Biology subjects

Hosaka, A.

Publications and source records attributed to Hosaka, A..

3 recordsLinked to original sources

bioRxiv2025

Database Chemistry for Genomics-Based Safety and Quality Evaluation of Biologics

Genomics-based safety and quality evaluation studies are advancing the bioindustry by enhancing various aspects, including viral safety, host cell protein (HCP) control, product heterogeneity control, cellular heterogeneity control, and process reproducibility. High-throughput instruments and genome-scale databases are essential in genomics, with the reference genome sequence being the most critical database. The completeness and accuracy of these genome sequences depend on DNA quality, sequencing instruments, read coverage, and assembly strategies. Significant efforts are being made to perfect genome assembly and continuously improve it. However, the quantitative impact of reference genome sequence accuracy on the safety of biologics is not yet fully understood. In this study, we compared and benchmarked six Chinese hamster genomes, including four newly sequenced genomes derived from Chinese hamster cell lines, from an industrial perspective. We also developed database assembly techniques to enhance the safety of biologics. We recommend using two or more independent reference genomes for viral safety studies. For HCP control, we suggest using protein sequences in which trypsin degradation peptides that overlap with high-risk proteins should be masked and unified. Additionally, we can predict microenvironments using single-cell transcriptome data. In bioengineering processes, any nucleotide samples have potential commercial benefits.

bioengineering↗

bioRxiv2023

Identification of active transposable element candidates from ROH in a de novo assembled chromosome-scale genome of a Nishikigoi, an ornamental fish derived from Common carp (Cyprinus carpio)

Transposable Elements (TEs) are major components of the genome. To understand their function and evolution, it is necessary to identify active TEs from a diverse range of organisms. Here, I report the genome of the Nishikigoi, an ornamental fish derived from the Common carp, and the novel approach to detecting active TE candidates. I constructed a chromosome-scale assembly using long-read sequencing and Hi-C methods. It revealed that Nishikigoi has Robertsonian-like chromosomal translocations not seen in Common carp. I also found that Nishikigoi has a significantly different genetic background from Common carp, reflecting the intensive breeding history. Furthermore, by focusing on Runs of Homozygosity (ROH) islands in the Nishikigoi genome and analyzing structural variations with long-read sequencing, I identified several active TE candidates. This study not only revealed the unique genetic features of Nishikigoi but also demonstrated the potential for a novel approach in the search for active TEs.

genomics↗

bioRxiv2022

The arms race in noncoding regions of transposable element: the evolution of anti-silencing and RNAi

Transposable elements (TEs) are among the most dynamic parts of genomes. Since TEs are potentially deleterious, eukaryotes silence them through epigenetic mechanisms such as DNA methylation and RNAi. We have previously reported that Arabidopsis TEs, called VANDALs, counteract epigenetic silencing through a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to noncoding regions of specific VANDAL copies and induce a loss of silent chromatin marks. Sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here, we show that RNAi efficiently targets noncoding regions of VANDAL TEs to silence them de novo. Target motifs of VANC, in turn, evolved to escape RNAi. Escaping RNAi could be the primary event leading to the differentiation of sequence-specific anti-silencing systems. We propose that this selfish behaviour of TEs paradoxically could make them less harmful to the host.

genetics↗