Biology subjects

Takenaka, S.

Publications and source records attributed to Takenaka, S..

4 recordsLinked to original sources

bioRxiv2024

Modeling of transcriptomic variation among subgenomes in 25 accessions of common wheat reveals cis- and trans-regulation architectures

Common wheat is an allohexaploid plant, thus making it difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3 RNA-seq, is efficient for obtaining homoeolog-distinguished transcriptomes and can thus overcome this measurement difficulty. This study obtained transcriptome data from the seedlings, second leaves, and root tips of 25 lines from mainly eastern transmitted area using Lasy-Seq. Roots and seedlings exhibited similar transcriptome profiles; however, they were different from those of the leaves. We determined the effects of subgenomes, lines and their interactions with leaves, roots, and seedlings on the expression levels of each homoeolog triad. Of the 19,805 homoeolog triads, 50.9-55.4%, 24.2-29.5%, and 7.7-9.0% showed significant effects on their expression levels from subgenome, line, and interaction, respectively. 51-55% and 24-30% have genetic variation in the cis- and trans-regulation. Hierarchical clustering and co-trans regulation network analysis of homoeolog triads revealed that the patterns of expression polymorphisms among the lines were shared in different genes. The triads in which the statistical model detected as line effects imply that expression variation between lines is caused by changes in a smaller number of common trans-factors. We assigned gene ontology (GO) terms of the Arabidopsis orthologs to wheat homoeolog triads via reciprocal BLAST between common wheat and Arabidopsis, thus improving the percentage of gene-assigned GO terms to all analyzed GO terms from 19.1% to 90.6%. GO term enrichment analysis revealed that GO terms related to each tissue type function were enriched in genes expressed in the leaves and roots. Our information provides fundamental knowledge for the future breeding of plants possessing complex gene regulatory networks such as common wheat.

plant biology↗

bioRxiv2023

Zinc controls histone acetyltransferase KAT7 activity to maintain cellular zinc homeostasis

Zinc is an indispensable micronutrient for optimal physiological functions, and zinc deficiency has been implicated in the pathogenesis of various human diseases. One potential mechanism underlying such pathogenic effects is the alteration of gene expression caused by zinc deficiency; however, the details of this process remain largely unexplored. Here, we show that during zinc deficiency, the histone acetyltransferase KAT7 loses its enzymatic activity, leading to the attenuated acetylation of histone H3 at Lys14 (H3K14ac) at enhancer regions. Physiologically, the decrease in H3K14ac leads to the upregulation of the expression of ZIP10, a plasma membrane-localized zinc transporter, thereby facilitating the import of extracellular zinc to maintain cellular zinc homeostasis. Moreover, prolonged zinc deficiency in mice induced by a zinc-deficient diet or high-fat diet, accompanied by decreased H3K14ac levels in the liver, upregulated the expression of genes associated with intracellular lipid droplet formation, leading to the accumulation of lipids within liver tissue. Our findings demonstrate that cells respond to zinc deficiency by converting it into an epigenetic signal that drives physiological or pathophysiological biological processes.

cell biology↗

bioRxiv2023

SHARPIN enhances ferroptosis in synovial sarcoma cells via NF-κB- and PRMT5-mediated PGC1α reduction

Sarcoma is a rare type of cancer for which new therapeutic agents are required. Ferroptosis is a nonapoptotic cell death triggered by iron-mediated lipid peroxidation. We found that transferrin receptor 1 (TFRC), an iron uptake protein, was expressed at higher levels in sarcoma cell lines than in noncancer and carcinoma cell lines. Glutathione peroxidase 4 (GPX4) protects cells against ferroptosis, and its inhibition using RAS-selective lethal 3 (RSL3) had an antitumor effect that was more pronounced in sarcoma cell lines, particularly synovial sarcoma cells, than in non-sarcoma cells. Because NF-{kappa}B can provoke ferroptosis, we examined the role of SHARPIN, an activator of NF-{kappa}B, in sarcoma. We found that SHARPIN expression is significantly associated with reduced survival in cohorts of patients with cancer, including sarcoma. In addition, SHARPIN promotes the sensitivity of sarcoma cells to ferroptosis. Further analyses revealed that the PGC1/NRF2/SLC7A11 axis and BNIP3L/NIX-mediated mitophagy are regulated through NF-{kappa}B and PRMT5 downstream of SHARPIN. Our findings suggest that ferroptosis could have a therapeutic effect in sarcoma, particularly in subpopulations with high TFRC and SHARPIN expression.

cancer biology↗

bioRxiv2022

Analysis of genetic relatedness between gastric and oral H. pylori in patients with early gastric cancer using multilocus sequence typing

Although oral cavity is the second most colonized site after the stomach, the association between gastric and oral Helicobacter pylori remains unclear. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer by multilocus sequence typing (MLST) analysis using seven housekeeping genes. Gastric biopsy specimens and oral samples, including saliva, supragingival dental biofilm, and superficial layers of the tongue, were collected from 21 patients positive for H. pylori by a fecal antigen test. The number of H. pylori allelic profiles of seven loci obtained from oral and gastric samples ranged from zero to seven since the yield of DNA was small even when the nested PCR was performed. The alleles of seven loci from both collection sites were determined from only one patient, and two out of seven alleles matched between oral and gastric samples. MLST analysis revealed that only one sample had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in two patients was markedly similar to gastric H. pylori, implying that the the origins of two strains may be the same, and the stomach and the oral cavity may be infected at the same time. In brief, although different genotypes of H. pylori exist in the oral cavity independently of H. pylori present in the stomach, there are rare cases in which the same H. pylori is present in the stomach and the oral cavity. It is necessary to establish a culture method for oral H. pylori for elucidating whether the oral cavity will act as the source of the gastric infection, as our analysis was based on a limited number of allele sequences. Author summaryHericobacter pylori is a clinically important pathogen that causes chronic gastritis and peptic ulcers, which are associated with gastric carcinoma. Oral H. pylori DNA has also been detected in a range of oral specimens, including saliva, supra- or sub-gingival biofilm, dentin caries, dental pulp, infected root canal, and coating of the tongue. Thus, researchers speculate that the main route of transmission of gastric H. pylori infections is via the oral cavity, however, there is inadequate evidence to support this suggestion. This study aimed to investigate if the oral and gastric H. pylori have the same origin using multilocus sequence typing. The results of this study provided some insight into the role of oral cavity as the source of H. pylori infections in stomach.

microbiology↗