Rippei Hayashi

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

Integrated transcriptomics and proteomics define the TRP channel hierarchy in mouse cortex

The paper quantifies TRP channel expression in mouse cortex using transcriptomics and proteomics, revealing dominant subfamilies and low abundance of others.

Conserved but mechanistically diverse piRNA defence against gypsy LTR retrotransposons in insect ovaries

The paper shows that piRNA pathways in insect ovaries defend against gypsy retrotransposons, with lineage-specific mechanisms across species.

A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements

The paper shows piRNA specificity arises from tissue-specific modules acting on non-specific RNA sampling, with Yb guiding processing in somatic cells and catalytic Argonaute triggering amplification in germline cells.

Single-molecule multimodal timing of in vivo mRNA synthesis

This study directly sequences pre-mRNA to resolve transcription and processing at single-molecule resolution, revealing delayed splicing and m6A methylation preceding splicing.

Non-gonadal PIWI protein, Aubergine, regulates regenerative stem cell proliferation and tumourigenesis in the Drosophila adult intestine.

This study shows Aubergine regulates ISC proliferation and tumourigenesis in Drosophila intestine through protein synthesis, independent of its piRNA function.

R2Dtool: Integration and visualization of isoform-resolved RNA features

R2Dtool integrates and visualizes isoform-resolved RNA features using transcript and genome annotations to enable comprehensive analysis of RNA modifications and structures.

A germline PAF1 paralog complex ensures cell type-specific gene expression

The paper shows that testis-specific PAF1C paralogs (tPAF) are essential for transcription termination and cell type-specific gene expression in Drosophila spermatocytes.

Mechanistic divergence of piRNA biogenesis in Drosophila

The paper shows that Drosophila species can generate piRNAs without Yb or Ago3, using alternative mechanisms for transposon silencing.

Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex.

This study identifies the interaction between Pla1 and Red1 in the MTREC complex and shows its role in polyadenylation of CUTs and heterochromatic island assembly.

Prediction of m6A and m5C at single-molecule resolution reveals a cooccurrence of RNA modifications across the transcriptome

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.