Research Articles

  1. Kirihara T, Luo Z, Chow SYA, Misawa R, Kawada J, Shibata S, Khoyratee F, Vollette CA, Volz V, Levi T, Fujii T, Ikeuchi Y. “A Human Induced Pluripotent Stem Cell-Derived Tissue Model of a Cerebral Tract Connecting Two Cortical Regions.” iScience 2019, 14, 301-311
  2. Chen X, Chanda A, Ikeuchi Y, Zhang X, Goodman JV, Reddy NC, Majidi SP, Wu DY, Smith SE, Godec A, Oldenborg A, Gabel HW, Zhao G, Bonni S, Bonni A. "The Transcriptional Regulator SnoN Promotes the Proliferation of Cerebellar Granule Neuron Precursors in the Postnatal Mouse Brain." Journal of Neuroscience 2019, 39, 44-62
  3. Cheng C, Deng PY, Ikeuchi Y, Yuede C, Li D, Rensing N, Huang J, Baldridge D, Maloney SE, Dougherty JD, Constantino J, Jahani-Asl A, Wong M, Wozniak DF, Wang T, Klyachko VA, Bonni A. "Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome." Cell Reports 2018, 25, 1404-1414
  4. Umegaki Y, Brotons AM, Nakanishi Y, Luo Z, Zhang H, Bonni A, Ikeuchi Y. "Palladin Is a Neuron-Specific Translational Target of mTOR Signaling That Regulates Axon Morphogenesis." Journal of Neuroscience 2018, 38, 4985-4995
  5. Asano K, Suzuki T, Saito A, Wei FY, Ikeuchi Y, Numata T, Tanaka R, Yamane Y, Yamamoto T, Goto T, Kishita Y, Murayama K, Ohtake A, Okazaki Y, Tomizawa K, Sakaguchi Y, Suzuki T."Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease." Nucleic Acids Research 2018, 46, 1565-1583
  6. Stephany Mai Nishikawa, Soo Hyeon Kim, Zhongyue Luo, Takaaki Kirihara, Yoshiho Ikeuchi, Teruo Fujii, Timothée Levi. "Biomimetic microfluidic neurons for bio-hybrid experiments" Artificial Life and Robotics 2018
  7. Levi T, Khoyratee F, Saïghi S, Ikeuchi Y. "Digital implementation of Hodgkin–Huxley neuron model for neurological diseases studies" Artificial Life and Robotics 2018, 23, 10-14
  8. Kawada J, Kaneda S, Kirihara T, Levi T, Maroof A, Eggan K, Fujii T, Ikeuchi Y. "Generation of a Motor Nerve Organoid with Human Stem Cell-Derived Neurons" Stem Cell Reports 2017 朝日新聞、日経新聞、毎日新聞、科学新聞(一面)などで紹介されました。
  9. Sayaka Tachizawa, Haruko Takahashi, Young-Jin Kim, Aoi Odawara, Joris Pauty, Yoshiho Ikeuchi, Ikuro Suzuki, Akihiko Kikuchi, and Yukiko T. Matsunaga "Bundle Gel Fibers with a Tunable Microenvironment for in Vitro Neuron Cell Guiding" ACS Applied Materials & Interfaces 2017
  10. Kaneda S, Kawada J, Akutsu H, Ichida J, Ikeuchi Y, Fujii T. "Compartmentalized embryoid body culture for induction of spatially patterned differentiation" Biomicrofluidics vol 11, 041101, 2017
  11. Huang J, Ikeuchi Y, Malumbres M, Bonni A. "A Cdh1-APC/FMRP Ubiquitin Signaling Link Drives mGluR-Dependent Synaptic Plasticity in the Mammalian Brain" Neuron vol 86, pp 726-39, 2015
  12. Ito H, Shiwaku H, Yoshida C, Homma H, Luo H, Chen X, Fujita K, Musante L, Fischer U, Frints SG, Romano C, Ikeuchi Y, Shimamura T, Imoto S, Miyano S, Muramatsu SI, Kawauchi T, Hoshino M, Sudol M, Arumughan A, Wanker EE, Rich T, Schwartz C, Matsuzaki F, Bonni A, Kalscheuer VM, Okazawa H. "In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells." Mol Psychiatry vol 20, pp459-71, 2015
  13. Ikeuchi Y, Dadakhujaev S, Chandhoke AS, Huynh MA, Oldenborg A, Ikeuchi M, Deng L, Bennett EJ, Harper JW, Bonni A, Bonni S. "TIF1γ protein regulates epithelial-mesenchymal transition by operating as a small ubiquitin-like modifier (SUMO) E3 ligase for the transcriptional regulator SnoN1" J Biol Chem vol 289, pp25067-78, 2014
  14. Ito S, Akamatsu Y, Noma A, Kimura S, Miyauchi K, Ikeuchi Y, Suzuki T, Suzuki T. "A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae" J Biol Chem vol 289, pp26201-12, 2014
  15. Kimura S, Miyauchi K, Ikeuchi Y, Thiaville PC, Crécy-Lagard Vd, Suzuki T. "Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs" Nucleic Acids Res vol 42, pp9350-65, 2014
  16. Ikeuchi Y, de la Torre-Ubieta L, Matsuda T, Steen H, Okazawa H, Bonni A. “The XLID Protein PQBP1 and the GTPase Dynamin 2 Define a Signaling Link that Orchestrates Ciliary Morphogenesis in Postmitotic Neurons.” Cell Reports vol 4, pp879-89, 2013
  17. Mejia LA, Litterman N, Ikeuchi Y, de la Torre-Ubieta L, Bennett EJ, Zhang C, Harper JW, Bonni A. “A Novel Hap1-Tsc1 Interaction Regulates Neuronal mTORC1 Signaling and Morphogenesis in the Brain” Journal of Neuroscience vol 33, pp18015-21, 2013
  18. Zhang C, Mejia LA, Huang J, Valnegri P, Bennett EJ, Anckar J, Jahani-Asl A, Gallardo G, Ikeuchi Y, Yamada T, Rudnicki M, Harper JW, Bonni A. “The X-linked intellectual disability protein PHF6 associates with the PAF1 complex and regulates neuronal migration in the mammalian brain,” Neuron vol 78, pp986-93, 2013
  19. Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. “Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity.” Nucleic Acid Research vol 40, pp4071-85, 2012
  20. Huynh MA, Ikeuchi Y, Netherton S, de la Torre-Ubieta L, Kanadia R, Stegmuller J, Cepko C, Bonni S, Bonni A. "An isoform-specific SnoN1-FOXO1 repressor complex controls neuronal morphogenesis and positioning in the mammalian brain." Neuron vol 69, pp930-44, 2011
  21. Litterman N, Ikeuchi Y, Gallardo G, O'Connell BC, Sowa ME, Gygi SP, Harper JW, Bonni A. “An OBSL1-Cul7Fbxw8 ubiquitin ligase signaling mechanism regulates Golgi morphology and dendrite patterning.” PLoS Biology Vol 9, 2011
  22. Puram SV, Kim AH, Ikeuchi Y, Wilson-Grady JT, Merdes A, Gygi SP, Bonni A. “A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain.” Nature Neuroscience Vol 14, pp 973-83, 2011
  23. Puram SV, Riccio A, Koirala S, Ikeuchi Y, Kim AH, Corfas G, Bonni A. “A TRPC5-regulated calcium signaling pathway controls dendrite patterning in the mammalian brain.” Genes Development Vol 25, 2011
  24. Bilimoria PM, de la Torre-Ubieta L, Ikeuchi Y, Becker EB, Reiner O, Bonni A. “A JIP3-Regulated GSK3β/DCX Signaling Pathway Restricts Axon Branching.” Journal of Neuroscience vol 30, pp16766-76, 2010
  25. de la Torre-Ubieta L, Gaudillière B, Yang Y, Ikeuchi Y, Yamada T, DiBacco S, Stegmüller J, Schüller U, Salih DA, Rowitch D, Brunet A, Bonni A. “A FOXO-Pak1 transcriptional pathway controls neuronal polarity.” Genes Development vol 24, pp 799-813, 2010
  26. Ikeuchi Y, Stegmüller J, Netherton S, Huynh MA, Masu M, Frank D, Bonni S, Bonni A. “A SnoN–Ccd1 Pathway Promotes Axonal Morphogenesis in the Mammalian Brain.” Journal of Neuroscience vol 29, pp 4312-4321, 2009
  27. Kim AH, Puram SV, Bilimoria PM, Ikeuchi Y, Keough S, Wong M, Rowitch D, Bonni A. “A centrosomal Cdc20-APC pathway controls dendrite morphogenesis in postmitotic neurons.” Cell vol 136, pp 322-36, 2009
  28. Yang Y, Kim AH, Yamada T, Wu B, Bilimoria PM, Ikeuchi Y, de la Iglesia N, Shen J, Bonni A. “A Cdc20-APC ubiquitin signaling pathway regulates presynaptic differentiation.” Science vol 326, pp 575-8, 2009
  29. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. “Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.” Nature Chemical Biology vol 6, pp 277-82, 2010
  30. Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. “Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity.” Nucleic Acid Research 2011
  31. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I. “RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon.” EMBO Journal vol. 28, pp1362-73, 2009
  32. Ikeuchi Y, Kitahara K, Suzuki T. “The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon.” EMBO Journal vol. 27, pp 2194-203, 2008
  33. Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O. “Snapshots of tRNA sulphuration via an adenylated intermediate.” Nature vol 442, pp 419-24, 2006
  34. Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. “Mechanistic insights into sulfur-relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions.” Molecular Cell vol 21, pp 97-108, 2006
  35. Takeda H, Toyooka T, Ikeuchi Y, Yokobori S, Okadome K, Takano F, Oshima T, Suzuki T, Endo Y, Hori H. “The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus.” Genes Cells vol. 11, pp1353-65, 2006
  36. Noma A, Kirino Y, Ikeuchi Y, Suzuki T. “Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA.” EMBO Journal vol. 25, pp2142-54, 2006
  37. Numata T, Ikeuchi Y, Fukai S, Adachi H, Matsumura H, Takano K, Murakami S, Inoue T, Mori Y, Sasaki T, Suzuki T, Nureki O. “Crystallization and preliminary X-ray analysis of the tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA(Glu).” Acta Crystallograph Sect F Struct Biol Cryst Commun vol. 62, pp368-71, 2006
  38. Takano Y, Takayanagi N, Hori H, Ikeuchi Y, Suzuki T, Kimura A, Okuno T. “A gene involved in modifying transfer RNA is required for fungal pathogenicity and stress tolerance of Colletotrichum lagenarium.” Molecular Microbiology vol. 60, pp81-92, 2006
  39. Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O. “Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex.” Structure vol. 14, pp357-66, 2006
  40. Ote T, Hashimoto M, Ikeuchi Y, Su'etsugu M, Suzuki T, Katayama T, Kato J. “Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.” Molecular Microbiology vol. 59, pp265-75, 2006
  41. Ikeuchi Y, Soma A, Ote T, Kato J, Sekine Y, Suzuki T. “Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition.” Molecular Cell vol 19, pp 235-46, 2005
  42. Nakanishi K, Fukai S, Ikeuchi Y, Soma A, Sekine Y, Suzuki T, Nureki O. “Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.” Proc Natl Acad Sci U S A vol. 24, pp7487-92, 2005
  43. Okamoto H, Watanabe K, Ikeuchi Y, Suzuki T, Endo Y, Hori H. “Substrate tRNA recognition mechanism of tRNA (m7G46)methyltransferase from Aquifex aeolicus.” J Biol Chem vol. 19, pp49151-9, 2004
  44. Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T. “An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.” Molecular Cell vol 12, pp689-98, 2003

Reviews

  1. Chow A, Ikeuchi Y. "New approaches to understand dynamics of protein synthesis in neurons" SEISAN KENKYU vol 69, pp 115-121, 2017
  2. Pot I, Ikeuchi Y, Bonni A, Bonni S. “SnoN: bridging neurobiology and cancer biology.” Current Molecular Medicine vol 10, pp667-73, 2010
  3. Suzuki T, Ikeuchi Y, Noma A, Suzuki T, Sakaguchi Y. “Mass spectrometric identification and characterization of RNA-modifying enzymes. ” Methods in Enzymology vol 425, pp211-29, 2007

日本語論文・総説

  1. 梅垣祐介,池内与志穂 「神経特異的な制御を受けて生産される新生タンパク質の探索」 生産研究 vol 68, pp 201-204, 2016
  2. 川田治良,藤井輝夫,池内与志穂 「神経変性疾患の理解と治療へ向けた研究の概況と新しいアプローチ」 生産研究 vol 68, pp 205-210, 2016
  3. 池内 与志穂,鈴木 勉. 「RNA修飾に関わる硫黄リレータンパク質群の同定」 細胞工学 vol 25, pp 400-1, 2006
  4. 鈴木 勉,池内 与志穂,鈴木 健夫. 「機能性RNAのマススペクトロメトリー」 実験医学増刊 vol 22, pp 2511-22, 2004
  5. 池内 与志穂,鈴木 勉. 「リボヌクレオーム解析:RNA修飾遺伝子の網羅的探索」細胞工学 vol 22, pp 945-50, 2003