Database

Publications

Database

fanta.bio

A database of cis-regulatory elements (CREs) with their genomic locations, activities in various cell types and states, and related genomic variations in human, mouse, and non-human primate genomes.

D3G

A database for the community of oligonucleotide therapeutics, from developers to regulatory authority. In particular, original data are included for non-human primates, for pre-clinical trial.

Publications

2024

Ueno, Y., Yoshida, E., Nojiri, S., Kato, T., Ohtsu, T., Takeshita, T., Suzuki, S., Yoshida, H., Kato, K., Itoh, M., Notomi, T., Usui, K., Sozu, T., Terao, Y., Kawaji, H., & Kato, H. Use of clinical variables for preoperative prediction of lymph node metastasis in endometrial cancer. Japanese Journal of Clinical Oncology, 54(1), 38–46 (2024).

Kuroda, T., Yasuda, S., Matsuyama, S., Miura, T., Sawada, R., Matsuyama, A., Yamamoto, Y., Morioka, M. S., Kawaji, H., Kasukawa, T., Itoh, M., Akutsu, H., Kawai, J., & Sato, Y. ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons. Scientific Reports, 14(1), 690 (2024).

2023

Kanamori, K., Suina, K., Shukuya, T., Takahashi, F., Hayashi, T., Hara, K., Saito, T., Mitsuishi, Y., Shimamura, S. S., Winardi, W., Tajima, K., Ko, R., Mimori, T., Asao, T., Itoh, M., Kawaji, H., Suehara, Y., Takamochi, K., Suzuki, K., & Takahashi, K. CALML5 is a novel diagnostic marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. Thoracic Cancer, 14(12), 1089–1097 (2023).

Koido, M., Hon, C.-C., Koyama, S., Kawaji, H., Murakawa, Y., Ishigaki, K., Ito, K., Sese, J., Parrish, N. F., Kamatani, Y., Carninci, P., & Terao, C. Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nature Biomedical Engineering, 7(6), 830–844 (2023).

Hara, Y., & Kuraku, S. The impact of local genomic properties on the evolutionary fate of genes. eLife, 12 (2023).

Kubiura-Ichimaru, M., Penfold, C., Kojima, K., Dollet, C., Yabukami, H., Semi, K., Takashima, Y., Boroviak, T., Kawaji, H., Woltjen, K., Minoda, A., Sasaki, E., & Watanabe, T. mRNA-based generation of marmoset PGCLCs capable of differentiation into gonocyte-like cells. Stem Cell Reports, 18(10), 1987–2002 (2023).

Miura, T., Kouno, T., Takano, M., Kuroda, T., Yamamoto, Y., Kusakawa, S., Morioka, M. S., Sugawara, T., Hirai, T., Yasuda, S., Sawada, R., Matsuyama, S., Kawaji, H., Kasukawa, T., Itoh, M., Matsuyama, A., Shin, J. W., Umezawa, A., Kawai, J., & Sato, Y. Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia. Stem Cells Translational Medicine, 12(6), 379–390 (2023).

Nakamura, A., Sakai, S., Taketomi, Y., Tsuyama, J., Miki, Y., Hara, Y., Arai, N., Sugiura, Y., Kawaji, H., Murakami, M., & Shichita, T. PLA2G2E-mediated lipid metabolism triggers brain-autonomous neural repair after ischemic stroke. Neuron, 111(19), 2995–3010.e9 (2023).

Nemeth, T., Yoshizawa-Sugata, N., Pallier, A., Tajima, Y., Ma, Y., Tóth, É., Masai, H., & Yamakoshi, Y. Water-Soluble Gd(III)-Porphyrin Complexes Capable of Both Photosensitization and Relaxation Enhancement. Chemical & Biomedical Imaging, 1(2), 157–167 (2023).

Tomita, Y., Suzuki, K., Yamasaki, S., Toriumi, K., Miyashita, M., Ando, S., Endo, K., Yoshikawa, A., Tabata, K., Usami, S., Hiraiwa-Hasegawa, M., Itokawa, M., Kawaji, H., Kasai, K., Nishida, A., & Arai, M. Urinary exosomal microRNAs as predictive biomarkers for persistent psychotic-like experiences. Schizophrenia (Heidelberg, Germany), 9(1), 14 (2023).

Toyama, S., Honda, T., Iwabuchi, S., Hashimoto, S., Yamaji, K., Tokunaga, Y., Matsumoto, Y., Kawaji, H., Miyazaki, T., Kikkawa, Y., & Kohara, M. Application of spatial transcriptomics analysis using the Visium system for the mouse nasal cavity after intranasal vaccination. Frontiers in Immunology, 14, 1209945 (2023).

Yoshizawa-Sugata, N. & Masai, H. Histone Modification Analysis of Low-Mappability Regions. Methods Mol. Biol. 2519, 163–185 (2023).

2022

Mukae, J., Sadato, D., Toya, T., Watanabe, S., Hirama, C., Konuma, R., Shimizu, H., Najima, Y., Kobayashi, T., Kato, M., Ohki, K., Oboki, K., Harada, H., Ohashi, K., Deguchi, T., Harada, Y. & Doki, N. Labile CD22 and CD19 expression in a case of Philadelphia chromosome-like acute lymphoblastic leukemia. Leuk. Lymphoma 63, 3261–3264 (2022).

Nakagawa, R., Takasawa, K., Gau, M., Tsuji-Hosokawa, A., Kawaji, H., Murakawa, Y., Takada, S., Mikami, M., Narumi, S., Fukami, M., Sreenivasan, R., Maruyama, T., Tucker, E. J., Zhao, L., Bowles, J., Sinclair, A., Koopman, P., Hayashizaki, Y., Morio, T. & Kashimada, K. Two ovarian candidate enhancers, identified by time series enhancer RNA analyses, harbor rare genetic variations identified in ovarian insufficiency. Hum. Mol. Genet. 31, 2223–2235 (2022).

Yoshikawa, A., Kushima, I., Miyashita, M., Suzuki, K., Iino, K., Toriumi, K., Horiuchi, Y., Kawaji, H., Ozaki, N., Itokawa, M. & Arai, M. Exonic deletions in IMMP2L in schizophrenia with enhanced glycation stress subtype. PLoS One 17, e0270506 (2022).

Morikawa, T., Fukami, T., Gotoh-Saito, S., Nakano, M. & Nakajima, M. PPARα regulates the expression of human arylacetamide deacetylase involved in drug hydrolysis and lipid metabolism. Biochem. Pharmacol. 199, 115010 (2022).

Vuoristo, S., Bhagat, S., Hydén-Granskog, C., Yoshihara, M., Gawriyski, L., Jouhilahti, E.-M., Ranga, V., Tamirat, M., Huhtala, M., Kirjanov, I., Nykänen, S., Krjutškov, K., Damdimopoulos, A., Weltner, J., Hashimoto, K., Recher, G., Ezer, S., Paluoja, P., Paloviita, P., Takegami, Y., Kanemaru, A., Lundin, K., Airenne, T. T., Otonkoski, T., Tapanainen, J. S., Kawaji, H., Murakawa, Y., Bürglin, T. R., Varjosalo, M., Johnson, M. S., Tuuri, T., Katayama, S. & Kere, J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 25, 104137 (2022).

Negishi, R., Yamakawa, H., Kobayashi, T., Horikawa, M., Shimoyama, T., Koizumi, F., Sawada, T., Oboki, K., Omuro, Y., Funasaka, C., Kageyama, A., Kanemasa, Y., Tanaka, T., Matsunaga, T. & Yoshino, T. Transcriptomic profiling of single circulating tumor cells provides insight into human metastatic gastric cancer. Commun Biol 5, 20 (2022).

Das, S. K., Kuzin, V., Cameron, D. P., Sanford, S., Jha, R. K., Nie, Z., Rosello, M. T., Holewinski, R., Andresson, T., Wisniewski, J., Natsume, T., Price, D. H., Lewis, B. A., Kouzine, F., Levens, D. & Baranello, L. MYC assembles and stimulates topoisomerases 1 and 2 in a ‘topoisome’. Mol. Cell 82, 140–158.e12 (2022).

Gotoh‐Saito, S., Sadato, D. & Shibasaki, F. INT6 / eIF3e represses E‐cadherin expression through HIF2α in lung carcinoma A549 cells. Genes to Cells 27, 689–705 (2022)

2021

Wiegard, A., Kuzin, V., Cameron, D. P., Grosser, J., Ceribelli, M., Mehmood, R., Ballarino, R., Valant, F., Grochowski, R., Karabogdan, I., Crosetto, N., Lindqvist, A., Bizard, A. H., Kouzine, F., Natsume, T. & Baranello, L. Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1. Mol. Cell 81, 5007–5024.e9 (2021).

Yoshizawa-Sugata, N., Yamazaki, S., Mita-Yoshida, K., Ono, T., Nishito, Y. & Masai, H. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation. J. Biol. Chem. 297, 101367 (2021).

Adachi, H., Sadato, D., Toya, T., Hirama, C., Haraguchi, K., Mukae, J., Shingai, N., Shimizu, H., Najima, Y., Kobayashi, T., Okuyama, Y., Oboki, K., Harada, H., Sakamaki, H., Ohashi, K., Harada, Y. & Doki, N. Donor-derived gene mutations in sex chromosome loss after stem cell transplantation. Br. J. Haematol. 195, e142–e146 (2021).

Kurosawa, S., Toya, T., Sadato, D., Hishima, T., Hirama, C., Najima, Y., Kobayashi, T., Haraguchi, K., Okuyama, Y., Oboki, K., Harada, H., Sakamaki, H., Ohashi, K., Harada, Y. & Doki, N. Mutation profiles of diffuse large B-cell lymphoma transformation of splenic B-cell lymphoma/leukemia, unclassifiable on whole-exome sequencing. EJHaem 2, 854–860 (2021).

Sadato, D., Hirama, C., Kaiho-Soma, A., Yamaguchi, A., Kogure, H., Takakuwa, S., Ogawa, M., Doki, N., Ohashi, K., Harada, H., Oboki, K. & Harada, Y. Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. PLoS One 16, e0255257 (2021).

Hara, Y., Shibahara, R., Kondo, K., Abe, W. & Kunieda, T. Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer. Open Biol. 11, 200413 (2021).

Jayakumar, V., Nishimura, O., Kadota, M., Hirose, N., Sano, H., Murakawa, Y., Yamamoto, Y., Nakaya, M., Tsukiyama, T., Seita, Y., Nakamura, S., Kawai, J., Sasaki, E., Ema, M., Kuraku, S., Kawaji, H. & Sakakibara, Y. Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset. Sci Data 8, 159 (2021).

Tanaka, R., Ito-Hirano, R., Fujimura, S., Arita, K., Hagiwara, H., Mita, T., Itoh, M., Kawaji, H., Ogawa, T., Watada, H., Masuda, H., Asahara, T. & Mizuno, H. Ex vivo conditioning of peripheral blood mononuclear cells of diabetic patients promotes vasculogenic wound healing. Stem Cells Transl. Med. 10, 895–909 (2021).

Yoshikawa, A., Kushima, I., Miyashita, M., Toriumi, K., Suzuki, K., Horiuchi, Y., Kawaji, H., Takizawa, S., Ozaki, N., Itokawa, M. & Arai, M. Dysregulation of post-transcriptional modification by copy number variable microRNAs in schizophrenia with enhanced glycation stress. Transl. Psychiatry 11, 331 (2021).

Iwai, M., Tulafu, M., Togo, S., Kawaji, H., Kadoya, K., Namba, Y., Jin, J., Watanabe, J., Okabe, T., Hidayat, M., Sumiyoshi, I., Itoh, M., Koyama, Y., Ito, Y., Orimo, A., Takamochi, K., Oh, S., Suzuki, K., Hayashizaki, Y., Yoshida, K. & Takahashi, K. Cancer-associated fibroblast migration in non-small cell lung cancers is modulated by increased integrin α11 expression. Mol. Oncol. 15, 1507–1527 (2021).

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).

Klein, K. N., Zhao, P. A., Lyu, X., Sasaki, T., Bartlett, D. A., Singh, A. M., Tasan, I., Zhang, M., Watts, L. P., Hiraga, S.-I., Natsume, T., Zhou, X., Baslan, T., Leung, D., Kanemaki, M. T., Donaldson, A. D., Zhao, H., Dalton, S., Corces, V. G. & Gilbert, D. M. Replication timing maintains the global epigenetic state in human cells. Science 372, 371–378 (2021).

Hirabayashi, S., Shirakawa, K., Horisawa, Y., Matsumoto, T., Matsui, H., Yamazaki, H., Sarca, A. D., Kazuma, Y., Nomura, R., Konishi, Y., Takeuchi, S., Stanford, E., Kawaji, H., Murakawa, Y. & Takaori-Kondo, A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochem. Biophys. Res. Commun. 546, 178–184 (2021).

Takahashi, T., Kawaji, H., Murakawa, Y., Hayashizaki, Y., Murakami, T., Yabushita, Y., Homma, Y., Kumamoto, T., Matsuyama, R. & Endo, I. Significance of HMGA2 expression as independent poor prognostic marker in perihilar and distal cholangiocarcinoma resected with curative intent. Eur. J. Surg. Oncol. 47, 394–400 (2021).

Najima, Y., Sadato, D., Harada, Y., Oboki, K., Hirama, C., Toya, T., Doki, N., Haraguchi, K., Yoshifuji, K., Akiyama, M., Inamoto, K., Igarashi, A., Kobayashi, T., Kakihana, K., Okuyama, Y., Sakamaki, H., Harada, H. & Ohashi, K. Prognostic impact of TP53 mutation, monosomal karyotype, and prior myeloid disorder in nonremission acute myeloid leukemia at allo-HSCT. Bone Marrow Transplant. 56, 334–346 (2021).

Abugessaisa, I., Ramilowski, J. A., Lizio, M., Severin, J., Hasegawa, A., Harshbarger, J., Kondo, A., Noguchi, S., Yip, C. W., Ooi, J. L. C., Tagami, M., Hori, F., Agrawal, S., Hon, C. C., Cardon, M., Ikeda, S., Ono, H., Bono, H., Kato, M., Hashimoto, K., Bonetti, A., Kato, M., Kobayashi, N., Shin, J., de Hoon, 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).

Sobue, A., Komine, O., Hara, Y., Endo, F., Mizoguchi, H., Watanabe, S., Murayama, S., Saito, T., Saido, T. C., Sahara, N., Higuchi, M., Ogi, T. & Yamanaka, K. Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer’s disease. Acta Neuropathol Commun 9, 1 (2021).

2020

Fracassi, A., Cao, J., Yoshizawa-Sugata, N., Tóth, É., Archer, C., Gröninger, O., Ricciotti, E., Tang, S. Y., Handschin, S., Bourgeois, J.-P., Ray, A., Liosi, K., Oriana, S., Stark, W., Masai, H., Zhou, R. & Yamakoshi, Y. LDL-mimetic lipid nanoparticles prepared by surface KAT ligation for in vivo MRI of atherosclerosis. Chem. Sci. 11, 11998–12008 (2020).

Kato, H., Asamitsu, K., Sun, W., Kitajima, S., Yoshizawa-Sugata, N., Okamoto, T., Masai, H. & Poellinger, L. Cancer-derived UTX TPR mutations G137V and D336G impair interaction with MLL3/4 complexes and affect UTX subcellular localization. Oncogene 39, 3322–3335 (2020).

Yasukawa, M., Ando, Y., Yamashita, T., Matsuda, Y., Shoji, S., Morioka, M. S., Kawaji, H., Shiozawa, K., Machitani, M., Abe, T., Yamada, S., Kaneko, M. K., Kato, Y., Furuta, Y., Kondo, T., Shirouzu, M., Hayashizaki, Y., Kaneko, S. & Masutomi, K. CDK1 dependent phosphorylation of hTERT contributes to cancer progression. Nat. Commun. 11, 1557 (2020).

Abugessaisa, I., Ramilowski, J. A., Lizio, M., Severin, J., Hasegawa, A., Harshbarger, J., Kondo, A., Noguchi, S., Yip, C. W., Ooi, J. L. C., Tagami, M., Hori, F., Agrawal, S., Hon, C. C., Cardon, M., Ikeda, S., Ono, H., Bono, H., Kato, M., Hashimoto, K., Bonetti, A., Kato, M., Kobayashi, N., Shin, J., de Hoon, 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).

Morioka, M. S., Kawaji, H., Nishiyori-Sueki, H., Murata, M., Kojima-Ishiyama, M., Carninci, P. & Itoh, M. Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods Mol. Biol. 2120, 277–301 (2020).

2019

Yoshida, T., Naito, Y., Yasuhara, H., Sasaki, K., Kawaji, H., Kawai, J., Naito, M., Okuda, H., Obika, S. & Inoue, T. Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells. Genes Cells 24, 827–835 (2019).

Hirabayashi, S., Bhagat, S., Matsuki, Y., Takegami, Y., Uehata, T., Kanemaru, A., Itoh, M., Shirakawa, K., Takaori-Kondo, A., Takeuchi, O., Carninci, P., Katayama, S., Hayashizaki, Y., Kere, J., Kawaji, H. & Murakawa, Y. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat. Genet. 51, 1369–1379 (2019).