Biology subjects

Kawahara, Y.

Publications and source records attributed to Kawahara, Y..

18 recordsLinked to original sources

bioRxiv2026

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

Transcription and mRNA processing are integrated into appropriate mRNA export pathway(s) enabling fine-tuned gene expression. The closely related RNA helicases, UAP56 and URH49, form distinct complexes known as the apo-TREX and the apo-AREX complexes, respectively, which remodel into the ATP-TREX complexes, thus forming multiple mRNA export pathways. However, the mechanisms by which helicases and their complexes shape these pathways remain unclear. Here, we showed that UAP56 and URH49 play general roles in mRNA splicing ahead of export. Further analyses revealed three patterns of splicing regulation and their association with mRNA export: Type I, in which both helicases redundantly or synergistically regulate splicing within the same transcripts, associated with cooperative mRNA export; Type II, in which either helicase preferentially regulates splicing in distinct transcripts; and Type III, in which the helicases exert opposing splicing effects within the same transcripts. Type II and III regulation was associated with selective mRNA export. Moreover, we demonstrated that the distinct complex formation influenced the splicing patterns regulated by the two helicases. Our findings reveal an additional layer of transcriptome regulation mediated by UAP56, URH49, and their complexes, extending beyond their canonical roles in mRNA export.

molecular biology↗

bioRxiv2026

Rice Annotation Project Database (RAP-DB): literature-curated gene annotation and integrated omics resources for rice functional genomics and molecular breeding

High-throughput sequencing technologies have enabled the generation of high-quality reference genomes for numerous rice cultivars. However, inferring gene functions, associated phenotypes, and causal variants from these sequences remains challenging. The Rice Annotation Project Database (RAP-DB; https://rapdb.dna.affrc.go.jp) is a curated genomic resource that provides comprehensive gene annotations for the reference genome of Oryza sativa ssp. japonica cv. Nipponbare. Since its major update in 2013, gene models and functional annotations have been continuously revised through expert manual curation of newly published literature related to rice genes. As of March 2025, a total of 6,631 transcripts corresponding to 6,371 loci have been curated based on 4,699 peer-reviewed publications. These curated genes are functionally characterized and are frequently associated with agronomic traits, including yield components, stress tolerance, and disease resistance. To support molecular breeding, RAP-DB now provides a curated catalogue of 904 agronomically important loci, including gene symbols, functional descriptions, and associated traits, together with more than 1,000 functionally characterized alleles compiled from the literature. In addition to in-house expert curation, RAP-DB integrates community-curated datasets for major gene families, such as WRKY transcription factors, S-domain receptor-like kinases, and leucine-rich repeat-containing receptors, thereby expanding coverage of key regulatory and defense-related genes. RAP-DB also incorporates reanalyzed RNA sequencing expression profiles alongside microarray-based expression data and co-expression networks, offering gene-centric views of expression patterns across tissues, conditions, and developmental stages. Furthermore, RAP-DB is linked to genome-wide variation datasets from diverse rice varieties through the TASUKE+ genome browser, enabling exploration of allelic diversity across varieties. To enhance annotation quality and long-term sustainability, AI-assisted literature screening and a web-based feedback system have been introduced, allowing users to submit corrections to gene models and report newly characterized genes or relevant publications. Together, these developments strengthen RAP-DB as a primary, literature-based gene annotation resource and provide a practical foundation for molecular breeding in rice.

bioinformatics↗

bioRxiv2025

Non-linear gene sets for digital biomarkers of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by the loss of motor neurons. Accurate and accessible blood-based diagnosis of neurodegenerative diseases, including ALS, is becoming increasingly critical. It would be of a major clinical advantage to be able to distinguish ALS based on gene expression profiles of blood cells, but this still remains to be established. We analyzed existing data of peripheral blood mononuclear cells (PBMCs) of ALS patients by machine learning, the Maximum Mean Discrepancy (MMD), minimizing the issue of multi-collinearity shown in a multiple regression model, and identified a non-linear combination of gene sets to classify healthy controls and ALS, since non-linear approaches can capture intricate gene-gene interactions and threshold effects, which are often critical for accurately distinguishing disease from healthy states. In the gene expression profiles of PBMCs, a combination of expression levels in 3 genes, PRKAR1A, QPCT, and TMEM71, enabled us to classify ALS with an area under the curve (AUC) accuracy of 0.83 from the public database, which were then confirmed by laboratory blood samples with an AUC accuracy of 0.85. Furthermore, we found the expression levels of PRKAR1A, QPCT, and TMEM71 in motor neurons derived from induced pluripotent stem cells (iPSCs), the cell type at the core of the pathology, classified ALS with an accuracy of AUC 0.79. This approach of discriminating ALS with non-linear gene combinations may be useful for identifying ALS molecular biomarkers for blood-based diagnosis as well as for arriving at a completely new perspective of ALS pathogenesis.

molecular biology↗

bioRxiv2025

Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population

O_LICrop breeding assembles genomic variants into cultivars via crossing and selection. Phenotypic selection has improved yield and lodging tolerance but has limited genetic insights. We show how specific genomic variants and their combinations underpin advances in modern rice breeding in Japan. C_LIO_LIThrough genome-wide association study using a multi-parent advanced-generation intercross population derived from four temperate japonica cultivars, we identified 11 quantitative trait loci (QTLs) for key agronomic traits, including days to heading, shoot biomass, panicle length, and culm length under field conditions. GA20ox1, GA20ox2, and Hd1 were among the QTLs, and their natural variants were well conserved in temperate japonica cultivars bred in Japan, underscoring distinct selection pressures at these loci. C_LIO_LIBy integrating genotype data with 5-year yield-performance-evaluation trials of elite cultivars, we found that cultivars carrying multiple-copy GA20ox1 and functional Hd1, together with non-functional ga20ox2, tended to have shorter culms and higher grain yield than cultivars with multiple-copy GA20ox1, functional Hd1, and GA20ox2. This yield advantage was consistent across latitudes in Japan. C_LIO_LIThese results reveal favorable genotype combinations underlying modern japonica improvement and provide a genomic framework for breeding semi-dwarf, high-yielding cultivars adapted to temperate rice-growing regions in Asia. C_LI

genomics↗

bioRxiv2025

Multi-omics profiling with indoor-unmanned phenotyping reveals drought adaptation through constitutive ABF1 expression in wild rice

Improving drought resistance is crucial for stable crop production under climate change. Identifying the mechanisms of drought resistance using diverse genetic resources, including crop wild relatives, would be beneficial for molecular breeding. Here, we developed an indoor, unmanned phenotyping platform that can noninvasively and automatically collect temporal data on plant responses to drought stress. Using this system, we analyzed the phenotypic, transcriptomic, and environmental data of four cultivated rice varieties and five wild relatives. Multi-omics analysis revealed that one wild rice species exhibited drought adaptation through the constitutive expression of ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1 (ABF1), which encodes a transcription factor that regulates drought resistance, before drought stress. Drought testing of introgression lines of cultivated rice with constitutive ABF1 expression revealed higher drought tolerance than in cultivars without a growth penalty. Our findings suggest that constitutive ABF1 expression contributes to drought adaptation in both cultivated and wild rice.

plant biology↗

bioRxiv2025

Self-organization of high-dimensional geometry of neural activity in culture

A vast number of neurons exhibit high-dimensional coordination for brain computation, both in processing sensory input and in generating spontaneous activity without external stimuli. Recent advancements in large-scale recordings have revealed that this high-dimensional population activity exhibits a scale-free structure, characterized by power law and distinct spatial patterns in principal components (PCs). However, the mechanisms underlying the formation of this high-dimensional neural coordination remain poorly understood. Specifically, it is unclear whether the characteristic high-dimensional structure of population activity emerges through self-organization or is shaped by the learning of sensory stimuli in animals. To address this question and clearly differentiate between these two possibilities, we investigated large-scale neural activity in dissociated neuronal culture using high-density multi-electrode arrays. Our findings demonstrate that the high-dimensional structure of neural activity self-organizes during network development in the absence of explicit sensory stimuli provided to animals. As the cultures mature, the PC variance exhibits a power-law decay, and the spatial structures of PCs transition from global to localized patterns, driven by the temporal correlations of neural activity. Furthermore, we observed an unexpected co-occurrence between the power-law decay in PCA and neuronal avalanches, suggesting a link between self-organized criticality and high-dimensional activity. To uncover the mechanism behind this co-occurrence, we developed a new theoretical framework and demonstrated that it arises from heavy-tailed synaptic connectivity. By highlighting a developmental origin of the high-dimensional structure of neural activity, these findings deepen our understanding of how coordinated neural computations are achieved in the brain. SignificanceOne of the most intriguing questions in neuroscience is how the extremely high-dimensional yet efficiently orchestrated coordination of neural activity is organized. Central to this question lies the "nature versus nurture" debate: Is the high-dimensional coordination self-organized during development, or is it acquired through learning in animals? We take a novel approach by applying cutting-edge analytical techniques to study high-dimensional neural activity in dissociated neuronal cultures. Our findings reveal that fundamental features characterizing the high-dimensional coordination of neurons, including the scale-free geometry of the neural manifold and the intrinsic spatial structure of neural dynamics, are self-organized without sensory stimuli. Remarkably, we also discover that this high-dimensional geometry emerges concurrently with neuronal avalanches, a hallmark of self-organized criticality in neural circuits.

neuroscience↗

bioRxiv2024

Fine-Tuning TAWAWA1-Mediated Panicle Architecture by Genome Editing of a Downstream Conserved Noncoding Sequence in Rice

Genome editing is a promising tool to enhance plant breeding, particularly for the generation of practical quantitative traits. We focused on the rice yield-related gene TAWAWA1 (TAW1) and produced various degrees of increased panicle branching phenotypes by modifying its downstream conserved noncoding sequence (CNS). Differential modification of two highly conserved regions containing putative repressive elements in this CNS caused transcriptional upregulation of TAW1, resulting in diverse phenotypes.

plant biology↗

bioRxiv2023

Haploid-resolved and chromosome-scale genome assembly in Citrus unshiu and its parental species, C. nobilis and C. kinokuni

Citrus, a member of the Rutaceae family, is a widely cultivated crop with numerous cultivars. In Japan, citrus fruits account for a significant portion of agricultural production. Although several new citrus varieties have been developed through conventional breeding programs, satsuma mandarin remains the dominant cultivar. In this study, chromosome-scale and haploid-resolved reference genome sequences of satsuma mandarin (Citrus unshiu Marc) and its parental varaieties, kishu mandarin (C. kinokuni hort. ex Tanaka) and kunenbo mandarin (C. nobilis Lour. var. kunip Tanaka) were generated using long-read sequencing and Hi-C technologies. The comparison of haploid and unphased genomes revealed structural differences between them, indicating distinct regions in each haploid. In addition, genetic linkage maps were constructed, and genetic and physical distances were compared. The results showed variations in polymorphism density across different regions of the chromosomes. Together, the obtained results provide valuable insights into the genomic characteristics and structural variations of satsuma mandarin and related citrus varieties. These insights will lead to the further elucidation and improvement of citrus cultivars through genome breeding strategies.

genomics↗

bioRxiv2023

RNA editing of AZIN1 coding sites is catalyzed by ADAR1 p150 after splicing

Adenosine-to-inosine RNA editing is catalyzed by nuclear ADAR1 p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize double-stranded RNAs (dsRNAs) as targets. Although its frequency is quite rare, RNA editing occurs in coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 prior to splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double knockout mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw264.7 and human HEK293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 knockout mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.

molecular biology↗

bioRxiv2022

Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Hybridization is a widespread phenomenon in plants and is a pathway for the evolution of adaptive traits. However, this process may also affect the persistence of combinations of adaptive alleles evolved through natural selection when hybridization occurs between adapted and non-adapted populations. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. In this study, we explored the influence of hybridization on the conservation of combinations of adaptive alleles by evaluating the natural variation in and the genetic structure of genomic regions associated with seed dormancy. Based on sequence variation in the genomic regions associated with seed dormancy, we revealed that hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait that were observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, the hybrid-derived weedy rice strains had deeper seed dormancy than their parental weedy rice strains. This study suggests that hybridization between weedy rice (having adaptive allelic combinations for seed dormancy) and cultivated rice (having non-adaptive combinations) generates weedy rice strains that express deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and non-adapted populations seems to be reinforcing the trajectory towards the evolution of adaptive traits.

evolutionary biology↗

bioRxiv2021

Post-transcriptionally regulated genes are essential for pluripotent stem cell survival

The effects of transcription factors on the maintenance and differentiation of pluripotent stem cells (PSCs) have been well studied. However, the importance of post-transcriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 post-transcriptionally regulated genes with strict upregulation of the protein level in PSCs. Among them, we found that 84 genes were vital for the survival of PSCs and HDFs, including 20 genes that were specifically necessary for the survival of PSCs. These 20 proteins were upregulated only in PSCs and not in differentiated cells derived from the three germ layers. Subcellular fractionation of the mRNA showed that the expression of most of the 20 proteins was regulated at the mRNA localization stage from the nucleus to the cytoplasm, but their translation efficiency was constant. Together, these results revealed that post-transcriptionally regulated genes have a crucial role in PSC survival.

molecular biology↗

bioRxiv2021

A stress-reduced passaging technique improves the viability of human pluripotent cells

Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, yet some problems, such as the reproducibility among the experiments, remain. Here we describe an improved method for the subculture of human PSCs. The revised method significantly enhanced the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing, gene delivery, and directed differentiation. Furthermore, the method did not alter PSC characteristics after long-term culture and attenuated the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application. HighlightsO_LIThe revised passaging method significantly increases the viability of human PSCs. C_LIO_LIThe method triggers less DNA damage and apoptosis signals compared to the conventional method. C_LIO_LIThe stress-reduced method improves the results of downstream applications. C_LIO_LIThe method does not alter PSC characters and attenuates the overgrowth of abnormal subpopulations. C_LI

cell biology↗

bioRxiv2021

HCN2 in cholinergic interneurons of the nucleus accumbens mediates reward response

Cholinergic interneurons (ChIs) of the nucleus accumbens (NAc) are important for mediating the behavioral response to rewarding stimuli. A major role for these cells is to regulate dopamine (DA) transmission by activating cholinergic receptors at local DAergic nerve terminals. However, the mechanisms that enable cholinergic neurons to enhance DA release in response to reward remain unknown. Here we report that the hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2) in NAc ChIs mediates an enhancement in DA signaling in response to rewarding stimuli. The HCN current in NAc ChIs and its modulation by DA, as well as the increase in cholinergic efflux by local cocaine infusion were impaired in mice with deletion of HCN2 in cholinergic cells. Enhancement in the DA efflux and signaling in the NAc in response to rewarding stimuli, as well as cocaine conditioning were also dependent on HCN2 in ChIs. These results provide a mechanistic link between the activity of NAc ChIs and reward encoding.

neuroscience↗

bioRxiv2021

Predicting behavior through dynamic modes in resting-state fMRI data

Dynamic properties of resting-state functional connectivity (FC) provide rich information on brainbehavior relationships. Dynamic mode decomposition (DMD) has been used as a method to characterize FC dynamics. However, it remains unclear whether dynamic modes (DMs), spatial-temporal coherent patterns computed by DMD, provide information about individual behavioral differences. This study established a methodological approach to predict individual differences in behavior using DMs. Furthermore, we investigated the contribution of DMs within each of seven specific frequency bands (0-0.1,...,0.6-0.7 Hz) for prediction. To validate our approach, we confirmed whether each of 59 behavioral measures could be predicted by performing multivariate pattern analysis on a gram matrix, which was created using subject-specific DMs computed from resting-state functional magnetic resonance imaging (rs-fMRI) data of individuals. The prediction was successful, and DMD outperformed temporal independent component analysis, a conventional data decomposition method for extracting spatial activity patterns. Most of the behavioral measures that showed significant prediction accuracies in a permutation test were cognitive-behavioral measures. Our results suggested that DMs within frequency bands <0.2 Hz primarily contributed to prediction. In addition, we found that DMs <0.2 Hz had spatial structures similar to several common resting-state networks. We demonstrated the effectiveness of DMs, indicating that DMD is a key approach for extracting spatiotemporal features from rs-fMRI data.

neuroscience↗

bioRxiv2020

Disruption of Z-RNA-binding of ADAR1 induces Aicardi-Goutieres syndrome-like encephalopathy in mice

ADAR1 p150 is an enzyme responsible for adenosine-to-inosine RNA editing. Deletion of ADAR1 p150 results in embryonic lethality with a type I interferon (IFN) signature, caused by aberrant MDA5 sensing unedited transcripts. ADAR1 p150 contains a unique Z-DNA/RNA-binding domain (Z); however, the role of this domain remains unknown. A mutation has been identified in this domain in patients with Aicardi-Goutieres syndrome (AGS), an inherited interferonopathy, suggesting an essential role in avoiding MDA5 activation. Here, we show that a mutation in the Z domain reduces the editing activity of ADAR1 p150 by comparing activity between wild-type and mutated isoforms expressed in Adar1/Adar2 knockout cells. Furthermore, we created Z domain-mutated knock-in mice, which displayed severe growth retardation with abnormal organ development, including AGS-like encephalopathy with a type I IFN signature. These abnormalities were ameliorated by the concurrent deletion of MDA5. Collectively, Z-RNA-recognition contributes to ADAR1 p150-mediated RNA editing, which prevents MDA5 activation.

immunology↗

bioRxiv2019

Alignment of time-course single-cell RNA-seq data with CAPITAL

Recent techniques on single-cell RNA sequencing have boosted transcriptome-wide observation of gene expression dynamics of time-course data at a single-cell scale. Typical examples of such analysis include inference of a pseudotime cell trajectory, and comparison of pseudotime trajectories between different experimental conditions will tell us how feature genes regulate a dynamic cellular process. Existing methods for comparing pseudotime trajectories, however, force users to select trajectories to be compared because they can deal only with simple linear trajectories, leading to the possibility of making a biased interpretation. Here we present CAPITAL, a method for comparing pseudotime trajectories with tree alignment whereby trajectories including branching can be compared without any knowledge of paths to be compared. Computational tests on time-series public data indicate that CAPITAL can align non-linear pseudotime trajectories and reveal gene expression dynamics.

bioinformatics↗

bioRxiv2019

A comparative analysis among ADAR mutant mice reveals site-specific regulation of RNA editing

Adenosine-to-inosine RNA editing is an essential posttranscriptional modification catalyzed by adenosine deaminase acting on RNA (ADAR)1 and ADAR2 in mammals. For numerous sites in coding sequences (CDS) and microRNAs (miRNAs), editing is highly conserved and has significant biological consequences, for example, by altering amino acid residues and target recognition. However, technical limitations have prevented a comprehensive and quantitative study to determine how specific ADARs contribute to each site. Here, we developed a simple method in which each RNA region with an editing site was amplified separately and combined for deep sequencing. Using this method, we compared the editing ratios of all sites that were either definitely or possibly conserved in CDS and miRNAs in the cerebral cortex and spleen of wild-type mice, Adar1E861A/E861AIfih-/- mice expressing inactive ADAR1 (Adar1 KI) and Adar2-/-Gria2R/R (Adar2 KO) mice. We found that the editing ratio was frequently upregulated in either Adar mutant mouse strain. In contrast, we found that the presence of both ADAR1 and ADAR2 was required for the efficient editing of specific sites. In addition, some sites, such as miR-3099-3p, showed no preference for either ADAR. We further created double mutant Adar1 KI Adar2 KO mice and observed viable and fertile animals with complete absence of editing, suggesting that ADAR1 and ADAR2 are the sole enzymes responsible for all editing sites in vivo. Collectively, these findings indicate that editing is regulated in a site-specific manner by the different interplay between ADAR1 and ADAR2.

molecular biology↗

bioRxiv2019

Data-driven spectral analysis for coordinative structures in periodic systems with unknown and redundant dynamics

Living organisms dynamically and flexibly operate a great number of components. As one of such redundant control mechanisms, low-dimensional coordinative structures among multiple components have been investigated. However, structures extracted from the conventional statistical dimensionality reduction methods do not reflect dynamical properties in principle. Here we regard coordinative structures in biological periodic systems with unknown and redundant dynamics as a nonlinear limit-cycle oscillation, and apply a data-driven operator-theoretic spectral analysis, which obtains dynamical properties of coordinative structures such as frequency and phase from the estimated eigenvalues and eigenfunctions of a composition operator. First, from intersegmental angles during human walking, we extracted the speed-independent harmonics of gait frequency. Second, we discovered the speed-dependent time-evolving behaviors of the phase on the conventional low-dimensional structures by estimating the eigenfunctions. Our approach contributes to the understanding of biological periodic phenomena with unknown and redundant dynamics from the perspective of nonlinear dynamical systems.

neuroscience↗