Group of Gene Expression and Regulation, Nagoya University

2025

• eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.
  Nucleic Acids Res., 53(22): gkaf1322, 2025.

  We revealed that eIF2D is important for recycling the 40S ribosomal subunit stalled during intrinsic ribosome destabilization (IRD). While the MCTS1–DENR complex is known to mediate 40S recycling at stop codons, the homologous protein eIF2D functions in a distinct pathway, with its central domain determining the selectivity between the stop-codon– and IRD-mediated recycling mechanisms.

• Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities.
  Nat. Commun., 16(1): 9599, 2025.

  A frameshift mutation in CHD1 disrupts condensate formation by removing its IDR, driving oncogenic transcription and highlighting the critical role of chromatin remodeler condensates.

• Translon: a single term for translated regions.
  Nat. Methods., 22(10): 2002-2006, 2025.

  The term “ORF” (Open Reading Frame) is originally a predictive concept based on nucleotide sequence information, and it often does not correspond to regions that are actually translated (CDSs). To address this, we propose the adoption of a new term, “translon”, which defines regions based on the act of translation itself. This proposal is a collaborative effort by numerous researchers worldwide, including two research groups from Japan, one of which is ours.

2024

• Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction.
  J. Gastroenterol., 59(7): 629-640, 2024.

  Although “Classical” and “Basal-like” molecular subtypes have been proposed for pancreatic ductal adenocarcinoma (PDAC), the establishment of patient-derived organoids (PDOs) for PDAC allows for morphological subtype classification, facilitating prediction of clinical outcome.

• The complex etiology of autism spectrum disorder due to missense mutations of CHD8.
  Mol. Phychiatry, 29(7): 2145-2160, 2024.

  CHD8 is most frequently mutated gene in patients with autism spectrum disorder (ASD). We characterized CHD8 missense mutations and examined the effects of such mutations on the biochemical activities of CHD8, neural differentiation of embryonic stem cells, and mouse behavior.

2023

• Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide.
  Cell Rep. 42(12): 113569, 2023.

  The detailed mechanism of intrinsic ribosomal destabilization (IRD) in Escherichia coli has been analyzed. Translation of acidic-rich amino acid sequences results in an abnormal conformational change of the 70S ribosome, resulting in non-canonical translation termination.

• RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  Nat. Commun. 14(1): 2131, 2023.

  RPL3L-containing ribosomes (Myo-ribosomes) efficiently translate genes involved in cardiac contraction, and mice lacking Myo-ribosome showed impaired cardiac contractility.

• The ASC-1 complex promotes translation initiation by scanning ribosomes.
  EMBO J. 42(12): e112869, 2023.

  By developing Sel-TCP-MS, we found that the ASC-1 complex binds to scanning ribosomes as well as disomes, and that the loss of the ASC-1 complex disrupts the dynamics of scanning ribosomes.

2022

• Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis.
  Nat. Commun. 13(1): 1071, 2022.

  We identified two novel polypeptides translated from a single lncRNA locus, which we named Kastor and Polluks (derived from Gemini). Both Kastor and Polluks bound to VDAC, and male mice lacking them were infertile.

2021

• A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing.
  PLOS Genet. 17(8): e1009686, 2021.

  TINCR was one of the well-known noncoding RNAs in dermatology, but we found that TINCR translates a protein with a ubiquitin-like domain. This protein promoted skin regeneration.

• Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
  Nucleic Acids Res. 49(13): 7298-7317, 2021.

  TISCA was developed to precisely identify translation initiation sites. TISCA revealed that many proteins are translated from the Non-AUG initiation codons, which is eIF2-dependent, not eIF2A or eIF2D.

2017

• mTORC1 and muscle regeneration are regulated by the LINC00961 encoded SPAR polypeptide.
  Nature 12;541(7636): 228-232, 2017.

  We found that LINC00961, which was thought to be a noncoding RNA, translates a polypeptide, and that the polypeptide regulates amino acid-dependent mTORC1 signaling.

2025

• Structural insights into the role of eIF3 in translation mediated by the HCV IRES.
  Iwasaki W., Kashiwagi K., Sakamoto A., Nishimoto M., Takahashi M., Machida K., Imataka H., Matsumoto A., Shichino Y., Iwasaki S., Imami K., Ito T.
  Proc. Natl. Acad. Sci. U.S.A., 122(49): e2505538122, 2025.
• eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.
  Ichihara K.^†, Shiraishi T.^†, Chadani Y., Kito Y., Shiraishi C., Hirata M., Takahashi Y., Kobo A., Hatano A., Matsumoto M., Machida K., Imataka H., Toyoda A., Mishiro-Sato E., Nojima T., Ito T., Taguchi H., Nakayama KI.*, Matsumoto A.*
  (†co-first author, *corresponding authors)
  Nucleic Acids Res., 53(22): gkaf1322, 2025.
• Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities.
  Tsukamoto Y., Kawamura A., Yurtsever A., Suzuki H., Rojas-Chverra NM., Sato H., Ino D., Ichikawa T., Wei W., Haji S., Voon DCC., Matsumoto A., Matsumoto K., Takahashi H, Kodera N., Fukuma T., Ogawa Y., Nishiyama M., Sakai K.
  Nat. Commun., in press.
• Inducible tag-free degradation of endogenous proteins with AlissAID and development of a photoactivable inducer.
  Ogawa Y., Nishimura K., Nambo M., Tsuchiya Y., Oka S., Fujimori T., Ichihara K., Matsumoto A., Obara K., Kamura T.
  Commun. Biol., 8(1): 1546, 2025.
• Translon: a single term for translated regions.
  Świrski MI., Tierney JAS., (incl. Matsumoto A.), Valen E., Baranov PV.
  Nat. Methods., 22(10): 2002-2006, 2025.
• Transient dietary intervention induces healthy adipose tissue expansion and metabolically healthy obesity in mice.
  Wada E., Hosono H., Tanaka M., Miyakawa F., Ochi K., Kohda H., Tanno H., Shimano R., Ito A., Kitaura Y., Ichihara K., Matsumoto A., Ogi T., Satoh-Asahara N., Murohara T., Suganami T.
  FASEB J., 39(14): e70847, 2025.
• Selection of short 5' UTR of chemically synthesized mRNA to improve translation efficiency.
  Ohashi S., Ishiguro S., Fukunaga T., Matsumoto A., Hirata M., Inagaki M., Abe N., Hashiya F., Abe H.
  Chem. Pharm. Bull., 73(5): 449-456, 2025.
• From non-coding to coding: The importance of long non-coding RNA translation in de novo gene birth.
  Shiraishi T., Matsumoto A.
  Biochim. Biophys. Acta., 1869(2): 130747, 2025.

2024

• Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction.
  Matsumoto K., Fujimori N., Ichihara K., Takeno A., Murakami M., Ohno A., Kakehashi S., Teramatsu K., Ueda K., Nakata K., Sugahara O., Yamamoto T., Matsumoto A., Nakayama KI., Oda Y., Nakamura M., Ogawa Y.
  J. Gastroenterol., 59(7): 629-640, 2024.
• The complex etiology of autism spectrum disorder due to missense mutations of CHD8.
  Shiraishi T., Katayama Y., Nishiyama M., Shoji H., Miyakawa T., Mizoo T., Matsumoto A., Hijikata A., Shirai T., Mayanagi K., Nakayama KI.
  Mol. Phychiatry, 29(7): 2145-2160, 2024.
• Large-scale animal model study uncovers altered brain pH and lactate levels as a transdiagnostic endophenotype of neuropsychiatric disorders involving cognitive impairment.
  Hagihara H., International Brain pH Project Consortium, and Miyakawa T.
  eLife, 12: RP89376, 2024.

2023

• Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide.
  Chadani Y., Kanamori T., Niwa T., Ichihara K., Nakayama KI., Matsumoto A., Taguchi H.
  Cell Rep. 42(12): 113569, 2023.
• RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  Shiraishi C.^†, Matsumoto A.^†*, Ichihara K., Yamamoto T., Yokoyama T., Mizoo T., Hatano A., Matsumoto M., Tanaka Y., Matsuura-Suzuki E., Iwasaki S., Matsushima S., Tsutsui H., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nat. Commun. 14(1): 2131, 2023.
• The ASC-1 complex promotes translation initiation by scanning ribosomes.
  Kito Y.^†, Matsumoto A.^†*, Ichihara K.^†, Shiraishi C., Tang R., Hatano A., Matsumoto M., Han P., Iwasaki S., Nakayama KI.*
  (†co-first author, *corresponding authors)
  EMBO J. 42(12): e112869, 2023.
• Identification of unannotated coding sequences and their physiological functions.
  Ichihara K., Nakayama KI.*, Matsumoto A.*
  (*corresponding authors)
  J. Biochem. 173(4): 237-242, 2023.

2022

• Spatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epithelium.
  Higa T., Okita Y., Matsumoto A., Nakayama S., Oka T., Sugahara O., Koga D., Takeishi S., Nakatsumi H., Hosen N., Robine S., Taketo MM., Sato T., Nakayama KI.
  Nat. Commun. 13(1): 1500, 2022.
• Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis.
  Mise S.^†, Matsumoto A.^†*, Shimada K., Hosaka T., Takahashi M., Ichihara K., Shimizu H., Shiraishi C., Saito D., Suyama M., Yasuda T., Ide T., Izumi Y., Bamba T., Kimura-Someya T., Shirouzu M., Miyata H., Ikawa M., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nat. Commun. 13(1): 1071, 2022.

2021

• A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing.
  Nita A., Matsumoto A.*, Tang R., Shiraishi C., Ichihara K., Saito D., Suyama M., Yasuda T., Tsuji G., Furue M., Katayama B., Ozawa T., Murata T., Dainichi T., Kabashima K., Hatano A., Matsumoto M., Nakayama KI.*
  (*corresponding authors)
  PLOS Genet. 17(8): e1009686, 2021.
• Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
  Ichihara K.^†, Matsumoto A.^†*, Nishida H., Kito Y., Shimizu H., Shichino Y., Iwasaki S., Imami K., Ishihama Y., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nucleic Acids Res. 49(13): 7298-7317, 2021.
• The autism-related protein CHD8 contributes to the stemness and differentiation of mouse hematopoietic stem cells.
  Nita A., Muto Y., Katayama Y., Matsumoto A., Nishiyama M., Nakayama KI.
  Cell Rep. 34(5): 108688, 2021.

2020

• A lipid bilayer formed on a hydrogel bead for single ion channel recordings.
  Hirano M., Yamamoto D., Asakura M., Hayakawa T., Mise S., Matsumoto A., Ide T.
  Micromachines 11(12): 1070, 2020.
• Cell cycle-dependent localization of the proteasome to chromatin.
  Kito Y., Matsumoto M., Hatano A., Takami T., Oshikawa K., Matsumoto A., Nakayama KI.
  Sci. Rep. 10(1): 5801 – 5801, 2020.

2019

• Intragenic antagonistic roles of protein and circRNA in tumorigenesis.
  Guarnerio J., Zhang Y., Cheloni G., Panella R., Mae Katon J., Simpson M., Matsumoto A., Papa A., Loretelli C., Petri A., Kauppinen S., Garbutt C., Nielsen GP., Deshpande V., Castillo-Martin M., Cordon-Cardo C., Dimitrios S., Clohessy JG., Batish M., Pandolfi PP.
  Cell Res. 29(8): 628-640, 2019.

2018

• Hidden peptides encoded by putative noncoding RNAs.
  Matsumoto A.*, Nakayama KI.
  (*corresponding author)
  Cell. Struct. Funct. 43(1): 75-83, 2018.

2006~2017

• SPAR, a lncRNA encoded mTORC1 inhibitor.
  Matsumoto A., Clohessy JG, Pandolfi PP.
  Cell Cycle 16(9): 815-816, 2017.
• mTORC1 and muscle regeneration are regulated by the LINC00961 encoded SPAR polypeptide.
  Matsumoto A., Pasut A., Matsumoto M., Yamashita R., Fung J., Monteleone E. Saghatelian A., Nakayama KI., Clohessy JG, Pandolfi PP.
  Nature 541(7636): 228-232, 2017.
• The pleiotropic role of non-coding genes in development and cancer.
  Pasut A, Matsumoto A., Clohessy JG, Pandolfi PP.
  Curr. Opin. Cell Biol. 43: 104-113, 2016.
• Fbw7 targets GATA3 through CDK2-dependent proteolysis and contributes to regulation of T-cell development.
  Kitagawa K., Shibata K., Matsumoto A., Matsumoto M., Ohhata T., Nakayama KI., Niida H., Kitagawa M.
  Mol. Cell. Biol. 34(14): 2732-2744, 2014.
• p57 regulates T cell development and prevents lymphomagenesis by balancing p53 activity and pre-TCR signaling.
  Matsumoto A.^†, Takeishi S.^†, Nakayama KI.
  (†co-first author)
  Blood 123(22): 3429-3439, 2014.
• Zoledronic acid enhances lipopolysaccharide-stimulated proinflammatory reactions through controlled expression of SOCS1 in macrophages.
  Muratsu D., Yoshiga D., Taketomi T., Onimura T., Seki Y., Matsumoto A., Nakamura S.
  PLOS One 8(7): e67906, 2013.
• p57 controls adult neural stem cell quiescence and modulates the pace of lifelong neurogenesis.
  Furutachi S., Matsumoto A., Nakayama KI., Gotoh Y.
  EMBO J. 32(7): 970-981, 2013.
• Ablation of Fbxw7 eliminates leukemia-initiating cells by preventing quiescence.
  Takeishi S., Matsumoto A., Onoyama I., Naka K., Hirao A., Nakayama KI.
  Cancer Cell 23(3): 347-361, 2013.
• Role of key regulators of the cell cycle in maintenance of hematopoietic stem cells.
  Matsumoto A., Nakayama KI.
  Biochim. Biophys. Acta. 1830(2): 2335-2344, 2013.
• Development of mice without Cip/Kip CDK inhibitors.
  Tateishi Y., Matsumoto A., Kanie T., Hara E., Nakayama K., Nakayama KI.
  Biochem. Biophys. Res. Commun. 427(2): 285-292, 2012.
• Increased efficiency in the generation of induced pluripotent stem cells by Fbxw7 ablation.
  Okita Y.^†, Matsumoto A.^†, Yumimoto K., Isoshita R., Nakayama KI.
  (†co-first author)
  Genes Cells 17(9): 768-777, 2012.
• SCF^Fbw7 modulates the NFκB signaling pathway by targeting NFκB2 for ubiquitination and destruction.
  Fukushima H.^†, Matsumoto A.^†, Inuzuka H.^†, Zhai B., Lau A., Wan A., Gao D., Shaik S., Yuan M., Gygi S., Jimi E., Asara J., Nakayama K., Nakayama KI., Wei W.
  (†co-first author)
  Cell Rep. 1(5): 434-443, 2012.
• Genetic reevaluation of the role of F-box proteins in cyclin D1 degradation.
  Kanie T., Onoyama I., Matsumoto A., Yamada M., Nakatsumi H., Tateishi Y., Yamamura S., Tsunematsu R., Matsumoto M., Nakayama KI.
  Mol. Cell. Biol. 32(3): 590-605, 2012.
• p57 is required for quiescence and maintenance of adult hematopoietic stem cells.
  Matsumoto A., Takeishi S., Kanie T., Susaki E., Onoyama I., Tateishi Y., Nakayama K., Nakayama KI.
  Cell Stem Cell 9(3): 262-271, 2011.
• Deregulation of the p57-E2F1-p53 axis results in nonobstructive hydrocephalus and cerebellar malformation in mice.
  Matsumoto A., Susaki E., Onoyama I., Nakayama K., Mikio H., Nakayama KI.
  Mol. Cell. Biol. 31(20): 4176-4192, 2011.
• Fbxw7-dependent degradation of Notch is required for control of "stemness" and neuronal-glial differentiation in neural stem cells.
  Matsumoto A., Onoyama I., Sunabori T., Kageyama R., Okano H., Nakayama KI.
  J. Biol. Chem. 286(15): 13754-13764, 2011.
• Fbxw7β resides in the endoplasmic reticulum membrane and protects cells from oxidative stress.
  Matsumoto A., Tateishi Y., Onoyama I., Okita Y., Nakayama K., Nakayama KI.
  Cancer Sci. 102(4): 749-755, 2011.
• Fbxw7 regulates lipid metabolism and cell fate decisions in the mouse liver.
  Onoyama I., Suzuki A., Matsumoto A., Tomita K., Katagiri H., Oike Y., Nakayama K., Nakayama KI.
  J. Clin. Invest. 121(1): 342-354, 2011.
• Conditional inactivation of Fbxw7 impairs cell-cycle exit during T cell differentiation and results in lymphomatogenesis.
  Onoyama I., Tsunematsu R., Matsumoto A., Kimura T., de Alboran I. M., Nakayama K., Nakayama KI.
  J. Exp. Med. 204(12): 2875-2888, 2007.
• Expression of mouse Fbxw7 isoforms is regulated in a cell cycle- or p53-dependent manner.
  Matsumoto A., Onoyama I., Nakayama KI.
  Biochem. Biophys. Res. Commun. 350(1): 114-119, 2006.
• Fbxw7 contributes to tumor suppression by targeting multiple proteins for ubiquitin-dependent degradation.
  Fujii Y., Yada M., Nishiyama M., Kamura T., Takahashi H., Tsunematsu R., Susaki E., Nakagawa T., Matsumoto A., Nakayama KI.
  Cancer Sci. 97(8): 729-736, 2006.