Shintaro Iwasaki

RNA-dependent RNA amplification as a strategy to perform tRNA sequencing on low-input samples

The paper introduces a method to quantify tRNA in low-input samples using RNA-dependent RNA amplification with T7 polymerase, showing reproducible and quantitative results.

Neuronal stop-codon readthrough is associated with ribosome pausing and appends lineage-restricted extensions that can alter protein localization in Drosophila

The paper identifies neuronal stop-codon readthrough in Drosophila, showing it produces C-terminal extensions that alter protein localization.

Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts

The paper investigates mitochondrial translation termination, recycling, and quality control mechanisms using Ribo-Seq and Disome-Seq, revealing roles of release factors and rescue mechanisms.

Activity-dependent synthesis of translational machinery through dynamic remodeling of ribonucleoprotein granules

The paper uses optogenetic stimulation and Ribo-seq in Drosophila to show that neuronal activity triggers two phases of translation: one for synaptic factors and another for ribosomal proteins, regulated by TOP motifs and La-related protein.

NudC moonlights in ribosome biogenesis and homeostasis in Drosophila melanogaster polyploid cells

This study identifies NudC as a novel regulator of ribosome biogenesis and homeostasis in Drosophila polyploid cells, independent of its known role in dynein regulation.

Ribosome stalling facilitates chloroplast targeting of nuclear-encoded proteins

The paper identifies ribosome stalling as a mechanism that enhances chloroplast targeting of nuclear-encoded proteins in Arabidopsis thaliana.

Translational regulation of GAD1 identified by circadian and light-responsive ribosome-bound transcriptome analysis in the mouse hypothalamic suprachiasmatic nucleus

The paper identifies translational regulation of GAD1 in the mouse SCN using Ribo-seq and RNA-seq, showing light-induced ribosome binding without mRNA changes.

Giant virus creates subcellular environment to overcome codon-tRNA mismatch

The paper shows how mimiviruses create a subcellular environment to overcome codon-tRNA mismatch by localizing viral mRNAs and proteins at the periphery of a viral factory.

Revisiting the in vivo functions of coilin in mice: Requirement for snRNA modifications and formation of novel condensates in elongating spermatids

This study investigates the role of coilin in mice by generating coilin mutants, revealing its involvement in snRNA modifications and the formation of novel condensates in spermatids.

Ultra-parallel ribosome profiling platform with RNA-dependent RNA amplification

The paper develops a semi-automated Ribo-Seq and Disome-Seq platform to analyze translation status across many samples, identifying factors regulating translation and revealing links between stop codon readthrough and mitochondrial translation deficiency in COVID-19.

Sequence features and dynamics of subcellular translation revealed by APEX-Ribo-Seq

APEX-Ribo-Seq maps local translation across organelles and identifies compartment-specific transcripts, revealing sequence features and dynamics of subcellular translation.

eIF4G2-Mediated Translation Initiation of Histone Modifiers Is Essential for Intestinal Stem Cell Maintenance and Differentiation

This study shows that eIF4G2 is essential for intestinal stem cell maintenance and differentiation by facilitating the translation of histone modifiers.

Sense codon-misassociated eRF1 elicits ribosome stalling and induction of quality control

This study shows that eRF1 transiently binds to UUA sense codons, causing ribosome stalling and triggering quality control mechanisms in human cells.

Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

The paper investigates the coordination of chloroplast and cytoplasmic protein synthesis during light/dark transitions in plants, revealing translational control in chloroplasts and mRNA abundance control in the cytoplasm.

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

The paper examines translation variation across yeast genetic backgrounds and identifies a post-transcriptional buffering signature that affects essential genes and low-transcribed genes.

Translational regulation enhances distinction of cell types in the nervous system

The paper shows that translational regulation, particularly through 5' leader uORFs, enhances cell-type distinction in the Drosophila nervous system by preferentially translating neuronal proteins in neurons.

Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

This paper identifies pateamine A as a small-molecule compound that selectively represses mRNA translation by anchoring eIF4A and DDX3 to GNG motifs.

Mettl1-dependent m7G tRNA modification is essential for maintaining spermatogenesis and fertility in Drosophila melanogaster

This study shows that Mettl1-dependent m7G tRNA modification is essential for spermatogenesis and fertility in Drosophila, as its loss leads to sterility and tRNA instability.

The complexity and dynamics of in organello translation assessed by high-resolution mitochondrial ribosome profiling

This study develops a high-resolution mitochondrial ribosome profiling technique to analyze translation dynamics and regulation in mammals.

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.

Absolute calibration of ribosome profiling assesses the dynamics of ribosomal flux on transcripts

This paper introduces methods to absolute quantify ribosome flux on transcripts, revealing ribosome allocation under stress, aging, and across cell types.

CRISPRδ: dCas13-mediated translational repression for accurate gene silencing in mammalian cells

CRISPRδ uses dCas13 to specifically block translation without affecting mRNA stability, achieving high gene knockdown specificity in mammalian cells.

Gravitational and mechanical forces drive mitochondrial translation

The paper shows that gravity and mechanical forces influence mitochondrial translation by affecting signaling pathways and malonylation of the translational machinery.

Thor-Ribo-Seq: ribosome profiling tailored for low input with RNA-dependent RNA amplification

Thor-Ribo-Seq enables ribosome profiling on low-input samples using RNA-dependent RNA amplification to assess ribosome traversal with codon resolution.

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

The paper identifies a fungal mutation that allows survival on plants producing toxic rocaglates by altering eIF4A, a target of these compounds.

The requirement of GW182 in miRNA-mediated gene silencingin Drosophila larval development

This study shows that GW182 is essential for miRNA-mediated gene silencing in Drosophila, affecting larval development despite some survival and repression capabilities.

Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization of NEAT1 in Naked Mole-rat

The paper investigates paraspeckle formation in naked mole-rats, finding that nNEAT1_2 recruits different RNA binding proteins compared to mice.

METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

This study identifies METTL18 as a histidine methyltransferase that modifies RPL3, slowing ribosome translocation on tyrosine codons to aid protein folding and prevent aggregation.

Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation

The paper develops mito-FUNCAT-FACS to measure mitochondrial translation activity in individual cells and detects heterogeneity in cancer cells.

Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish

The paper identifies codon-mediated mRNA decay in zebrafish embryos, showing ribosome decoding kinetics affect mRNA stability independently of Znf598 and stall-dependent decay.