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Coauthors
Hodaka Fujii Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Japan
2 protocols
Coreviewers
Antoine de Morree Stanford university
27 protocols

Clara Lubeseder-Martellato Technical University of Munich
5 protocols

Lee-Hwa Tai Universite de Sherbrooke
20 protocols

Modesto Redrejo-Rodriguez Centro de Biología Molecular Severo Ochoa
14 protocols

Reviewer
Toshitsugu Fujita
  • Hirosaki University Graduate School of Medicine
Research focus
  • Molecular biology
Contributions
  • 2 Author merit
  • 5 Reviewer merit

Education

Ph.D. in Science, Department of Biological Sciences, Graduate school of Science, Osaka University, Japan, 2004

Current position

Associate professor, Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Japan

Publications

  1. Fujita, T., Kitaura, F., Yuno, M., Suzuki, Y., Sugano, S. and Fujii, H. (2017). Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line. DNA Res 24(5): 537-548.
  2. Fujita, T., Yuno, M., Suzuki, Y., Sugano, S. and Fujii, H. (2017). Identification of physical interactions between genomic regions by enChIP-Seq. Genes Cells 22(6): 506-520.
  3. Fujita, T. and Fujii, H. (2016). Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies. Gene Regul Syst Bio 10(Suppl 1): 1-9.
  4. Fujita, T., Yuno, M. and Fujii, H. (2016). Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus. Sci Rep 6: 30485.
  5. Fujita, T., Yuno, M. and Fujii, H. (2016). Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells 21(4): 370-377.
  6. Fujita, T. and Fujii, H. (2015). Isolation of specific genomic regions and identification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Methods Mol Biol 1288: 43-52.
  7. Fujita, T. and Fujii, H. (2015). Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research. Int J Mol Sci 16(10): 23143-23164.
  8. Fujita, T. and Fujii, H. (2015). Isolation of specific genomic regions and identification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Methods Mol Biol 1288: 43-52.
  9. Fujita, T., Yuno, M., Okuzaki, D., Ohki, R. and Fujii, H. (2015). Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. PLoS One 10(4): e0123387.
  10. Fujita, T., Kitaura, F. and Fujii, H. (2015). A critical role of the Thy28-MYH9 axis in B cell-specific expression of the Pax5 gene in chicken B cells. PLoS One 10(1): e0116579.
  11. Fujita, T. and Fujii, H. (2015). Isolation of specific genomic regions and identification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Methods Mol Biol 1288: 43-52.
  12. Fujita, T. and Fujii, H. (2014). Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins. BMC Mol Biol 15: 26.
  13. Tanigawa, N., Fujita, T. and Fujii, H. (2014). Oligoribonucleotide (ORN) interference-PCR (ORNi-PCR): a simple method for suppressing PCR amplification of specific DNA sequences using ORNs. PLoS One 9(11): e113345.
  14. Fujita, T. and Fujii, H. (2014). Identification of proteins associated with an IFNgamma-responsive promoter by a retroviral expression system for enChIP using CRISPR. PLoS One 9(7): e103084.
  15. Fujita, T. and Fujii, H. (2013). Locus-specific biochemical epigenetics/chromatin biochemistry by insertional chromatin immunoprecipitation. ISRN Biochem 2013: 913273.
  16. Fujita, T., Asano, Y., Ohtsuka, J., Takada, Y., Saito, K., Ohki, R. and Fujii, H. (2013). Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP). Sci Rep 3: 3171.
  17. Fujita, T. and Fujii, H. (2013). Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochem Biophys Res Commun 439(1): 132-136. 
  18. Fujita, T. and Fujii, H. (2012). Efficient isolation of specific genomic regions by insertional chromatin immunoprecipitation (iChIP) with a second-generation tagged LexA DNA-binding domain. Advances in Bioscience & Biotechnology 3(5).
  19. Fujita, T. and Fujii, H. (2012). Transcription start sites and usage of the first exon of mouse Foxp3 gene. Mol Biol Rep 39(10): 9613-9619.
  20. Fujita, T. and Fujii, H. (2011). Direct identification of insulator components by insertional chromatin immunoprecipitation. PLoS One 6(10): e26109.
  21. Fujita, T. and Fujii, H. (2011). Species-specific 5'-genomic structure and multiple transcription start sites in the chicken Pax5 gene. Gene 477(1-2): 24-31.
  22. Fujita, T., Piuz, I. and Schlegel, W. (2010). Transcription elongation factors are involved in programming hormone production in pituitary neuroendocrine GH4C1 cells. Mol Cell Endocrinol 319(1-2): 63-70.
  23. Yamazaki, T., Walchli, S., Fujita, T., Ryser, S., Hoshijima, M., Schlegel, W., Kuroda, S. and Maturana, A. D. (2010). Splice variants of enigma homolog, differentially expressed during heart development, promote or prevent hypertrophy. Cardiovasc Res 86(3): 374-382.
  24. Maturana, A. D., Fujita, T. and Kuroda, S. (2010). Functions of fasciculation and elongation protein zeta-1 (FEZ1) in the brain. ScientificWorldJournal 10: 1646-1654.
  25. Fujita, T. and Schlegel, W. (2010). Promoter-proximal pausing of RNA polymerase II: an opportunity to regulate gene transcription. J Recept Signal Transduct Res 30(1): 31-42.
  26. Fujita, T., Piuz, I. and Schlegel, W. (2009). The transcription elongation factors NELF, DSIF and P-TEFb control constitutive transcription in a gene-specific manner. FEBS Lett 583(17): 2893-2898.
  27. Fujita, T., Piuz, I. and Schlegel, W. (2009). Negative elongation factor NELF controls transcription of immediate early genes in a stimulus-specific manner. Exp Cell Res 315(2): 274-284.
  28. Charital, Y. M., van Haasteren, G., Massiha, A., Schlegel, W. and Fujita, T. (2009). A functional NF-kappaB enhancer element in the first intron contributes to the control of c-fos transcription. Gene 430(1-2): 116-122.
  29. Fujita, T., Ryser, S., Piuz, I. and Schlegel, W. (2008). Up-regulation of P-TEFb by the MEK1-extracellular signal-regulated kinase signaling pathway contributes to stimulated transcription elongation of immediate early genes in neuroendocrine cells. Mol Cell Biol 28(5): 1630-1643.
  30. Fujita, T., Maturana, A. D., Ikuta, J., Hamada, J., Walchli, S., Suzuki, T., Sawa, H., Wooten, M. W., Okajima, T., Tatematsu, K., Tanizawa, K. and Kuroda, S. (2007). Axonal guidance protein FEZ1 associates with tubulin and kinesin motor protein to transport mitochondria in neurites of NGF-stimulated PC12 cells. Biochem Biophys Res Commun 361(3): 605-610.
  31. Ikuta, J., Maturana, A., Fujita, T., Okajima, T., Tatematsu, K., Tanizawa, K. and Kuroda, S. (2007). Fasciculation and elongation protein zeta-1 (FEZ1) participates in the polarization of hippocampal neuron by controlling the mitochondrial motility. Biochem Biophys Res Commun 353(1): 127-132.
  32. Fujita, T., Ryser, S., Tortola, S., Piuz, I. and Schlegel, W. (2007). Gene-specific recruitment of positive and negative elongation factors during stimulated transcription of the MKP-1 gene in neuroendocrine cells. Nucleic Acids Res 35(3): 1007-1017.
  33. Ryser, S., Fujita, T., Tortola, S., Piuz, I. and Schlegel, W. (2007). The rate of c-fos transcription in vivo is continuously regulated at the level of elongation by dynamic stimulus-coupled recruitment of positive transcription elongation factor b. J Biol Chem 282(7): 5075-5084.
  34. Suzuki, T., Okada, Y., Semba, S., Orba, Y., Yamanouchi, S., Endo, S., Tanaka, S., Fujita, T., Kuroda, S., Nagashima, K. and Sawa, H. (2005). Identification of FEZ1 as a protein that interacts with JC virus agnoprotein and microtubules: role of agnoprotein-induced dissociation of FEZ1 from microtubules in viral propagation. J Biol Chem 280(26): 24948-24956.
  35. Fujita, T., Ikuta, J., Hamada, J., Okajima, T., Tatematsu, K., Tanizawa, K. and Kuroda, S. (2004). Identification of a tissue-non-specific homologue of axonal fasciculation and elongation protein zeta-1. Biochem Biophys Res Commun 313(3): 738-744.
  36. Fujita, T., Ikuta, J., Maturana, A., Okajima, T., Tatematsu, K., Tanizawa, K., and Kuroda, S. (2004). UNC-76/FEZ family is essential for axonal guidance. Recent Res. Devel. Biophys. Biochem. 4, 313-320.
  37. Miyoshi, K., Honda, A., Baba, K., Taniguchi, M., Oono, K., Fujita, T., Kuroda, S., Katayama, T. and Tohyama, M. (2003). Disrupted-In-Schizophrenia 1, a candidate gene for schizophrenia, participates in neurite outgrowth. Mol Psychiatry 8(7): 685-694.
2 Protocols published
In vitro Engineered DNA-binding Molecule-mediated Chromatin Immunoprecipitation (in vitro enChIP) Using CRISPR Ribonucleoproteins in Combination with Next-generation Sequencing (in vitro enChIP-Seq) for the Identification of Chromosomal Interactions
Authors:  Toshitsugu Fujita and Hodaka Fujii, date: 11/20/2017, view: 32, Q&A: 0
We have developed locus-specific chromatin immunoprecipitation (locus-specific ChIP) technologies consisting of insertional ChIP (iChIP) and engineered DNA-binding molecule-mediated ChIP (enChIP). Locus-specific ChIP is a method to isolate a genomic ...
Identification of Proteins Interacting with Genomic Regions of Interest in vivo Using Engineered DNA-binding Molecule-mediated Chromatin Immunoprecipitation (enChIP)
Authors:  Toshitsugu Fujita and Hodaka Fujii, date: 05/20/2014, view: 4832, Q&A: 0
Elucidation of molecular mechanisms of genome functions requires identification of molecules interacting with genomic regions of interest in vivo. To this end, it is useful to isolate the target regions retaining molecular interactions. We ...
5 Protocols reviewed
Nucleosome Positioning Assay
Authors:  Zhongliang Zhao and Holger Bierhoff, date: 05/20/2017, view: 1311, Q&A: 0
The basic unit of chromatin is the nucleosome, a histone octamer with 147 base pairs of DNA wrapped around it. Positions of nucleosomes relative to each other and to DNA elements have a strong impact on chromatin structure and gene activity and are ...
More >
Macrophage Polarization by Tumor-induced MDSCs Assay
Authors:  Felipe Vences-Catalán, Minu K. Srivastava and Shoshana Levy, date: 08/20/2016, view: 2750, Q&A: 0
Myeloid derived suppressor cells (MDSCs) are a subset of granulocytes (immature myeloid cells) that exploit a variety of mechanism to modulate the innate and adaptive immune system. MDSCs are present normally in the body, but their numbers increase ...
More >