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Department of Systems BioMedicine

Our aim is to reveal the molecular mechanisms underlying embryonic development, cell differentiation and tissue formation and apply our findings to understand the causes of developmental diseases.


Our department consists of the Division of Functional Genomics and the Division of Tissue Regeneration. Our combined areas of expertise include post-genome sequencing analysis, systems biology, bioinformatics, molecular
biology, developmental biology, and epigenetics.

Our research

1. Gene expression databases

We are currently constructing gene expression databases to identify genes that play an important role in organ formation.

2. High-throughput gene expression system

By singly expressing genes in cultured cells, we can analyze the function of more than 6,000 genes at once.

3. Exploring the genome

We are trying to identify novel genomic regions that are relevant to developmental diseases.

4. Rapid generation of model mice

Taking advantage of new-generation genome editing techniques, we generate knockout mice?mouse models in which an existing gene has been modified?that recapitulate human disease symptoms.

5. Mutation analyses using next-generation sequencers

Combining next-generation sequencers and bioinformatic techniques, we search for mutations that could impair embryonic development and child health. This methodology is also applied to the detection of mutations in regenerative medicine.




  • Atsumi Tsuji-Hosokawa
  • Miho Terao



  1. Hara S, Muramatsu A, Terao M, Takada S: Efficient production and transmission of CRISPR/Cas9-mediated mutant alleles at the IG-DMR via generation of mosaic mice using a modified 2CC method. Scientific Reports, 9(1):20202 (2019).
  2. Kagami M, Yanagisawa A, Ota M, Matsuoka K, Nakamura A, Matsubara K, Nakabayashi K, Takada S, Fukami M, Ogata T: Temple syndrome in a patient with variably methylated CpGs at the primary MEG3/DLK1:IG-DMR and severely hypomethylated CpGs at the secondary MEG3:TSS-DMR. Clinical Epigenetics 11(1):42 (2019).
  3. Miyado M, Fukami M, Takada S, Terao T, Nakabayashi K, Hata K, Matsubara Y, Tanaka Y, Sasaki G, Nagasaki K,Shiina M, Ogata K, Masunaga Y, Saitsu H, Ogata T: Nephrogenic syndrome of inappropriate antidiuresis caused by germline-derived gain-of-function mutations of GNAS Gsα-coding exons. Journal of the American Society of Nephrology, 30(5):877-889 (2019).
  4. Maeoka Y, Okamoto, Wu Y, Saito A, Asada R, Matsuhisa K, Terao M, Takada S, Masaki T, Imaizumi K, Kaneko M: Renal medullary tonicity regulates RNF183 expression in the collecting ducts via NFAT5. Biochemical and Biophysical Research Communications, 25;514(2):436-442 (2019).
  5. Sasaki K, Shiba K, Nakamura A, Kawano N, Satouh Y, Yamaguchi H, Morikawa M, Shibata D, Yanase R, Jokura J, Nomura M, Miyado M, Takada S, Ueno H, Nonaka S, Baba T, Ikawa M, Kikkawa M, Miyado K, Inaba K: Calaxin is required for cilia-driven determination of vertebrate laterality. Communications Biology, 2:226 (2019).
  6. Yamoto K, Saitsu H, Nishimura G, Kosaki R, Takayama S, Haga N, Tonoki H, Okumura A, Horii E, Okamoto N, Suzumura H, Ikegawa S, Kato F, Fujisawa Y, Nagata E, Takada S, Fukami M, Ogata T: Comprehensive clinical and molecular studies in split-hand/foot malformation: identification of two plausible candidate genes (LRP6 and UBA2). European Journal of Human Genetics, 27(12):1845-1857 (2019).
  7. Yamashita S, Kataoka K, Yamamoto H, Kato T, Hara S, Yamaguchi K, Renard-Guillet C, Katou Y, Shirahige K, Ochi H, Ogino H, Uchida T, Inui M, Takada S, Shigenobu S, Asahara H: Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken. Scientific Reports, 9(1):12560 (2019).
  8. Sakai K, Ito C, Wakabayashi M, Kanzaki S, Ito T, Takada S, Toshimori K, Sekita Y, Kimura T: Usp26 mutation in mice leads to defective spermatogenesis depending on genetic background. Scientific Reports, 9(1):13757 (2019).
  9. Shindo M, Inui M, Kang W, Tamano M, Tingwei C, Takada S, Hibino T, Yoshida M, Yoshida K, Okada H, Iwamoto T, Miyado K, Kawano N: Deletion of a seminal gene cluster reinforces a crucial role of SVS2 in male fertility. International Journal of Molecular Sciences, 20(18) pii: E4557 (2019).


  1. Saito T, Hara S, Kato T, Tamano M, Muramatsu A, Asahara H, Takada S: A tandem repeat array in IG-DMR is essential for imprinting of paternal allele at the Dlk1-Dio3 domain during embryonic development. Human Molecular Genetics 27(18):3283-3292 (2018).
  2. Tsuji-Hosokawa A, Kashimada K, Kato T, Ogawa Y, Nomura R, Takasawa K, Lavery R, Coschiera A, Schlessinger D, Harley VR, Takada S, Morio T: Peptidyl arginine deiminase 2 (Padi2) is expressed in Sertoli cells in a specific manner and regulated by SOX9 during testicular development. Scientific Reports 8(1):13263 (2018).
  3. Osumi T, Tsujimoto SI, Tamura M, Uchiyama M, Nakabayashi K, Okamura K, Yoshida M, Tomizawa D, Watanabe A, Takahashi H, Hori T, Yamamoto S, Hamamoto K, Migita M, Ogata-Kawata H, Uchiyama T, Kizawa H, Ueno-Yokohata H, Shirai R, Seki M, Ohki K, Takita J, Inukai T, Ogawa S, Kitamura T, Matsumoto K, Hata K, Kiyokawa N, Goyama S, Kato M: Recurrent RARB translocations in acute promyelocytic leukemia lacking RARA translocation. Cancer Research 78(16):4452-4458 (2018).
  4. Inui M, Mokuda S, Sato T, Tamano M, Takada S, Asahara H: Dissecting the roles of miR-140 and its host gene. Nature Cell Biology 20(5):516-518 (2018).
  5. Hara S, Takada S: Genome editing for the reproduction and remedy of human diseases in mice. Journal of Human Genetics 63(2):107-113 (2018).
  6. Katoh-Fukui Y, Yatsuga S, Shima H, Hattori A, Nakamura A, Okamura K, Yanagi K, Iso M, Kaname T, Matsubara Y, Fukami M: An unclassified variant of CHD7 activates a cryptic splice site in a patient with CHARGE syndrome. Human Genome Variation 5:18006 (2018).
  7. Okuno M, Ayabe T, Yokota I, Musha I, Shiga K, Kikuchi T, Kikuchi N, Ohtake A, Nakamura A, Nakabayashi K, Okamura K, Momozawa Y, Kubo M, Suzuki J, Urakami T, Kawamura T, Amemiya S, Ogata T, Sugihara S, Fukami M: Protein-altering variants of PTPN2 in childhood-onset Type 1A diabetes. Diabetic Medicine 35(3):376-380 (2018).
  8. Takasawa K, Igarashi M, Ono M, Takemoto A, Takada S, Yamataka A, Ogata T, Morio T, Fukami M, Kashimada K: Phenotypic variation in 46,XX disorders of sex development due to the NR5A1 p.R92W variant: A sibling case report and literature review. Sexual Development 11(5-6):284-288 (2018).
  9. Steward O, Matsudaira Yee K, Farris S, Pirbhoy PS, Worley P, Okamura K, Okuno H, Bito H: Delayed degradation and impaired dendritic delivery of intron-lacking EGFP-Arc/Arg3.1 mRNA in EGFP-Arc transgenic mice. Frontiers in Molecular Neuroscience 10:435 (2018).


  1. Murakami M, Yoshimoto T, Nakabayashi K, Nakano Y, Fukaishi T, Tsuchiya K, Minami I, Bouchi R, Okamura K, Fujii Y, Hashimoto K, Hata KI, Kihara K, Ogawa Y: Molecular characteristics of the KCNJ5 mutated aldosterone-producing adenomas. Endocrine-related Cancer 24(10):531-541 (2017).
  2. Kajiwara K, Tanemoto T, Wada S, Karibe J, Ihara N, Ikemoto Y, Kawasaki T, Oishi Y, Samura O, Okamura K, Takada S, Akutsu H, Sago H, Okamoto A, Umezawa A: Fetal therapy model of myelomeningocele with three-dimensional skin using amniotic fluid cell-derived induced pluripotent stem cells. Stem Cell Reports 8(6):1701-1713 (2017).
  3. Hara S, Terao M, Takada S: A protocol for production of mutant mice using chemically synthesized crRNA/tracrRNA with Cas9 nickase and FokI-dCas9. Bio-protocol 7(11):e2340 (2017).
  4. Kagami M, Matsubara K, Nakabayashi K, Nakamura A, Sano S, Okamura K, Hata K, Fukami M, Ogata T: Genome-wide multilocus imprinting disturbance analysis in Temple syndrome and Kagami-Ogata syndrome. Genetics in Medicine 19(4):476-482 (2017).
  5. Kato T, Hara S, Goto Y, Ogawa Y, Okayasu H, Kubota S, Tamano M, Terao M, Takada S: Creation of mutant mice with megabase-sized deletions containing custom-designed breakpoints by means of the CRISPR/Cas9 system. Scientific Reports 7(1):59 (2017).
  6. Saito T, Hara S, Tamano M, Asahara H, Takada S: Deletion of conserved sequences in IG-DMR at Dlk1-Gtl2 locus suggests their involvement in expression of paternally expressed genes in mice. The Journal of Reproduction and Development 63(1):101-109 (2017).
  7. Sakaki M, Ebihara Y, Okamura K, Nakabayashi K, Igarashi A, Matsumoto K, Hata K, Kobayashi Y, Maehara K: Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses. PloS One 12(2):e0171431 (2017).
  8. Inui M, Tamano M, Kato T, Takada S: CRISPR/Cas9-mediated simultaneous knockout of Dmrt1 and Dmrt3 does not recapitulate the 46,XY gonadal dysgenesis observed in 9p24.3 deletion patients. Biochemistry and Biophysics Reports 9:238-244 (2017).
  9. Igarashi M, Takasawa K, Hakoda A, Kanno J, Takada S, Miyado M, Baba T, Morohashi KI, Tajima T, Hata K, Nakabayashi K, Matsubara Y, Sekido R, Ogata T, Kashimada K, Fukami M: Identical NR5A1 missense mutations in two unrelated 46,XX individuals with testicular tissues. Human Mutation 38(1):39-42 (2017).
  10. Kato T, Takada S: In vivo and in vitro disease modeling with CRISPR/Cas9. Briefings in Functional Genomics 16(1):13-24 (2017).
  11. Hirabayashi S, Ohki K, Nakabayashi K, Ichikawa H, Momozawa Y, Okamura K, Yaguchi A, Terada K, Saito Y, Yoshimi A, Ogata-Kawata H, Sakamoto H, Kato M, Fujimura J, Hino M, Kinoshita A, Kakuda H, Kurosawa H, Kato K, Kajiwara R, Moriwaki K, Morimoto T, Nakamura K, Noguchi Y, Osumi T, Sakashita K, Takita J, Yuza Y, Matsuda K, Yoshida T, Matsumoto K, Hata K, Kubo M, Matsubara Y, Fukushima T, Koh K, Manabe A, Ohara A, Kiyokawa N: ZNF384-related fusion genes define a subgroup of childhood B-cell precursor acute lymphoblastic leukemia with a characteristic immunotype. Haematologica 102(1):118-129 (2017).


  1. Akutsu H, Nasu M, Morinaga S, Motoyama T, Honma N, Machida M, Yamazaki-Inoue M, Okamura K, Nakabayashi K, Takada S, Nakamura N, Kanzaki S, Hata K, Umezawa A: In vivo maturation of human embryonic stem cell-derived teratoma over time. Regenerative Therapy 5:31-39 (2016).
  2. Miyado M, Inui M, Igarashi M, Katoh-Fukui Y, Takasawa K, Hakoda A, Kanno J, Kashimada K, Miyado K, Tamano M, Ogata T, Takada S, Fukami M: The p.R92W variant of NR5A1/Nr5a1 induces testicular development of 46,XX gonads in humans, but not in mice: phenotypic comparison of human patients and mutation-induced mice. Biology of Sex Differences 7:56 (2016).
  3. Hara S, Kato T, Goto Y, Kubota S, Tamano M, Terao M, Takada S: Microinjection-based generation of mutant mice with a double mutation and a 0.5 Mb deletion in their genome by the CRISPR/Cas9 system. The Journal of Reproduction and Development 62(5):531-536 (2016).
  4. Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M, Okamura K, Sakai A, Nakashima H, Hata K, Nakashima K, Hatada I: Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nature Biotechnology 34(10):1060-1065 (2016).
  5. Shima H, Yatsuga S, Nakamura A, Sano S, Sasaki T, Katsumata N, Suzuki E, Hata K, Nakabayashi K, Momozawa Y, Kubo M, Okamura K, Kure S, Matsubara Y, Ogata T, Narumi S, Fukami M: NR0B1 frameshift mutation in a boy with idiopathic central precocious puberty. Sexual Development 10(4):205-209 (2016).
  6. Nakamichi R, Ito Y, Inui M, Onizuka N, Kayama T, Kataoka K, Suzuki H, Mori M, Inagawa M, Ichinose S, Lotz MK, Sakai D, Masuda K, Ozaki T, Asahara H: Mohawk promotes the maintenance and regeneration of the outer annulus fibrosus of intervertebral discs. Nature Communications 7:12503 (2016).
  7. Terao M, Tamano M, Hara S, Kato T, Kinoshita M, Takada S: Utilization of the CRISPR/Cas9 system for the efficient production of mutant mice using crRNA/tracrRNA with Cas9 nickase and FokI-dCas9. Experimental Animals 65(3):275-283 (2016).
  8. Nakamura A, Hamaguchi E, Horikawa R, Nishimura Y, Matsubara K, Sano S, Nagasaki K, Matsubara Y, Umezawa A, Tajima T, Ogata T, Kagami M, Okamura K, Fukami M: Complex genomic rearrangement within the GNAS region associated with familial pseudohypoparathyroidism type 1b. The Journal of Clinical Endocrinology and Metabolism 101(7):2623-2627 (2016).
  9. Fujinaga H, Fujinaga H, Watanabe N, Kato T, Tamano M, Terao M, Takada S, Ito Y, Umezawa A, Kuroda M: Cord blood-derived endothelial colony-forming cell function is disrupted in congenital diaphragmatic hernia. American Journal of Physiology. Lung Cellular and Molecular Physiology 310(11):L1143-1154 (2016).
  10. Higasa K, Miyake N, Yoshimura J, Okamura K, Niihori T, Saitsu H, Doi K, Shimizu M, Nakabayashi K, Aoki Y, Tsurusaki Y, Morishita S, Kawaguchi T, Migita O, Nakayama K, Nakashima M, Mitsui J, Narahara M, Hayashi K, Funayama R, Yamaguchi D, Ishiura H, Ko WY, Hata K, Nagashima T, Yamada R, Matsubara Y, Umezawa A, Tsuji S, Matsumoto N, Matsuda F: Human genetic variation database, a reference database of genetic variations in the Japanese population. Journal of Human Genetics 61(6):547-553 (2016).
  11. Okamura K, Sakaguchi H, Sakamoto-Abutani R, Nakanishi M, Nishimura K, Yamazaki-Inoue M, Ohtaka M, Periasamy VS, Alshatwi AA, Higuchi A, Hanaoka K, Nakabayashi K, Takada S, Hata K, Toyoda M, Umezawa A: Distinctive features of single nucleotide alterations in induced pluripotent stem cells with different types of DNA repair deficiency disorders. Scientific Reports 6:26342 (2016).
  12. Hayashi K, Kawai YL, Yura K, Yoshida MA, Ogura A, Hata K, Nakabayashi K, Okamura K: Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans. Mitochondrial DNA 27(3):1842-3 (2016).
  13. Miyamoto Y, Tamano M, Torii T, Kawahara K, Nakamura K, Tanoue A, Takada S, Yamauchi J: Data supporting the role of Fyn in initiating myelination in the peripheral nervous system. Data in Brief 7:1098-1105 (2016).


  1. Miyata T, Sonoda K, Tomikawa J, Tayama C, Okamura K, Maehara K, Kobayashi H, Wake N, Kato K, Hata K, Nakabayashi K: Genomic, epigenomic, and transcriptomic profiling towards identifying omics features and specific biomarkers that distinguish uterine leiomyosarcoma and leiomyoma at molecular levels. Sarcoma 2015:412068 (2015).
  2. Tsumura H, Ito M, Takami M, Arai M, Li XK, Hamatani T, Igarashi A, Takada S, Miyado K, Umezawa A, Ito Y: Conditional deletion of CD98hc inhibits osteoclast development. Biochemistry and Biophysics Reports 5:203-210 (2015).
  3. Okamura K, Kawai T, Hata K, Nakabayashi K: Lists of HumanMethylation450 BeadChip probes with nucleotide-variant information obtained from the Phase 3 data of the 1000 Genomes Project. Genomics Data 7:67-69 (2015).
  4. Miyamoto Y, Torii T, Takada S, Ohno N, Saitoh Y, Nakamura K, Ito A, Ogata T, Terada N, Tanoue A, Yamauchi J: Involvement of the Tyro3 receptor and its intracellular partner Fyn signaling in Schwann cell myelination. Molecular Biology of the Cell 26(19):3489-3503 (2015).
  5. Kawai T, Yamada T, Abe K, Okamura K, Kamura H, Akaishi R, Minakami H, Nakabayashi K, Hata K: Increased epigenetic alterations at the promoters of transcriptional regulators following inadequate maternal gestational weight gain. Scientific Reports 5:14224 (2015).
  6. Yokoyama T, Miura F, Araki H, Okamura K, Ito T: Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape. BMC Genomics 16:594 (2015).
  7. Okamura K, Toyoda M, Hata K, Nakabayashi K, Umezawa A: Whole-exome sequencing of fibroblast and its iPS cell lines derived from a patient diagnosed with xeroderma pigmentosum. Genomics Data 6:4-6 (2015).
  8. Katoh-Fukui Y, Igarashi M, Nagasaki K, Horikawa R, Nagai T, Tsuchiya T, Suzuki E, Miyado M, Hata K, Nakabayashi K, Hayashi K, Matsubara Y, Baba T, Morohashi K, Igarashi A, Ogata T, Takada S, Fukami M: Testicular dysgenesis/regression without campomelic dysplasia in patients carrying missense mutations and upstream deletion of SOX9. Molecular Genetics & Genomic Medicine 3(6):550-557 (2015).
  9. Hara S, Tamano M, Yamashita S, Kato T, Saito T, Sakuma T, Yamamoto T, Inui M, Takada S: Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Scientific Reports 5:11221 (2015).
  10. Matsubara Y, Kato T, Kashimada K, Tanaka H, Zhi Z, Ichinose S, Mizutani S, Morio T, Chiba T, Ito Y, Saga Y, Takada S, Asahara H: TALEN-mediated gene disruption on Y chromosome reveals critical role of EIF2S3Y in mouse spermatogenesis. Stem Cells and Development 24(10):1164-1170 (2015).
  11. Otabe K, Nakahara H, Hasegawa A, Matsukawa T, Ayabe F, Onizuka N, Inui M, Takada S, Ito Y, Sekiya I, Muneta T, Lotz M, Asahara H: Transcription factor Mohawk controls tenogenic differentiation of bone marrow mesenchymal stem cells in vitro and in vivo. Journal of Orthopaedic Research 33(1):1-8 (2015).
  12. Miyata K, Miyata T, Nakabayashi K, Okamura K, Naito M, Kawai T, Takada S, Kato K, Miyamoto S, Hata K, Asahara H: DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation. Human Molecular Genetics 24(2):410-423 (2015).
  13. Kawai YL, Yura K, Shindo M, Kusakabe R, Hayashi K, Hata K, Nakabayashi K, Okamura K: Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum. Mitochondrial DNA 26(6):863-864 (2015).

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