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Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

ABSTRACT: Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

PROVIDER: PRJNA776169 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16633400.fastq.gz	Fastqsanger.gz
	SRR16633401.fastq.gz	Fastqsanger.gz
	SRR16633402.fastq.gz	Fastqsanger.gz
	SRR16633403.fastq.gz	Fastqsanger.gz
	SRR16633404.fastq.gz	Fastqsanger.gz

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Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

Project description:Upf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.

2022-10-21 | GSE186795 | GEO

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

2022-10-21 | PXD029577 | Pride

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance.

Project description:Upf1, Upf2, and Upf3, the central regulators of nonsense-mediated mRNA decay (NMD), appear to exercise their NMD functions while bound to elongating ribosomes, and evidence for this conclusion is particularly compelling for Upf1. Hence, we used selective profiling of yeast Upf1:ribosome association to define that step in greater detail, understand whether the nature of the mRNA being translated influences Upf1:80S interaction, and elucidate the functions of ribosome-associated Upf1. Our approach has allowed us to clarify the timing and specificity of Upf1 association with translating ribosomes, obtain evidence for a Upf1 mRNA surveillance function that precedes the activation of NMD, identify a unique ribosome state that generates 37-43 nt ribosome footprints whose accumulation is dependent on Upf1's ATPase activity, and demonstrate that a mutated form of Upf1 can interfere with normal translation termination and ribosome release. In addition, our results strongly support the existence of at least two distinct functional Upf1 complexes in the NMD pathway.

| S-EPMC9670811 | biostudies-literature

Head and Embryo 80S monosomes are much more translationally active than 80S in other tissues

Project description:Translational regulation at the stage of initiation impacts the number of ribosomes translating each mRNA molecule. For example, multiple ribosomes can engage on a single mRNA forming a polysome, resulting in highly efficient protein synthesis. However, the translational activity of single 80S ribosomes on mRNA (monosomes) is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in many tissues. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs. Overall, these findings highlight that regulation of translation initiation, and therefore the number of ribosomes bound per mRNA, varies substantially across tissues.

2025-03-24 | GSE267425 | GEO

RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis

Project description:Immunoprecipitation of Upf1-bound RNA from the cytoplasmic and synaptosomal compartments followed by RNA sequencing identified unique populations of NMD-associated transcripts and altered levels after status epilepticus.

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Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

Project description:Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

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Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast

Project description:Upf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In S. cerevisiae, Upf1 exists in two distinct complexes with factors that mediate NMD activation or 5'-3' mRNA degradation. We combined endogenous purifications and biochemical reconstitutions of yeast Upf1 complexes with structural analyses and biochemical assays to elucidate the molecular mechanisms driving the mutually exclusive organization of the Upf1-5'-3' and Upf1-2-3 complexes. We show that yeast Upf1 is in a constitutive complex whereby its CH, RecA and C-terminal domains interact with the mRNA decapping factor Dcp2, NMD-associated proteins Nmd4 and Ebs1, and the 5'-3' exoribonuclease Xrn1, respectively. Together, the interacting surfaces and closed conformation of Upf1 in the Upf1-5'-3' complex sterically obstruct the binding of Upf2-3. Our work points to a major restructuring upon recruitment of these factors during NMD and provides insights into evolutionary divergence amongst species.

2025-10-15 | GSE307461 | GEO

Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

Project description:Fe-BABE probing of Upf1 binding site on yeast ribosome

2017-12-06 | GSE104072 | GEO

Phosphorylated UPF1 (p-UPF1) RIP-seq using mouse Neuro-2A (N2A) neuroblastoma cells

Project description:To identify high-confidence NMD targets in mouse N2A neuroblastoma cells, we used our established transcriptome-wide RNA sequencing (RNA-seq) methodologies. Through parallel analyses of RNA-seq upon UPF1-knockdown (KD) and RNA immunoprecipitation (RIP-seq) footprinting of p-UPF1-bound RNAs, we identified 1027 high-confidence neuronal NMD targets.

2021-10-25 | GSE180134 | GEO

Determination the direct binding target transcripts of UPF1 in B cell.

Project description:To determine the direct binding targets of UPF1, we performed RNA-immunoprecipitation sequencing (RIP-seq), in which mRNAs bound to phosphorylated (NMD-active) UPF1 were immunoprecipitated. And then, we analyzed the pUPF1-bound RNAs by RNA sequencing.

2024-05-30 | GSE234827 | GEO

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