A5045068486- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Pluripotent Stem Cells Research
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Machine Learning in Bioinformatics
- RNA Interference and Gene Delivery
- Reproductive Biology and Fertility
- Advanced biosensing and bioanalysis techniques
- Genetic diversity and population structure
- Animal Ecology and Behavior Studies
- Genetic Neurodegenerative Diseases
- DNA Repair Mechanisms
- Fish biology, ecology, and behavior
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Neurodevelopmental Disorders
- Biochemical and Structural Characterization
- Gene Regulatory Network Analysis
- Prenatal Screening and Diagnostics
- MicroRNA in disease regulation
Southern University of Science and Technology
2018-2025
National Institute of Genetics
2013-2020
The Graduate University for Advanced Studies, SOKENDAI
2013-2016
Abstract Transposable elements (TEs) make up a majority of typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools explore cells, however analysis is typically gene-centric TE expression has not been addressed. Here, we develop single-cell processing pipeline, scTE, report the TEs single cells range biological contexts. Specific types expressed subpopulations embryonic stem dynamically regulated during...
Abstract The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs increasingly recognized for their important biological functions, they a potential danger genomic stability and carefully regulated by the epigenetic system. However, full complexity this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that suppressed heterochromatic marks like H3K9me3, also labelled all major types chromatin modification in complex patterns,...
CTCF mediates chromatin insulation and long-distance enhancer-promoter (EP) interactions; however, little is known about how these regulatory functions are partitioned among target genes in key biological processes. Here, we show that Ctcf expression progressively increased during induced pluripotency. In this process, first as a insulator responsible for direct silencing of the somatic gene program and, interestingly, elevated next ensures accessibility contributes to EP interactions...
CTCF plays key roles in gene regulation, chromatin insulation, imprinting, X chromosome inactivation and organizing the higher-order architecture of mammalian genomes. Previous studies have mainly focused on canonical isoform. Here, we explore functions an alternatively spliced human isoform which exons 3 4 are skipped, producing a shorter (CTCF-s). Functionally, find that CTCF-s competes with genome binding binds similar DNA sequence. disrupts CTCF/cohesin binding, alters CTCF-mediated...
Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II be copied as parts primary transcripts; however, their full contribution mature transcript sequences remains unresolved. Here, using long short read (LR SR) sequencing data, we show that 26% coding 65% noncoding transcripts in human pluripotent stem cells...
Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around 16th century. The unique demographic history Mauritian cynomolgus provides opportunity not only examine genetic background well-established nonhuman primates for biomedical research but also understand effect an extreme population bottleneck on pattern polymorphisms in genomes. We sequenced whole genomes six and obtained average 20-fold coverage genome sequences each individual. overall...
The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles mouse reprogramming. On one side, induces pro-senescence factor Ink4a degrades pluripotency regulator PHF20 a factor-independent manner. other specifically recruited by to reduce H3K27me3 at both enhancers...
Experimental studies have found the involvement of certain conserved noncoding sequences (CNSs) in regulation proximal protein-coding genes mammals. However, reported cases long range enhancer activities and inter-chromosomal suggest that proximity CNSs to might not be important for regulation. To test importance CNS genomic location, we extracted between chicken four mammalian species (human, mouse, dog, cattle). These were confirmed under purifying selection. The intergenic are often...
Around 60% of in vitro fertilized (IVF) human embryos irreversibly arrest before compaction between the 3- to 8-cell stage, posing a significant clinical problem. The mechanisms behind this are unclear. Here, we show that arrested enter senescent-like state, marked by cell cycle arrest, down-regulation ribosomes and histones MYC p53 activity. can be divided into 3 types. Type I fail complete maternal-zygotic transition, II/III have low levels glycolysis either high (Type II) or III)...
Abstract The complicated process of neuronal development is initiated early in life, with the genetic mechanisms governing this yet to be fully elucidated. Single-cell RNA sequencing (scRNA-seq) a potent instrument for pinpointing biomarkers that exhibit differential expression across various cell types and developmental stages. By employing scRNA-seq on human embryonic stem cells, we aim identify differentially expressed genes (DEGs) crucial early-stage development. Our focus extends beyond...
Endogenous retroviruses (ERVs) occupy a significant part of the human genome, with some encoding proteins that influence immune system or regulate cell-cell fusion in early extra-embryonic development. However, whether ERV-derived somatic development is unknown. Here, we report developmental function for primate-specific ERVH48-1 (SUPYN/Suppressyn). encodes fragment viral envelope expressed during embryonic Loss led to impaired mesoderm and cardiomyocyte commitment diverted cells an...
Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution CNSs in four mammalian orders: primates, rodents, carnivores, cetartiodactyls. defined two thresholds for CNS using conservation level coding genes; all three positions only first second codon positions. The varied among lineages, primates rodents having highest lowest number CNSs, respectively, whereas...
Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior intellectual abilities. Despite the increasing genome data, however, genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes highly conserved noncoding sequences (HCNSs) are among high-potential evolutionary candidates involved in driving clade-specific characters phenotypes. On this premise, we analyzed whole along with gene orthology data retrieved from...
β-Catenin recruits BRD4 and other coregulators to protect pluripotency gene transcription against network perturbation.
Investigating the functions and activities of genes requires proper annotation transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in number transcripts, especially so for noncoding transcripts. This heterogeneity assembled sets might be partially explained by sequencing depth. Here, we used real simulated short-read data as well long-read to systematically investigate impact depths on accuracy We analyzed transcripts from 671 human four sets....
Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are resistant to reprogramming. Epigenetic barriers must block from reprogramming, but the nature of those is unclear. In this study, we generated a systematic panel mouse embryonic fibroblasts (MEFs) using transgenes discovered lines compatible with when transfected Oct4/Sox2/Klf4/Myc. By comparing reprogramming-capable incapable identified multiple stages failure in process....
Abstract Capybara (Hydrochoerus hydrochaeri) is the largest species among extant rodents. The draft genome of capybara was sequenced with estimated size 2.6 Gb. Although about 60 times larger than guinea pig, comparative analyses revealed that neutral evolutionary rates two were not substantially different. However, 39 mammalian genomes very heterogeneous rates. highest rate, 8.5 higher human found in Cricetidae–Muridae common ancestor after divergence Spalacidae. Muridae, family number...
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Species of the genus Pagurus have diversified into a wide variety marine habitats across world. Despite their worldwide abundance, diversity and biogeographical relationship are relatively less understood at species-level. We evaluated phylogenetic genetic among species based on publicly available mitochondrial nuclear markers. While independent analyses different markers allowed for larger coverage taxa produced largely consistent results, concatenation 16S COI partial sequences led to...
Abstract Transposable elements (TEs) are genomic that found in multiple copies mammalian genomes. TEs were previously thought to have little functional relevance but recent studies reported TE roles biological processes, particularly embryonic development. To investigate the expression dynamics of during human early development, we used long-read sequence data generated from vitro differentiation pluripotent stem cells (hPSCs) endoderm, mesoderm, and ectoderm lineages construct...