Toshifumi Inada

RiboPipe: efficient per-transcript codon-resolution ribo-seq coverage imputation for low-coverage transcripts

RiboPipe imputes codon-resolution Ribo-seq coverage for low-coverage transcripts using a unified framework that improves accuracy and efficiency.

Parallel ZNF598 and GIGYF2 pathways mediate conserved collision-dependent mRNA decay with distinct endonucleolytic features

The paper shows that two pathways, ZNF598 and GIGYF2, mediate mRNA decay due to ribosome collisions in yeast and mammals, with distinct endonucleolytic features.

Cytoplasmic roles of HSATIII RNAs in RNA granule assembly and production of actin cytoskeleton-associated repeat-containing proteins

This study identifies cytoplasmic roles of HSATIII RNAs in forming RNA granules and producing proteins during thermal stress recovery.

Editing of the polyubiquitin architecture on the collided ribosome maintains persistent RQC activity

The paper identifies the roles of Ubp2 and Ubp3 in editing polyubiquitin chains on ribosomes to maintain RQC activity.

HemK2 functions for sufficient protein synthesis and RNA stability through eRF1 methylation during Drosophila oogenesis

This study identifies HemK2 as a methyltransferase that methylates eRF1, essential for protein synthesis and RNA stability during Drosophila oogenesis.

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in vertebrates

The paper investigates how Znf598-mediated no-go decay (NGD) degrades mRNAs encoding C2H2-ZF domains during zebrafish development, preventing ribosome collisions and maintaining translational homeostasis.

Recognition and deubiquitination of free 40S for translational reset by Otu2

The paper identifies Otu2's role in deubiquitinating eS7 on recycled 40S ribosomal subunits to reset translation, revealing structural mechanisms for this process.

Ribosome collision sensor Hel2 recognizes mistargeting secretory ribosome-nascent chain complexes

This study identifies Hel2 as a sensor for ribosome collision in secretory pathways, showing it binds to mistargeted ribosome-nascent chain complexes and contributes to mitochondrial function.

Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome

This study shows that eS7A ubiquitination during ER stress in yeast regulates mRNA translation and affects stress outcomes.

Age-dependent ribosomal DNA variations and their effect on cellular function in mammalian cells

This study identifies age-dependent changes in rDNA copy number, methylation, and sequence variations in mice, linking these alterations to reduced pre-rRNA levels and shortened yeast lifespan.

Genome-wide survey of ribosome collision

The paper identifies genome-wide ribosome collision sites in humans and zebrafish, revealing their sequence motifs and functional roles in protein synthesis.

The Ccr4-Not complex monitors the translating ribosome for codon optimality

The paper shows the Ccr4-Not complex interacts with the ribosome's E-site when codon optimality is low, linking translation efficiency to mRNA stability.