline-lysine motif, stop codons, and 3′ UTR. The number of ribosomes in a collision is not limited to two, rather four to five, forming a queue of ribosomes. Especially, XBP1, a key modulator of unfolded protein response, shows striking queues of collided ribosomes thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and the consequences of ribosome slowdowns by dissecting the specific architecture of ribosomes.
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Project description:Kinetochores assemble on centromeres via histone H3 variant CENP-A and low levels of noncoding centromere transcripts (cenRNAs). The latter are ensured by downregulation of RNA polymerase II (RNAPII) and turnover by the nuclear exosome. Using S. cerevisiae, we now add kinase Rio1 to this scheme. Yeast cenRNAs are produced in very low amounts either as short (median lengths of 231nt) or long (4,458nt) transcripts, in a 1:1 ratio. Rio1 limits their production by reducing RNAPII access and transcription activity, and promotes their turnover by the 5’-3’exoribonuclease Rat1. Rio1 similarly curtails the concentrations of noncoding pericenRNAs, which also exist as short transcripts (225nt) at a magnitude higher level than the cenRNAs. In yeast depleted of Rio1, cen- and pericenRNAs accumulatre, and kinetochores misform causing chromosomal instability. The latter phenotypes were also observed with human cells lacking orthologue RioK1, suggesting that CEN regulation by Rio1/RioK1 is evolutionary conserved.
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Project description:In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. Here we surveyed the position of ribosome collisions, caused by ribosome pausing, at a genome-wide level using the modified ribosome profiling in human and zebrafish. The collided ribosomes, i.e. disome, emerge at various sites; the proline-proline-lysine motif, stop codons, and 3′ UTR. The number of ribosomes in a collision is not limited to two, rather four to five, forming a queue of ribosomes. Especially, XBP1, a key modulator of unfolded protein response, shows striking queues of collided ribosomes thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and the consequences of ribosome slowdowns by dissecting the specific architecture of ribosomes.
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