応用ゲノム解析技術研究チーム

論文

 

  1. Yuuri Yasuoka, “Tissue-specific expression of carbohydrate sulfotransferases drives keratan sulfate biosynthesis in the notochord and otic vesicles of Xenopus embryos.” Front. Cell Dev. Biol. 11, 957805 (2023)
  2. Imai-Okazaki A, Nitta KR, Yatsuka Y, Sugiura A, Arao M, Shimura M, Ebihara T, Onuki T, Ichimoto K, Ohtake A, Murayama K, Okazaki Y. Impact of measuring heteroplasmy of a pathogenic mitochondrial DNA variant at the single-cell level in individuals with mitochondrial disease. J Inherit Metab Dis 45, 1143-1150 (2022)
  3. Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 41, 111893 (2022)
  4. Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Rep 38, 110364 (2022)
  5. de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs. Genome Res 32, 1727-35 (2022)
  6. Ozaki K, Irioka T, Uchihara T, Yamada A, Nakamura A, Majima T, Igarashi S, Shintaku H, Yakeishi M, Tsuura Y, Okazaki Y, Ishikawa K, Yokota T. Neuropathology of SCA34 showing widespread oligodendroglial pathology with vacuolar white matter degeneration: a case study. Acta Neuropathol Commun 9, 172 (2021)
  7. Kato T, Manabe RI, Igarashi H, Kametani F, Hirokawa S, Sekine Y, Fujita N, Saito S, Kawashima Y, Hatano Y, Ando S, Nozaki H, Sugai A, Uemura M, Fukunaga M, Sato T, Koyama A, Saito R, Sugie A, Toyoshima Y, Kawata H, Murayama S, Matsumoto M, Kakita A, Hasegawa M, Ihara M, Kanazawa M, Nishizawa M, Tsuji S, Onodera O. Candesartan prevents arteriopathy progression in cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy model. J Clin Invest 131, e140555 (2021)
  8. Hashimoto M, Saito Y, Nakagawa R, Ogahara I, Takagi S, Takata S, Amitani H, Endo M, Yuki H, Ramilowski JA, Severin J, Manabe RI, Watanabe T, Ozaki K, Kaneko A, Kajita H, Fujiki S, Sato K, Honma T, Uchida N, Fukami T, Okazaki Y, Ohara O, Shultz LD, Yamada M, Taniguchi S, Vyas P, de Hoon M, Momozawa Y, Ishikawa F. Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia. Nat Cancer 2, 340-356 (2021)
  9. Kishita Y, Shimura M, Kohda M, Fushimi T, Nitta KR, Yatsuka Y, Hirose S, Ideguchi H, Ohtake A, Murayama K, Okazaki Y. Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2. Hum Mutat 42, 1422-1428 (2021)
  10. Imai-Okazaki A, Yagi N, Nitta KR, Murayama K, Ohtake A, Okazaki Y. Clinical heterogeneity in patients with m.4412G > A MT-TM mutation and different heteroplasmy levels. Mitochondrion 59, 214-215 (2021)
  11. Inaba A, Arinaga A, Tanaka K, Endo T, Hayatsu N, Okazaki Y, Yamane T, Oishi Y, Imai H, Iwatsuki K. Interleukin-4 Promotes Tuft Cell Differentiation and Acetylcholine Production in Intestinal Organoids of Non-Human Primate. Int J Mol Sci 22, 7921 (2021)
  12. Yasuoka Y, Taira M. LIM homeodomain proteins and associated partners: Then and now. Curr Top Dev Biol 145, 113-166 (2021)
  13.    Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski J, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, C.Frith M, FANTOM consortium, Chatelain C, Carninci P, deHoon M, W.Wasserman W, Bréhélin L, Lecellier C, Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 12, 3297 (2021)
  14. Abugessaisa I, Ramilowski J, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip C, LiChingOoi J, Tagami M, Hori F, Agrawal S, Hon C, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, deHoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.  Nucleic Acids Res 49, D892–D898 (2021)
  15.    Ito Y, Terao Y, Noma S, Tagami M, Yoshida E, Hayashizaki Y, Itoh M, Kawaji H, Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter. Sci Rep 11, 9355 (2021)
  16. Imai-Okazaki A, Matsunaga A, Yatsuka Y, Nitta KR, Kishita Y, Sugiura A, Sugiyama Y, Fushimi T, Shimura M, Ichimoto K, Tajika M, Ogawa-Tominaga M, Ebihara T, Matsuhashi T, Tsuruoka T, Kohda M, Hirata T, Harashima H, Nojiri S, Takeda A, Nakaya A, Kogaki S, Sakata Y, Ohtake A, Murayama K, Okazaki Y. Long-term prognosis and genetic background of cardiomyopathy in 223 pediatric mitochondrial disease patients. Int J Cardiol 341, 48-55 (2021)
  17. Yasuoka Y, Matsumoto M, Yagi K, Okazaki Y, Evolutionary History of GLIS genes illuminates their Roles in Cell Reprogramming and Ciliogenesis. Mol Biol Evol 37, 100-109 (2020)
  18. Ramilowski J, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy I, Mendez M, Ooi J, ..., Okazaki Y, Orlando V, Paquette D, Parr C, Rackham O, Rizzu P, Sanchez D, Sandelin A, Sanjana P, Semple C, Sharma H, Shibayama Y, Sivaraman D, Suzuki T, Szumowski S, Tagami M, Taylor M, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov I, Yamamoto C, Young R, Baillie JK, Forrest A, Guigó R, Hoffman M, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, FANTOM consortium, de Hoon M, Shin J, Carninci P. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. Genome Res. 30, 1060-1072 (2020)
  19. Borna NN, Kishita Y, Abe J, Furukawa T, Ogawa-Tominaga M, Fushimi T, Imai-Okazaki A, Takeda A, Ohtake A, Murayama K, Okazaki Y. NAD(P)HX dehydratase protein-truncating mutations are associated with neurodevelopmental disorder exacerbated by acute illness. Brain 143, e54 (2020)
  20. Borna NN, Kishita Y, Sakai N, Hamada Y, Kamagata K, Kohda M, Ohtake A, Murayama K, Okazaki Y. Leigh Syndrome Due to NDUFV1 Mutations Initially Presenting as LBSL. Genes (Basel) 11, 1325 (2020)
  21.    Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin JW, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P. Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians. Proc Natl Acad Sci U S A 116, 24242-24251 (2019)
  22.    Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. Zoological Lett 5, 27 (2019)
  23. Nindita Y, Cao Z, Fauzi AA, Teshima A, Misaki Y, Muslimin R, Yang Y, Shiwa Y, Yoshikawa H, Tagami M, Lezhava A, Ishikawa J, Kuroda M, Sekizuka T, Inada K, Kinashi H, Arakawa K. The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids. Sci Rep 9, 10973 (2019)
  24. Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, Hori C, Ishida JK, Kasahara H, Kiba T, Kim MS, Koo N, Laohavisit A, Lee YH, Lumba S, McCourt P, Mortimer JC, Mutuku JM, Nomura T, Sasaki-Sekimoto Y, Seto Y, Wang Y, Wakatake T, Sakakibara H, Demura T, Yamaguchi S, Yoneyama K, Manabe RI, Nelson DC, Schulman AH, Timko MP, dePamphilis CW, Choi D, Shirasu K. Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism. Curr Biol 29, 3041-3052.e4 (2019)
  25. Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W. Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Commun Biol 2, 263 (2019)
  26. Imai-Okazaki A, Kishita Y, Kohda M, Mizuno Y, Fushimi T, Matsunaga A, Yatsuka Y, Hirata T, Harashima H, Takeda A, Nakaya A, Sakata Y, Kogaki S, Ohtake A, Murayama K, Okazaki Y. Cardiomyopathy in children with mitochondrial disease: Prognosis and genetic background. Int J Cardiol 279, 115-121 (2019)