Mitsutaka Kadota

Ductal myofibroblasts reactivate contractile program to stabilize alveolar architecture during lung regeneration

The paper identifies ductal myofibroblasts as critical for maintaining alveolar structure during lung regeneration through reactivation of a contractile program.

Stressor-Selective Sympathetic Preganglionic Modules for Organ-Biased Control

The paper identifies stressor-selective sympathetic preganglionic modules in mice that link physiological demands to organ-biased sympathetic output.

A single-nucleus and spatial transcriptomic atlas of the Syrian hamster preoptic area across hibernation states

This study creates a transcriptomic atlas of the Syrian hamster preoptic area using snRNA-seq and spatial transcriptomics, comparing seasonal and hibernation states.

Transcriptomic Landscape of Microglia in Mouse Models of Social Dysfunction and Oxytocin-Mediated Recovery

The paper investigates how VPA exposure and OT neuron stimulation affect microglia in the PVH and finds that OT neuron activation can reverse some microglial gene downregulation.

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

The paper presents whole genome sequences of two elasmobranchs, analyzing genome size dynamics and genomic architecture, revealing correlations between chromosome size, repetitive elements, and gene duplication patterns.

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

This study reconstitutes gene-scale chromatin arrays with controlled histone modifications to show acetylation increases structural fluctuations and reduces nucleosome contact frequency.

Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms

This study identifies the oldest vertebrate sex chromosomes in sharks and rays, revealing a unique dosage-dependent sex determination mechanism distinct from other vertebrates.

RNA Dynamics Regulate Transcriptional Condensate Vivacity to Drive Gene Coordination

The paper shows RNA exosome activity maintains transcriptional condensate stability and fluidity, which is essential for coordinated gene expression and cellular homeostasis.

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

This study constructs a haplotype-phased genome assembly for Haliotis gigantea and identifies non-syntenic homologous chromosomes with structural variations that may contribute to functional diversification.

The Greenland shark genome: insights into deep-sea ecology and lifespan extremes

This paper presents the first chromosome-level genome assembly of the Greenland shark, identifying genetic features associated with its extreme longevity and deep-sea adaptations.

Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence

This study presents the first chromosome-scale genome assembly of a chimaera, identifies a sex chromosome in holocephalans, and reveals genomic features related to intron size and sex determination.

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

This study presents the first whole genome assembly of the Pacific saury using SMRT sequencing, providing resources for fishery science and comparative biology.

Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

The paper estimates genome sizes of elasmobranch species using optimized flow cytometry and qPCR methods, revealing large variation and enabling non-invasive analysis.

Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals

The paper identifies truncated radial glia (tRG) as a conserved progenitor subtype in ferret and human corticogenesis, showing their role in brain expansion.

Single-cell transcriptome atlas of Drosophila gastrula 2.0

The paper presents a single-cell transcriptome atlas of Drosophila gastrulae, identifying 65 clusters and revealing spatial gene expression patterns across germ layers.

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu fish

The paper identifies a shared supergene involved in sex chromosome turnover across three Takifugu species, showing repeated translocations of this supergene as the mechanism for sex determination locus changes.

Chromosomal-scale De novo Genome Assemblies of Cynomolgus Macaque and Common Marmoset

This study presents de novo chromosome-scale genome assemblies for cynomolgus macaque and common marmoset using long-read and Hi-C data, achieving high contiguity and accuracy.

Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri

The paper reconstructs a high-coverage coding gene set for the inshore hagfish Eptatretus burgeri using genome sequencing and RNA-seq data.

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

This study benchmarks Hi-C methods for chromosome-scale genome scaffolding, identifying key factors that improve scaffolding quality and introduces a new protocol.

Cell Type Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing

The paper introduces tChIP-Seq, a method to analyze cell type-specific epigenetic modifications, identifying neuronal genes and unknown functions in cortical neurons.