Biology subjects

Ninomiya, K.

Publications and source records attributed to Ninomiya, K..

6 recordsLinked to original sources

bioRxiv2025

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

HSATIII architectural lncRNAs are nuclear short-tandem repeat ncRNAs induced upon thermal stress and serve as scaffolding molecules for nuclear stress bodies (nSBs), stress-induced membraneless organelles in the nucleus. We report that HSATIII lncRNAs are exported to the cytoplasm during stress recovery, where they form novel cytoplasmic bodies with nucleocytoplasmic RNA-binding proteins, including PURA, PURB, and m6A reader proteins. Recruitment of ALYREF to nSBs promotes HSATIII RNA export. These HSATIII-based granules, named HERALDs (Heat-removal-associated scaffolds), are transported along microtubules and accumulate at distal cellular regions. We further show that cytoplasmic HSATIII RNAs are translated into MEWNG-rich proteins, which interact with actin filaments and form complexes with HSPA8 and stress granule proteins such as ZC3HAV1 and ATXN2L. Together, these findings reveal previously unrecognized cytoplasmic roles of HSATIII RNAs, functioning both as lncRNAs to scaffold RNA granules and as mRNAs to produce proteins during the late phase of thermal stress recovery.

molecular biology↗

bioRxiv2025

Thermo-Sensing Mechanisms of Splicing Control by Nuclear Stress Bodies

Nuclear stress bodies (nSBs) are stress-inducible membraneless organelles formed on HSATIII lncRNAs and regulate pre-mRNA splicing during thermal stress recovery. During stress, dephosphorylated SRSFs accumulate in nSBs, whereas upon stress removal, their kinase CLK1 is recruited to rephosphorylate SRSFs, thereby promoting intron detention in specific transcripts. However, the mechanism underlying CLK1 localization to nSBs in response to stress removal has remained unclear. Here, we identify phosphorylation of CLK1 at Ser341 as a critical determinant of its nSB localization. Ser341 is phosphorylated under normal conditions, dephosphorylated by PP1 during stress, and rephosphorylated by RIOK2 during recovery, enabling CLK1 localization to nSBs specifically during recovery. We further identify PPP1R2, an entirely intrinsically disordered PP1 inhibitory subunit, as a reversible thermosensor that dissociates under stress to activate PP1. Together, our findings reveal multilayered thermosensing mechanisms that coordinate the temporally staged localization of SRSFs and CLK1 to nSBs, thereby regulating temperature-dependent pre-mRNA splicing.

molecular biology↗

bioRxiv2024

Next-generation sequencing analysis with a population-specific reference genome

Next-generation sequencing (NGS) has become widely available and is routinely used in basic research and clinical practice. The reference genome sequence is an essential resource for NGS analysis, and several population-specific reference genomes have recently been constructed to provide a choice to deal with the vast genetic diversity of human samples. However, resources supporting population-specific references are insufficient, and it is burdensome to perform analysis using these reference genomes. Here, we constructed a set of resources to support NGS analysis using the Japanese reference genome sequence, JG. We created resources for variant calling, gene and repeat element annotations, variant-effect prediction, read mappability, and RNA-seq analysis. We also provide a resource for reference coordinate conversion for further annotation enrichment. We then provide a variant calling protocol using JG-based resources. Our resources provide a guide to prepare sufficient resources for the use of population-specific reference genomes and can facilitate the migration of reference genomes.

bioinformatics↗

bioRxiv2021

Nascent ribosomal RNA acts as surfactant that suppresses growth of fibrillar centers in nucleolus

Liquid-liquid phase separation (LLPS) has been thought to be the biophysical principle governing the assembly of the multiphase structures of nucleoli, the site of ribosomal biogenesis. Condensates assembled through LLPS increase their sizes to minimize the surface energy as far as their components are available. However, multiple microphases, fibrillar centers (FCs), dispersed in a nucleolus are stable and their sizes do not grow unless the transcription of pre-ribosomal RNA (pre-rRNA) is inhibited. To understand the mechanism of the suppression of the FC growth, we here construct a minimal theoretical model by taking into account the nascent pre-rRNAs tethered to the FC surfaces by RNA polymerase I. Our theory predicts that nascent pre-rRNAs generate the lateral osmotic pressure that counteracts the surface tension of the FCs and this suppresses the growth of the FCs over the stable size. The stable FC size decreases with increasing the transcription rate and decreasing the RNA processing rate. This prediction is supported by our experiments showing that RNA polymerase inhibitors increase the FC size in a dose-dependent manner. This theory may provide insight into the general mechanism of the size control of nuclear bodies. Significance statementThe nucleolus, a site of pre-ribosomal RNA (pre-rRNA) production, has a characteristic multiphase structure, which has been thought to be assembled through liquid-liquid phase separation (LLPS). Although condensates assembled through LLPS grow by coarsening or coalescence as far as the components are available, the multiple inner phases, fibrillar centers (FCs), are dispersed in a nucleolus. To investigate the underlying mechanism, we constructed a minimal theoretical model by considering nascent pre-rRNAs tethered to RNA polymerase I at the FC surface. This model is supported by our experiments and explains previous experimental observations. This work shed light on the role of nascent RNAs to control the size of nuclear bodies.

biophysics↗

bioRxiv2020

Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model

Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here we report our discovery that naphthyridine carbamate dimer (NCD) targets disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31 (SCA31). Structural analysis of the NCD-UGGAA/UGGAA complex by nuclear magnetic resonance (NMR) spectroscopy clarified the mode of binding that recognizes four guanines in UGGAA/UGGAA pentad by hydrogen bonding with four naphthyridine moieties of two NCD molecules. Biological studies show that NCD disrupts naturally occurring RNA foci built on r(UGGAA)n repeat RNA known as nuclear stress bodies (nSBs) by interfering with RNA-protein interactions resulting in the suppression of nSBs-mediated splicing event. Feeding NCD to larvae of the Drosophila model of SCA31 alleviates disease phenotype induced by toxic r(UGGAA)n repeat RNA. These studies demonstrated that small molecules targeting toxic repeat RNAs are a promising chemical tool for studies on repeat expansion diseases.

biochemistry↗

bioRxiv2019

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly dephosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.

molecular biology↗