Biology subjects

Kai, Y.

Publications and source records attributed to Kai, Y..

5 recordsLinked to original sources

bioRxiv2024

Evolution of Key Factors Influencing Performance Across Phases in Junior Short Sprints

Sprint performance plays a crucial role in various sports. Short sprints vary in court size and competitive characteristics but are common in many sports. Although the relationship between age and muscle strength has been explored in short sprints, there is limited understanding of how various physical factors interact, particularly concerning differences in the acceleration phase. This study examined the relationship between sprint times at 0-2.5 m, 2.5-5 m, and 5-10 m intervals and various factors in junior athletes. Results indicated that sprint times increased with age, and is correlated with muscle strength and flexibility. Partial correlation analysis showed that faster times in the 0-2.5 m interval were associated with higher hip flexibility; in the 2.5-5 m interval, faster times were associated with higher core flexibility; and in the 5-10 m interval, a relationship with standing long jump performance was confirmed. Furthermore, lower fat-free body weight translated to higher performance. In the acceleration phase of 10 m, flexibility immediately after the start and the subsequent horizontal propulsive force is important factors that are strongly related to performance change in each interval. The study results illuminate the mechanism behind short sprints in junior athletes and emphasize the importance of daily training, considering the sprint distance required for each sport.

animal behavior and cognition↗

bioRxiv2023

Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions

Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. Upon acute depletion of Matr3, gains in chromatin accessibility and MyoD binding were observed, prior to widespread loss in the steady-state Matr3-knockout. These initial changes correlated with gene expression changes later in development. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected in close proximity to enhancer and promoter regions, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.

molecular biology↗

bioRxiv2020

Multi-scale annotations of chromatin states in 127 human cell-types

Genome-wide profiling of chromatin states has been widely used to characterize the biological function of non-coding genomic sequences in a cell-type specific manner. However, the systematic, comprehensive annotations of chromatin states from experimental data are challenging and require not just extensive biological knowledge but also sophisticated computational modeling. Previously we developed a hierarchical hidden Markov model, named diHMM, to systematically annotate chromatin states at multiple scales based on the combination of histone mark and chromatin regulator binding profiles. Here, we have improved the method by optimizing computational efficiency and using an ensemble-clustering approach to achieve a unified annotation by integrating information from cell-type-specific models. We then applied this improved method to generate a unified multi-scale chromatin state map in 127 human cell types, based on public data generated by the Epigenome Roadmap and ENCODE consortia. We found cell types with similar origin are typically associated with similar chromatin states, but cultured cell lines have distinct structures than primary cells. The contribution of enhancer elements to gene regulation is mediated by the broader context of domain-state organization. Distinct domain-state patterns are associated with various 3D chromatin structures. As such, we have demonstrated the utility of the multi-scale chromatin state map in characterizing the biological function of the human genome.

genomics↗

bioRxiv2019

The reconstruction and functional mapping of a recurrent microcircuit in Drosophila mushroom body

In Drosophila melanogaster, mushroom body and anterior paired lateral (APL) neurons play important roles not only in learning and memory but also in high cognitive behavior, reversal learning. The circuit between APL neurons and Kenyon cells (KCs) in the mushroom body underlies this behavior, including reversal learning, and electron microscopy (EM) methods must be used to reveal this circuit. Here, we reconstructed the connections between mushroom body cells and APL neurons in the vertical lobe of the mushroom body via focused ion beam scanning electron microscopy (FIB-SEM) and sparse genetic horseradish peroxidase (HRP) labeling. We offer the first EM evidence that recurrent network and lateral inhibition connections exist between APL neurons and KCs in the vertical lobe of the mushroom body. This circuit is the neural basis of action selection decision making, associative learning and reversal learning. Additionally, dopamine neurons project to different areas of mushroom bodies and, together with extrinsic neurons and KC axons, form a compartmental structure of mushroom body axons, thereby restricting the KC-mushroom body output neuron (MBON) response to local compartments. Whether APL neurons also respond locally is uncertain. We found that APL neurons exhibited input and output synapses that were intermixed and arranged on enlarged and thin sections, respectively, resembling a string of beads. Different KCs were found to project to APL neurons nonrepetitively, forming a local circuit structure. Furthermore, using a single neurite calcium imaging method, we identified local calcium domains on this circuit, suggestive of individual electrical compartments. The electrically recorded APL neurons were nonspike neurons that selectively responded to odor in both the lobes and calyx. Thus, the localized APL neuron responses coordinate with mushroom body-dopamine-MBON compartmental function.

neuroscience↗

bioRxiv2017

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

The CCCTC-binding zinc finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we found that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here we present Lollipop--a machine-learning framework--which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrated that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell-types, and outperforms other methods based only on CTCF motif orientation. Predictions were confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach reveals novel determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.

systems biology↗