Biology subjects

Yamashita, Y. M. M.

Publications and source records attributed to Yamashita, Y. M. M..

4 recordsLinked to original sources

bioRxiv2025

Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila

Programmed DNA elimination (PDE), a phenomenon wherein cells eliminate a subset of genetic material during certain stages of development, is observed in a broad range of organisms. The fungus gnat Bradysia (formerly Sciara) coprophila undergoes a series of PDE events during their development, including elimination of germline-restricted chromosomes (called L chromosomes) in soma and elimination of paternal chromosomes during male meiosis. However, the underlying mechanisms of this phenomenon are poorly understood. Highly repetitive satellite DNA, which often shows chromosome specific distribution, is a possible candidate for sequences involved in PDE. In this study, we utilized recent genomic data and genome assemblies to identify new satellite DNA sequences of B. coprophila. Through characterization of satellite DNA distribution on chromosomes, we found that the X and autosomes do not share centromeric satellite DNA sequence with the L chromosomes. We further provide the cytological evidence that confirms a recent finding based on the genome assembly that there are two distinct L chromosomes that were not previously distinguished cytologically. Together, our work lays a foundation for future studies to explore the possible connection between satellite DNA and the mechanism of PDE in B. coprophila.

cell biology↗

bioRxiv2025

OmniSplice: a framework-free splicing event reporter

Splicing generates mature mRNA by removing introns from nascent transcripts and is widely studied using RNA sequencing. However, most RNA-seq analysis pipelines classify RNA-seq reads according to predefined splice-junction structures and discard those that do not conform to such predefined models, potentially obscuring biologically meaningful splicing events. In this study, we developed OmniSplice, a computational framework that captures and analyzes RNA-seq reads that overlap annotated exon ends without assuming predefined splicing architectures. This approach enables systematic detection of non-canonical splicing events that are often overlooked by conventional analyses. Applying OmniSplice to Drosophila splicing factor mutants and mouse TDP-43 mutant datasets, we found widespread splicing defects with non-canonical junctions that were not previously recognized, including back-splicing and trans-splicing. Together, these results demonstrate that RNA-seq datasets may contain a substantial reservoir of overlooked splicing information, warranting more comprehensive approaches for analyzing RNA-seq data for splicing events.

bioinformatics↗

bioRxiv2024

Self-restrained sex chromosome drive through sequential asymmetric meiosis

Meiotic drivers are selfish genetic elements that bias their own transmission, violating Mendels Law of Equal Segregation. It has long been recognized that sex chromosome-linked drivers present a paradox: their success in transmission can severely distort populations sex ratio and lead to extinction. How sex chromosome drivers may resolve this paradox remains unknown. Here, we show that D. melanogasters Stellate (Ste) is an X chromosome-linked driver with a self-restraining mechanism that weakens its drive and prevents extinction. Ste protein asymmetrically segregates into Y-bearing cells during meiosis I, subsequently causing their death. Surprisingly, Ste segregates asymmetrically again during meiosis II, sparing half of the Y-bearing spermatids from Ste-induced defects. Our findings reveal a novel class of sex chromosome drivers that resolve the paradox of suicidal success.

genetics↗

bioRxiv2022

ribosomal DNA instability as a potential cause of karyotype evolution

Karyotype refers to the configuration of the genome into a set of chromosomes. The karyotype difference between species is expected to impede various biological processes, such as chromosome segregation or meiotic chromosome pairing, potentially contributing to incompatibility. Karyotypes can rapidly change between closely related species and even among populations of the same species. However, the forces driving karyotype evolution are poorly understood. Here we describe a unique karyotype of a D. melanogaster strain isolated from the Seychelles archipelago. This strain has lost the ribosomal DNA (rDNA) locus on the X chromosome. Because the Y chromosome is the only other rDNA-bearing chromosome, all females carry at least one Y chromosome as the source of rDNA. Interestingly, we found that the strain also carries a truncated Y chromosome (YS) that is stably maintained in the population despite its inability to support male fertility. Our modeling and cytological analysis suggest that the Y chromosome has a larger negative impact on female fitness than the YS chromosome. Moreover, we generated an independent strain that lacks X rDNA and has a karyotype of XXY females and XY males. This strain quickly evolved multiple karyotypes: two new truncated Y chromosomes (similar to YS), as well as two independent X chromosome fusions that contain the Y-derived rDNA fragment, eliminating females dependence on the Y chromosome. Considering that Robertsonian fusions frequently occur at rDNA loci in humans, we propose that rDNA loci instability is a driving force of karyotype evolution.

genetics↗