Yutaka Nakachi

ORCID: 0000-0003-1964-2495
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About
Contact & Profiles
Research Areas
  • Epigenetics and DNA Methylation
  • Medical Imaging Techniques and Applications
  • Medical and Biological Sciences
  • Genomics and Chromatin Dynamics
  • CRISPR and Genetic Engineering
  • Pluripotent Stem Cells Research
  • Genetics and Neurodevelopmental Disorders
  • Peroxisome Proliferator-Activated Receptors
  • Immunotherapy and Immune Responses
  • RNA Research and Splicing
  • Cell Adhesion Molecules Research
  • Genetic Syndromes and Imprinting
  • RNA modifications and cancer
  • Mitochondrial Function and Pathology
  • RNA and protein synthesis mechanisms
  • Tryptophan and brain disorders
  • Metabolism and Genetic Disorders
  • Bone Metabolism and Diseases
  • Bipolar Disorder and Treatment
  • Adipose Tissue and Metabolism
  • Sex and Gender in Healthcare
  • Luminescence Properties of Advanced Materials
  • 3D Printing in Biomedical Research
  • Electronic and Structural Properties of Oxides
  • Virus-based gene therapy research

Saitama Medical University
2013-2025

Kumamoto University
2019-2025

Zero to Three
2024

Murata (United States)
2023

Kubota (Japan)
2023

Juntendo University
2023

Genomics (United Kingdom)
2016-2017

Hidaka Hospital
2015

Kyushu Institute of Technology
2006-2008

Advanced Engineering (Czechia)
2007

Peter Arner Carsten O. Daub Kristoffer Vitting‐Seerup Robin Andersson Berit Lilje and 95 more Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C. Freeman Ahmad M. N. Alhendi Peter Arner Richard A Axton J. Kenneth Baillie Anthony G Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret R. Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J. Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M. Forrester Dan Goldowitz Reto Guler Thomas J Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M. Khachigian S. Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine L. Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada Yasushi Okazaki Valerio Orlando Dmitry A. Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian‐Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst J. Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan E. Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D. Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F. Meehan Chris Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets genes has not been previously studied en masse. Exploiting the fact active are transcribed, we simultaneously measured their activity in 19 human 14 mouse time courses covering a wide range cell types biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated earliest responses....

10.1126/science.1259418 article EN Science 2015-02-13
Harukazu Suzuki Alistair R. R. Forrest Erik van Nimwegen Carsten O. Daub Piotr J. Balwierz and 95 more Katharine M. Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy L. Bailey Vladimir B. Bajić Denis C. Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M. Chalk Joe Chiba Nicole Cloonan Adam Dawe Josée Dostie Pär G. Engström Magbubah Essack Geoffrey J. Faulkner J. Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M. Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Yoshihide Hayashizaki Oliver Hofmann Michael Hörnquist Łukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders J. Skanderup Mandeep Kaur Hideya Kawaji Markus C. Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo T. Konno Anders Krogh Adéle Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Ross MacPherson Norihiro Maeda Christopher A. Maher Monique Maqungo Jessica C. Mar Nicholas Matigian Hideo Matsuda John S. Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto‐Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky

10.1038/ng.375 article EN Nature Genetics 2009-04-19

Mitochondrial disorders have the highest incidence among congenital metabolic characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic genetic heterogeneity. Mutations about 1,500 nuclear encoded mitochondrial proteins may cause dysfunction energy production disorders. More than 250 genes that been reported to date. However exact diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we...

10.1371/journal.pgen.1005679 article EN cc-by PLoS Genetics 2016-01-07

Abstract Meiosis is a unique process that allows the generation of reproductive cells. It remains largely unknown how meiosis initiated in germ cells and why non-germline do not undergo meiosis. We previously demonstrated knockdown Max expression, gene encoding partner MYC family proteins, strongly activates expression cell-related genes ESCs. Here we find complete ablation ESCs results profound cytological changes reminiscent undergoing meiotic cell division. Furthermore, our analyses...

10.1038/ncomms11056 article EN cc-by Nature Communications 2016-03-30

Excessive accumulation of bone marrow adipocytes observed in senile osteoporosis or age-related osteopenia is caused by the unbalanced differentiation MSCs into osteoblasts. Several transcription factors are known to regulate balance between adipocyte and osteoblast differentiation. However, molecular mechanisms that have yet be elucidated. To identify candidate genes associated with osteoporosis, we performed genome-wide expression analyses differentiating osteoblasts adipocytes. Among were...

10.1371/journal.pgen.1001019 article EN cc-by PLoS Genetics 2010-07-08

COVID-19, caused by SARS-CoV-2, has spread worldwide with dire consequences. To urgently investigate the pathogenicity of COVID-19 and develop vaccines therapeutics, animal models that are highly susceptible to SARS-CoV-2 infection needed. In present study, we established an model via intratracheal tract in CAG promoter–driven human angiotensin-converting enzyme 2–transgenic (CAG-hACE2) mice. The CAG-hACE2 mice showed several severe symptoms infection, definitive weight loss subsequent...

10.1172/jci.insight.152529 article EN cc-by JCI Insight 2021-08-31

Bipolar disorder (BD) is a severe mental characterized by repeated mood swings. Although genetic factors are collectively associated with the etiology of BD, underlying molecular mechanisms, particularly how environmental affect brain, remain largely unknown. We performed promoter-wide DNA methylation analysis neuronal and nonneuronal nuclei in prefrontal cortex patients BD (N = 34) controls 35). found decreased at promoters both cell types patients. Gene Ontology (GO) differentially...

10.1038/s41380-021-01079-0 article EN cc-by Molecular Psychiatry 2021-04-20

Intense green, orange or magenta luminescence was observed in rare-earth doped alkaline earth (Ca, Sr, and Ba) stannates, particularly strontium stannates with perovskite-related structures. Tb–Mg codoped SrSnO3 showed sharp emission lines corresponding to Tb ions as a green phosphor. Sm Sr3Sn2O7 exhibited pairs of an Eu–Ti Sr2SnO4 phosphor red luminescent Eu well broad blue band Ti-related complexes. It suggested that codoping and/or layered structures these phosphors are closely related...

10.1143/jjap.45.6981 article EN Japanese Journal of Applied Physics 2006-09-01

Abstract Once disseminated tumor cells (DTCs) arrive at a metastatic organ, they remain there, latent, and become seeds of metastasis. However, the clonal composition DTCs in latent state remains unclear. Here, we applied high-resolution DNA barcode tracking to mouse model that recapitulated dormancy head neck squamous cell carcinoma (HNSCC). We found clones abundantly circulated peripheral blood dominated DTCs. Through analyses multiple barcoded lines, identified specific subclonal...

10.1038/s41598-021-85743-z article EN cc-by Scientific Reports 2021-03-17

Recent success with the use of glucagon-like peptide-1 (GLP-1) receptor analogs and dipeptidyl peptidase-4 (DPP-4) inhibitors for treatment patients diabetes has highlighted role intestine as an endocrine organ. Gut-derived hormones, including GLP-1, glucose-dependent insulinotropic polypeptide (GIP), ghrelin, have important roles in control energy metabolism food intake, are associated metabolic syndrome. In this study, we isolated identified a new intestine-derived hormone, betagenin,...

10.1016/j.jbc.2025.108202 article EN cc-by Journal of Biological Chemistry 2025-01-01

Abstract Background Long interspersed nuclear element-1 (LINE1 or L1) is a major type of retrotransposons constituting about 20% mammalian genomes, some which still have retrotransposition ability. L1 the only transposon that can retrotranspose itself using its own proteins. Although strictly repressed by host-defense mechanism, it known somatic transiently activated in early neural development. We previously reported increased copy number brains patients as well animal models psychiatric...

10.1093/ijnp/pyae059.641 article EN cc-by-nc The International Journal of Neuropsychopharmacology 2025-02-01

Peroxisomes are subcellular organelles involved in lipid metabolic processes, including those of very-long-chain fatty acids and branched-chain acids, among others. Peroxisome matrix proteins synthesized the cytoplasm. Targeting signals (PTS or peroxisomal targeting signal) at C-terminus (PTS1) N-terminus (PTS2) mediate their import into organelle. In case PTS2-containing proteins, PTS2 signal is cleaved from protein when transported peroxisomes. The functional mechanism processing, however,...

10.1371/journal.pgen.1003286 article EN cc-by PLoS Genetics 2013-02-14

This report identifies a novel gene encoding Fam57b (family with sequence similarity 57, member B) as peroxisome proliferator-activated receptor γ (PPARγ)-responsive transmembrane that is related to obesity. The was identified based on an integrated bioinformatics analysis of the following three expression profiling data sets: adipocyte differentiation mouse stromal cells (ST2 cells), adipose tissues from obesity mice, and siRNA-mediated knockdown Pparγ using ST2 cells. consists variants...

10.1074/jbc.m112.440792 article EN cc-by Journal of Biological Chemistry 2012-12-29

Identification of a gene set capable driving rapid and proper reprogramming to induced pluripotent stem cells (iPSCs) is an important issue. Here we show that the efficiency kinetics iPSC are dramatically improved by combined expression Jarid2 genes encoding its associated proteins. We demonstrate forced JARID2 promotes suppressing Arf, known barrier, N-terminal half sufficient for such promotion. Moreover, accelerated silencing retroviral Klf4 transgene demethylation Nanog promoter,...

10.1002/stem.2243 article EN Stem Cells 2015-11-02

Background and AimsHepatocellular carcinoma (HCC) mainly develops from chronic hepatitis. Metabolic dysfunction-associated steatohepatitis (MASH) has gradually become the main pathogenic factor for HCC due to rising incidence of obesity metabolic diseases. 15-Hydroxyprostaglandin dehydrogenase (15-PGDH) is enzyme that degrades prostaglandin 2 (PGE2), which known exacerbate inflammatory responses. However, role PGE2 accumulation caused by 15-PGDH downregulation in development MASH-HCC not...

10.1016/j.jhepr.2023.100892 article EN cc-by-nc-nd JHEP Reports 2023-08-23

Correlation between amino acid composition and nucleotide is examined. Class III POU transcription factors having higher third GC contents showed of alanine, glycine, proline residues encoded by GC-rich nucleotides, vice versa. This correlation was observed even among various types from vertebrates invertebrates regardless functional structural constraints inherent to each protein. Furthermore, reptile class sequences revealed no evolutionary directionality increasing the cold- warm-blooded...

10.1093/oxfordjournals.molbev.a025710 article EN Molecular Biology and Evolution 1997-10-01

The epitaxial films of the recently developed calcium and strontium stannates phosphors with perovskite or its related structure were fabricated by pulsed-lased deposition method. all highly transparent in visible region, showed intense luminescence several colors under ultraviolet excitation. Light scattering at substrates' surfaces varied appearance photoluminescence. In combination epitaxial-film-growth technologies for many functional materials, obtained results provide a promise future...

10.1143/apex.1.015003 article EN Applied Physics Express 2008-01-17

Abstract Objective Mitochondrial respiratory chain disorder ( MRCD ) is an intractable disease of infants with variable clinical symptoms. Our goal was to identify the causative mutations in patients. Methods The subjects were 90 children diagnosed by enzyme assay. We analyzed whole mitochondrial DNA (mt sequences. A cybrid study performed two Whole exome sequencing for one these patients whose mt variant confirmed as non‐pathogenic. Results sequences identified 29 variants (13 previously...

10.1002/acn3.59 article EN cc-by-nc-nd Annals of Clinical and Translational Neurology 2014-04-28
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