Biology subjects

Nishijima, R.

Publications and source records attributed to Nishijima, R..

3 recordsLinked to original sources

bioRxiv2024

Effect of heterozygous deletions on phenotypic changes and dosage compensation in Arabidopsis thaliana

Heterozygous deletions, which include a large number of genes, are often caused by the induction of mutations. The induction of gene dosage compensation should be considered when assessing the effects of heterozygous deletions on phenotypic changes. This mechanism is known to balance the expression levels of genes with different copy numbers in sex chromosomes, but it is also known to operate in autosomes. In the present study, 12 Arabidopsis thaliana BC1 mutants with heterozygous deletions were produced by crossing wild-type Col-0 plants with mutants induced by heavy ion beams. The sizes of the deletions ranged from 50.9 kb to 2.03 Mb, and the number of deleted genes ranged from 8 to 92. Nine of the 12 BC1 mutants showed phenotypic changes in fresh weight 14 days after cultivation or during the flowering period. RNA-sequencing (RNA-seq) analyses of 14-day-old leaves, 40-day-old leaves, and flower buds showed that dosage compensation did not occur in any stage or tissue tested. These results indicate that heterozygous deletions cause phenotypic changes owing to the absence of dosage compensation. Article SummaryIn this study, we examined the impact of heterozygous deletions in Arabidopsis thaliana. By crossing wild-type Col-0 plants with mutants induced by heavy ion beams, we created 12 BC1 mutants, each having heterozygous deletions. The deletions ranged from 50.9 kb to 2.03 Mb, affecting 8 to 92 genes. Nine mutants showed changes in fresh weight or flowering time. RNA-seq analyses of leaves and flower buds revealed no gene dosage compensation. Our findings indicate that phenotypic changes result from the lack of dosage compensation in heterozygous deletions.

genetics↗

bioRxiv2020

The transcriptomic landscapes of diverse rice cultivars grown under mild drought conditions

Root system architecture affects plant drought tolerance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, especially for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field under mild drought stress. We found that four principal components explained the phenotypic variation and that accessions could be classified into four admixture groups (admixed, aus, indica, and japonica) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific admixture groups were enriched with stress response-related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and mild drought stress. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing (DAP-seq) analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under mild drought stress. ONE-SENTENCE SUMMARYCatalog of the phenomes and transcriptomes of rice cultivars grown in upland fields provides a resource for further studies toward breeding climate-resilient crops.

plant biology↗

bioRxiv2020

Alteration of mucins in the submandibular gland during aging in mice

ObjectiveMucins are large glycosylated glycoproteins that are produced in the salivary glands, and their changes may contribute to the development of xerostomia due to aging and the accompanying deterioration of oral hygiene. This study aimed to characterize the changes in the mucins produced in submandibular gland (SMG) during the aging process. MethodsSMG mucins derived from mice of each age were separated using supported molecular matrix electrophoresis (SMME). Subsequently, the membranes were stained with AB or blotted with MAL-II lectin. The SMME membranes stained with AB were subjected to densitometric analysis and glycan analysis. The detailed structures of O-glycan were investigated by MS/MS spectra. ResultsThe SMG of mice secreted three mucins with different glycan profiles: age-specific mucin, youth-specific mucin, and a mucin expressed throughout life, and the expression patterns of these mucins change during aging. Additionally, age-specific mucin began to be detected at about 12 months of age. A mucin expressed throughout life and age-specific mucin had the same mass of major glycans but different structures. Furthermore, the proportion of mucin glycan species expressed throughout life changed during the aging process, and aging tended to decrease the proportion of fucosylated glycans and increase the proportion of sialoglycans. ConclusionThere are three secretory mucins with different glycan profiles in the SMG of mice, and their expression patterns change according to the period of the aging process. The proportion of glycan species of mucin expressed throughout life also changes during the aging process. HighlightsO_LIThree secreted mucins with different glycan profiles are detected in SMG using SMME. C_LIO_LIEach mucin has its own peak production age during the aging process. C_LIO_LIAge-specific mucin begins to be detected at about 12 months of age. C_LIO_LISame mass of major glycans but different structures in mucins expressed throughout life vs. age-specific mucins. C_LIO_LIProportion of mucin glycan species expressed throughout life changes during aging. C_LI

biochemistry↗