- Double PHD finger proteins DPF3a and 3b are required as transcriptional coactivators in the SWI/SNF complex-dependent activation of the NF-κB RelA/p50 heterodimer.
Ishizaka A, Mizutani T, Kobayashi K, Tando T, Sakurai K, Fujiwara T, Iba H.
Journal of Biological Chemistry in press
- Mechanistic features of RNA-directed molecular asymmetry of amino acids
Koji Tamura
Viva Origino, Vol. 39, 2011, 39-44
- Origin of the peptide-forming function in the ribosome
Koji Tamura
Viva Origino, Vol. 39, 2011, 31-37
- Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development.
Ichiyanagi K, Li Y, Watanabe T, Ichiyanagi T, Fukuda K, Kitayama J, Yamamoto Y, Kuramochi-Miyagawa S, Nakano T, Yabuta Y, Seki Y, Saitou M, Sasaki H
Genome Res. 21(12):2058-66.(2011)
- Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.
Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H.
Science, 332(6031):848-52 (2011)
- MITOPLD is a mitochondrial protein essential for nuage nuage formation and piRNA buigenesis in the mouse germline.
Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakano T, Nakatsuji N, Lin H, Sasaki H.
Dev Cell. 23(3):364-75 (2011)
- Gtsf1/Cue110, a gene encoding a protein with two copies of a CHHC Zn-finger motif, is involved in spermatogenesis and retrotransposon suppression in murine testes.
Yoshimura T. Toyoda S. Kuramochi-Miyagawa S. Miyazaki T. Miyazaki S. Tashiro F. Yamato E. Nakano T. Miyazaki J.
Developmental Biology. 335(1):216-727
- The N domain of Argonaute drives duplex unwinding during RISC assembly
Pieter Bas Kwak, and Yukihide Tomar
Nat Struct Mol Biol. 10 January 2012 | doi:10.1038/nsmb.2232 [Epub ahead of print]
- Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2, and NPM3 during sperm chromatin remodeling
Mitsuru Okuwaki, Ayako Sumi, Miharu Hisaoka, Ai Satome, Satoko Akashi, Yoshifumi Nishimura, Kyosuke Nagata
Nucleic Acids Research, In press (2012)
- PRMT1 is required for RAP55 to localize to processing bodies
Ken Matsumoto, , Hiroshi Nakayama, Mami Yoshimura, Akiko Masuda, Naoshi Dohmae, Shogo Matsumoto and Masafumi Tsujimoto
RNA Biology in press
- Surmounting Chemoresistance by Targeting the Y-Box Binding Protein-1
Ikuko Inoue, Ken Matsumoto, Yingnan Yu, Boon-Huat Bay
The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology Volume 295, Issue 2, pages 215?222, February 2012
- PRAS40 is a functionally critical target for EWS repression in Ewing's sarcoma
Lin Huang, Yuji Nakai, Iku Kuwahara, and Ken Matsumoto
Cancer Research Published OnlineFirst January 12, 2012; doi: 10.1158/0008-5472.CAN-11-2254
- Molecular basis for RNA polymerization by Qbeta replicase
Daijiro Takeshita Kozo Tomita
Nature Structural & Molecular Biology Year published:(2012) DOI:doi:10.1038/nsmb.2204
- Dicer is dispensable for asymmetric RISC loading in mammals.
Juan Guillermo Betancur, Yukihide Tomari
RNA 2012 Jan; 18(1):24-30. Epub 2011 Nov 21.
- Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA modification enzyme, TiaS, complexed with tRNAIle2 and ATP
Takuo Osawa, Hideko Inanaga, Satoshi Kimura, Naohiro Terasaka Tsutomu Suzuki, Tomoyuki Numata
Acta Crystallographica Section F 67, 1414-1416 (2011)
- Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS
Naohiro Terasaka, Satoshi Kimura, Takuo Osawa, Tomoyuki Numata, Tsutomu Suzuki
Nature Structural & Molecular Biology 18, 1268-1274 (2011) Published online 16 October 2011
- Structural basis of tRNA agmatinylation essential for AUA codon decoding
Takuo Osawa, Satoshi Kimura, Naohiro Terasaka, Hideko Inanaga, Tsutomu Suzuki, Tomoyuki Numata
Nature Structural & Molecular Biology 18, 1275-1280 (2011) Published online 16 October 2011
- Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish
Mishima Y, Fukao A, Kishimioto T, Sakamoto H, Fujiwara, T., Inoue K.
Proc. Natl. Acad. Sci. USA (2011)、in press
- Functional and direct interaction between the RNA binding protein HuD and active Akt1
Fujiwara, T., Fukao, A.、Sasano Y, Matsuzaki H, Kikkawa U, Imataka H, Inoue K, Endo S, Sonenberg N, Thoma C, Sakamoto H
Nucleic Acids Research (2011)、Nov 10. [Epub ahead of print]
- Mechanisms of translational regulation by a human eIF5-mimic protein.
Singh CR, Watanabe R, Zhou D, Jennings MD, Fukao A, Lee B, Ikeda Y, Chiorini JA, Campbell SG, Ashe MP, Fujiwara, T., Wek RC, Pavitt GD, Asano K
Nucleic Acids Research 39, 8314-8328 (2011)
- Microtubule association of a neuronal RNA-binding protein HuD through its binding to the light chain of MAP1B.
Fujiwara, Y., Kasashima K, Saito K, Fukuda M, Fukao A, Sasano Y, Inoue K, Fujiwara, T.
Biochimie 93. 817-822 (2011)
- Single-embryo metabolomics and systematic prediction of developmental stage in zebrafish.
Hayashi, S., Yoshida, M., Fujiwara, T., Maegawa, S., Fukusaki, E.
Z Naturforsch C. 66, 191-198 (2011)
- A small nucleolar RNA functions in rRNA processing in C. elegans
Hokii, Y., Sasano Y, Sato M, Sakamoto H, Sakata K, Shingai R, Taneda A, Oka S, Himeno H, Muto A, Fujiwara, T.
Nucleic Acids Research 38, 5909-5918 (2010)
- DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish.
Takeda, Y., Mishima, Y., Fujiwara, T., Sakamoto, H., Inoue, K.
PLoS ONE 4, e7513 (2009)
- Positive autoregulation of a KNOX gene is essential for shoot meristem maintenance in rice.
Katsutoshi Tsuda, Yutaka Sato, Yukihiro Itoh, Nori Kurata
The Plant Cell Published online before print December 2011, doi: http://dx.doi.org/10.1105/tpc.111.090050
- RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice.
Daisuke Ogawa, Kiyomi Abe, Akio Miyao, Mikiko Kojima, Hitoshi Sakakibara, Megumi Mizutani, Haruka Morita, Yosuke Toda, Tokunori Hobo, Yutaka Sato, Tsukaho Hattori, Hirohiko Hirochika, Shin Takeda
Nature Communications Vol 2, 278, 2011
- Non-retroviral fossils in vertebrate genomes.
Masahiro Horie and Keizo Tomonaga
Viruses 3:1836-1848 (2011)
- A novel Borna disease virus vector system that stably expresses foreign proteins from an intercistronic noncoding region
Daito T, Fujino K, Honda T, Matsumoto Y, Watanabe Y and Tomonaga K.
Journal of Virology 85: 12170-12178 (2011)
- No evidence for natural selection on endogenous Borna-like nucleoprotein elements after the divergence of Old World and New World monkeys.
Kobayashi Y, Horie M, Tomonaga K and Suzuki Y.
PLoS One 6:e24403 (2011)
- Analysis of intracellular distribution of Borna disease virus glycoprotein fused with fluorescent markers in living cells.
Daito T, Fujino K, Watanabe Y, Ikuta K and Tomonaga K.
Journal of Veterinary Medical Science 73: 1243-1247 (2011)
- Upregulation of insulin-like growth factor binding protein 3 in astrocytes of transgenic mice that express Borna disease virus phosphoprotein.
Honda T, Fujino K, Okuzaki D, Ohtaki N, Matsumoto Y, Horie M, Daito T, Itoh M and Tomonaga K.
Journal of Virology 85: 4567-4571 (2011)
- Living fossil or evolving virus?
Keizo Tomonaga
EMBO Reports 11:327 (2010)
- Fluorescence Detection of Single Nucleotide Polymorphisms Using Nucleic Acid Probe Containing Tricyclic Base-linked Acyclonucleoside
Mayumi Hattori, Tokimitsu Ohki, Emiko Yanase, and Yoshihito Ueno
Bioorg. Med. Chem. Lett., 22, 253–257 (2012).
- Nucleic acid probe containing fluorescent tricyclic base-linked acyclonucleoside for detection of single nucleotide polymorphisms
Kinji Furukawa, Mayumi Hattori, Tokimitsu Ohki, Yoshiaki Kitamura, Yukio Kitade, and Yoshihito Ueno
Bioorg. Med. Chem., 20, 16–24 (2012).
- Incorporation of biaryl units into the 5′ and 3′ ends of sense and antisense strands of siRNA duplexes improves strand selectivity and nuclease resistance
Kayo Yoshikawa, Aya Ogata, Chiho Matsuda, Michinori Kohara, Hideo Iba, Yukio Kitade, and Yoshihito Ueno
Bioconjugate Chem., 22, 42–49 (2011).
- Biaryl modification of the 5′-terminus of one strand of a microRNA duplex induces strand specificity
Aya Ogata, Chihiro Furukawa, Kouhei Sakurai, Hideo Iba, Yukio Kitade, and Yoshihito Ueno
Bioorg. Med. Chem. Lett., 20, 7299–7302 (2010).
- Role of Template Activating Factor-I as a chaperone in linker histone dynamics
Kosuke Kato, Mitsuru Okuwaki, Kyosuke Nagata
Journal of Cell Science 2011.Oct.1 (Vol.124, p.3254-65)
- RMRP is a non-coding RNA essential for early murine development
Rosenbluh J, Nijhawan D, Chen Z, Wong KK, Masutomi K*, Hahn WC*(*: co-corresponding auther)
PLoS ONE,2011; 6: e26270 (2011/10/19)
- 55 amino acid linker between helicase and carboxyl terminal domains of RIG-I functions as a critical repression domain and determines inter-domain conformation.
Kageyama M, Takahasi K, Narita R, Hirai R, Yoneyama M, Kato H, Fujita T
Biochem. Biophys. Res. Commun., 415: 75-81, 2011.
- Mutations in POLR3A and POLR3B Encoding RNA Polymerase III Subunits Cause an Autosomal-Recessive Hypomyelinating Leukoencephalopathy.
Saitsu H, Osaka H, Sasaki M, Takanashi J, Hamada K, Yamashita A, Shibayama H, Shiina M, Kondo Y, Nishiyama K, Tsurusaki Y, Miyake N, Doi H, Ogata K, Inoue K, Matsumoto N.
The American Journal of Human Genetics 2011/10/28(e-pub)
- Ribosome evolution: Emergence of peptide synthesis machinery
Koji Tamura
Journal of Biosciences, Vol. 36, 921-928, 2011
- A plastid protein NUS1 is essential for build-up of the genetic system for early chloroplast development under cold stress conditions
Kensuke Kusumi, Chikako Sakata, Takahiro Nakamura, Shinji Kawasaki, Atsushi Yoshimura, Koh Iba
The Plant Journal (in press; doi: 10.1111/j.1365-313X.2011.04755.x.)
- Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein
Keiko Kobayashi, Masuyo Kawabata, Keizo Hisano, Tomohiko Kazama, Ken Matsuoka, Mamoru Sugita, Takahiro Nakamura
Nucleic Acids Research (in press; doi:10.1093/nar/gkr1084)
- N- and C-terminal Upf1 phosphorylations create binding platform for SMG-6 and SMG-5:-7 during NMD.
Yukiko Okada-Katsuhata, Y,Yamashita, A, Kutsuzawa K., Izumi N., Hirahara F., Ohno S.
Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr791
- Hsp90 is involved in the formation of P-bodies and stress granules
Ken Matsumotoab, Michiko Minamic, Fumika Shinozakic, Yukari Suzukid, Keiko Abed, Shuhei Zennoe, Shogo Matsumotoa , Yasufumi Minami
Biochemical and Biophysical Research Communications 2011 Apr 22;407(4):720-4.
- Hsp90 regulates PIKK family proteins together with the RUVBL1/2 and Tel2-containing co-factor complex
Izumi N, Yamashita A, Hiano H, Ohno S.
Cancer Science Article first published online: 24 OCT 2011 DOI: 10.1111/j.1349-7006.2011.02112.x
- Cyclophilin 40 Facilitates HSP90-mediated RISC Assembly in Plant.
Taichiro Iki, Manabu Yoshikawa, Tetsuo Meshi, Masayuki Ishikawa
EMBO Journal Journal advance online publication 1 November 2011; doi:10.1038/emboj.2011.395
- 3´end formation of PIWI-interacting RNAs in vitro
Shinpei Kawaoka, Natsuko Izumi, Susumu Katsuma and YukihideTomari
Molecular Cell. 2011 Sep16;43(6)1015-10222
- Recognition of the pre-miRNA structure by Drosophila Dicer-1
Akihisa Tsutsumi, Tomoko Kawamata, Natsuko Izumi, Hervé Seitz, and Yukihide Tomari
Nature Structural & Molecular Biology 2011 Sep 18 Epub ahead of print
- LAX PANICLE2 of Rice Encodes a Novel Nuclear Protein and Regulates the Formation of Axillary Meristems
Hiroaki Tabuchi, Yu Zhang, Susumu Hattori, Minami Omae, Sae Shimizu-Sato, Tetsuo Oikawa, Qian Qian, Minoru Nishimura, Hidemi Kitano, He Xie, Xiaohua Fang, Hitoshi Yoshida, Junko Kyozuka, Fan Chen, and Yutaka Sato
Plant Cell 2011 tpc.111.088765; First Published on September 30, 2011; doi:10.1105/tpc.111.088765
- A novel role for hSMG-1 in stress granule formation.
Brown JA. , Robert TL, Richards R , Woods R, Limα GB, Ohno S, Yamashita A, Abraham RT, Guevenα N, Lavin MF
Mol. Cell. Biol. doi:10.1128/MCB.05987-11
- The intron of tRNA-TrpCCA is dispensable for growth and translation of Saccharomyces cerevisiae.
Shunsuke Mori, Takuya Kajita, Toshiya Endo, and Tohru Yoshihisa
RNA , doi: 10.1261/rna.2851411
- Tumor-associated macrophages regulate tumorigenicity and anti-cancer drug responses of cancer stem/initiating cells
Jinushi M, Chiba S, Yoshiyama H, Masutomi K, Kinoshita I, Dosaka-Akita H, Yagita H, Takaoka A, Tahara H
Proc Natl Acad Sci U S A 2011; 108: 12425-12430
- eXIST with matrix-associated proteins
Shinichi Nakagawa and Kannanganattu V. Prasanth
Trends in Cell Biology June 2011, Vol. 21, No. 6, 321-327
- RNA-directed molecular asymmetry of amino acids
Koji Tamura
Viva Origino, Vol. 38, 2010, 18-22
- Molecular Basis for Chiral Selection in RNA Aminoacylation
Koji Tamura
International Journal of Molecular Sciences, Vol. 12, 4745-4757, 2011
- RIG-I-inducible miR-23b inhibits infections by minor group rhinoviruses through down-regulation of the receptor VLDLR.
Ouda R, Onomoto K, Takahasi K, Edwards MR, Kato H, Yoneyama M, Fujita T
J Biol Chem., 286, 26210-26219, 2011
- Comparison of telomere length and association with progenitor cell markers inlacrimal gland between Sjögren and non-Sjögren syndrome dry eye patients
Kawashima M, Kawakita T, Maida Y, Kamoi M, Ogawa Y, Shimmura S, Masutomi K, Tsubota K
Molecular Vision 2011;17:1397-1404, 2011/5/27
- Native Gel Analysis for RISC Assembly..
Kawamata T, Tomari Y
Methods Mol Biol. 2011;725:91-105.
- .Zygotic amplification of secondary piRNAs during silkworm embryogenesis.
Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S
RNA. 2011 Jul ;17(7): 1401-07
- .Multilayer checkpoints for microRNA authenticity during RISC assembly.
Kawamata T, Yoda M, Tomari Y
EMBO Rep. 2011 in press
- Maintenance of tumor initiating cells of defined genetic composition by a complex composed of nucleostemin, hTERT and BRG1
Okamoto N, Yasukawa M, Nguyen C, Maida Y, Possemato R, Shibata T, Fukami K, Hahn WC, Masutomi K
Proc Natl Acad Sci doi/10.1073/pnas.1015171108
- Competition between a noncoding exon and introns:Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1
Hitomi Tsuiji,Rei Yoshimoto,Yuko Hasegawa,Masaaki Furuno,Minoru Yoshida and Shinichi Nakagawa
Genes Cells. 2011 May; 16(5): 479–490.
- The microRNA pathway and cancer.
Kwak PB, Iwasaki S (equal contribution), *Tomari Y
Cancer Sci. 2010 Nov;101(11):2309-15.
- Retinoic Acid-inducible gene-I-like receptors.
Onoguchi K, Yoneyama M, Fujita T
J Interferon Cytokine Res., 31, 27-31, 2011
- Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice
Shinichi Nakagawa, Takao Naganuma, Go Shioi, and Tetsuro Hirose
J. Cell Biol. Vol. 193 No. 1 31–39
- Peptide Bond Formation: RNA's Big Bang
Koji Tamura
Journal of Cosmology, Vol. 13, 3800-3810, 2011
- Bacterial populations assimilating carbon from 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach.
Chol Gyu Lee, Takeshi Watanabe, Yutaka Sato, Jun Murase, Susumu Asakawa, Makoto Kimura
Siol Biol. Biochem. 43, 814-822, 2011.
- Hepatocellular carcinoma arising from ectopic liver tissue in the spleen producing insulin-like growth factor II.
M. Matsuyama, Sugiura S., Kakita A., Sato Y., Hayakawa N., Suzuki A., Yamada M., Miura K., Kameya T., Kuroda M
Pathology-Research and Practice, 2011 207, 124-126.
- Gateway binary vectors with the bialaphos resistance gene, bar, as a selection marker for plant transformation.
Shinya Nakamura, Shoji Mano, Yuji Tanaka, Masato Ohnishi, Chihiro Nakamori, Masami Araki, Tomoko Niwa, Mikio Nishimura, Hironori Kaminaka, Tsuyoshi Nakagawa, Yutaka Sato, Sumie Ishiguro
Biosci. Biotechnol. Biochem., 74, 1315-1319, 2010.
- WAVY LEAF 1, an Ortholog of Arabidopsis HEN1, Regulates Shoot Development by Maintaining microRNA and trans-acting siRNA Accumulation in Rice.
Masashi Abe, Takanori Yoshikawa, Misuzu Nosaka, Hitoshi Sakakibara, Yutaka Sato, Yasuo Nagato, Jun-ichi Itoh
Plant Physiol., 2010 154, 1335-1346.
- Y-box binding protein 1 is up-regulated in proliferative breast cancer and its inhibition deregulates the cell cycle.
Yu, Y.-N., Yip, G. W.-C., Tan, P.-H., Thike, A. A., Matsumoto, K., Tsujimoto, M., and Bay, B.-H
Int. J. Oncol. 2010 Aug; 37(2):483-92.
- MicroRNA Regulation of Glycoprotein B5R in Oncolytic Vaccinia Virus Reduces Viral Pathogenicity Without Impairing Its Antitumor Efficacy.
Hikichi M, Kidokoro M, Haraguchi T, Iba H, Shida H, Tahara H, Nakamura T.
Molecular Therapy, online March 8, 2011
- Nonsense-Mediated mRNA Decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8.
Arias-Palomo E, Yamashita A (co-first author), Fernández IS, Núñez-Ramírez R, Bamba Y, Izumi N, Ohno S, Llorca S
Genes and Development. 25(2):153-164. 2011.
- Post-transcriptional Defects of Antioxidant Selenoenzymes Cause Oxidative Stress under Methylmercury Exposure.
Usuki F, Yamashita A, Fujimura M
J. Biol. Chem. 2011 286: 6641-6649.
- Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex.
Fernández1 SI, Yamashita A (co-first author), Arias-Palomo E, Bamba Y, Bartolomé RA, Canales MA, Teixidó J, Ohno S, Llorca O
Nucleic Acids Research. 39(1):347-358. 2011. (Epub 2010 Sep 3)
- ASPP2 regulates epithelial cell polarity through the PAR complex.
Cong W, Hirose T, Harita Y, Yamashita A, Mizuno K, Hirano H, Ohno S
Curr Biol.;20(15):1408-1414. 2010
- Sde2: a novel nuclear protein essential for telomeric silencing and genomic stability in Schizosaccharomyces pombe
Rie Sugioka-Sugiyamaa, and Tomoyasu Sugiyama
BBRC doi:10.1016/j.bbrc.2011.02.068 Feb. 17, 2011 online
- Two-step cleavage of hairpin RNA with 5' overhangs by human DICER
Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K, Hayashizaki, Y
BMC Molecular Biology, online 2011.2.9
- RNA-dependent RNA polymerase in RNA silencing
Maida Y, Masutomi K
Biological Chemistry online 2011.2.7
- LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses.
Satoh T, Kato H, Kumagai Y, Yoneyama M, Sato S, Matsushita K, Tsujimura T, Fujita T, Akira S, Takeuchi O
Proc. Natl. Acad. Sci. USA,, 107, 1512-7, 2010
- Site-specific incorporation of 4-iodo-l-phenylalanine through opal suppression.
Kodama K, Nakayama H, Sakamoto K, Fukuzawa S, Kigawa T, Yabuki T, Kitabatake M, Takio K, Yokoyama S.
J Biochem. (2010) 148(2):179-187
- Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme
Wu J, Bu W, Sheppard K, Kitabatake M, Kwon ST, Soll D, Smith JL
J Mol Biol (2009) 391(4):703-716
- Roles of TOM70 in import of presequence-containing mitochondrial proteins.
Yamamoto, H., Fukui, K., Takahashi, H., Kitamura, S., Shiota, H., Terao, K., Uchida, M., Esaki, M., Nishikawa, S., Yoshihisa, T., Yamano, Y., and Endo, T.
J. Biol. Chem., 284, 31635-31646 (2009)
- Mechanism for the Alteration of the Substrate Specificities of Template-Independent RNA Polymerases
Yukimatsu Toh, Daijiro Takeshita, Takashi Nagaike, Tomoyuki Numata and Kozo Tomita
Structure, 2011 ; 19 (2), 232-243.
- Red1 promotes the elimination of meiosis-specific mRNAs in vegetatively growing fission yeast
Tomoyasu Sugiyama and Rie Sugioka-Sugiyama
The EMBO Journal advance online publication 11 February 2011; doi:10.1038/emboj.2011.32
- Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.
Maeda Y, Furuta H, Ikawa Y
J Biosci Bioeng. 2010 Dec 14. [Epub ahead of print]
- Development of Defective and Persistent Sendai Virus Vector: a Unique Gene Delivery/Expression System Ideal for Cell Reprogramming.
Ken Nishimura, Masayuki Sano, Manami Ohtaka, Birei Furuta, Yoko Umemura, Yoshiro Nakajima, Yuzuru Ikehara, Toshihiro Kobayashi, Hiroaki Segawa, Satoko Takayasu, Hideyuki Sato, Kaori Motomura, Eriko Uchida, Toshie Kanayasu-Toyoda, Makoto Asashima, Hiromitsu Nakauchi, Teruhide Yamaguchi and Mahito Nakanishi
Journal of Biological Chemistry 2010.12.7 Online (doi:10.1074/jbc.M110.183780)
- Transient activation of c-MYC expression is critical for efficient platelet generation from human induced pluripotent stem cells
Naoya Takayama, Satoshi Nishimura, Sou Nakamura, Takafumi Shimizu, Ryoko Ohnishi, Hiroshi Endo, Tomoyuki Yamaguchi, Makoto Otsu, Ken Nishimura, Mahito Nakanishi, Akira Sawaguchi, Ryozo Nagai, Kazutoshi Takahashi, Shinya Yamanaka, Hiromitsu Nakauchi, and Koji Eto
Journal of Experimental Medicine 207(13), 2817-2830, 20 December 2010
- Regulation of Nucleolar Chromatin by B23/Nucleophosmin Jointly Depends upon Its RNA Binding Activity and Transcription Factor UBF
Miharu Hisaoka, Shuhei Ueshima, Kensaku Murano, Kyosuke Nagata, and Mitsuru Okuwaki
Molecular and Cellular Biology, October 2010, p. 4952-4964, Vol. 30, No. 20
- Dual functions of yeast tRNA ligase in the unfolded protein response: unconventional cytoplasmic splicing of HAC1 pre-mRNA is not sufficient to release translational attenuation.
Ogasawara, Toshifumi Inada, Markus Englert, Hildburg Beier, Mine Takezawa, Toshiya Endo, and Tohru Yoshihisa
Molecular Biology of the Cell Vol. 21, Issue 21, 3722-3734, November 1, 2010
- The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA.
Hasegawa Y, Brockedorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S
Developmental Cell, Volume 19, Issue 3, 469-476, 14 September 2010
- Differential Replication of Two Chloroplast Genome Forms in Heteroplasmic Chlamydomonas reinhardtii Gametes Contributes to Alternate Inheritance Patterns.
Yoshiki Nishimura, David B Stern
Genetics 185, 1167-81, 2010
- Diazirine-containing RNA photocrosslinking probes for the study of siRNA-protein interactions
Satoru Kuboe, Mayuko Yoda, Aya Ogata, Yukio Kitade, Yukihide Tomari and Yoshihito Ueno
Chem. Commun., 2010, 46, 7367-7369
- Water-Soluble Doubly N-Confused Hexaphyrin: A Near-IR Fluorescent Zn(II) Ion Sensor in Water
Ikawa, Y.; Takeda, M.; Suzuki, M.; Osuka, A.; Furuta, H.
Chem. Commun. 2010, 46, 5689 - 5691
- Assembly of Qbeta viral RNA polymerase with host translational elongation factors EF-Tu and -Ts
Daijiro Takeshita and Kozo Tomita
PNAS September 7, 2010 vol. 107 no. 36 15733-15738
- Visualization and genetic analysis of alternative splicing regulation in vivo using fluorescence reporters in transgenic Caenorhabditis elegans
Hidehito Kuroyanagi,Genta Ohno,Hiroaki Sakane,Hiroyuki Maruoka& Masatoshi Hagiwara
Nature Protocols Volume 5 Pages 1495–1516 (2010) DOI doi:10.1038/nprot.2010.107
- Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis
T. Kondo, S. Plaza, J. Zanet, E. Benrabah, P. Valenti, Y. Hashimoto, S. Kobayashi, F. Payre, Y. Kageyama
Science 16 July 2010:Vol. 329. no. 5989, pp. 336 - 339DOI: 10.1126/science.1188158
- アミノ酸の非対称性の起源:RNAワールドの観点から
田村浩二
生物物理, Vol. 50, 180-181, 2010
- Ser386 phosphorylation of transcription factor IRF-3 induces dimerization and association with CBP/p300 without overall conformational change
Kiyohiro Takahasi, Masataka Horiuchi, Kiyonaga Fujii, Shingo Nakamura, Nobuo N Noda, Mitsutoshi Yoneyama, Takashi Fujita and Fuyuhiko Inagaki
Genes to Cells Vol.15, issue 8, 901-910, 2010 (published on line 6, Jul. 2010)
- Virus-Infection or 5′ppp-RNA Activates Antiviral Signal through Redistribution of IPS-1 Mediated by MFN1.
Kazuhide Onoguchi, Koji Onomoto, Shiori Takamatsu, Michihiko Jogi, Azumi Takemura, Shiho Morimoto, Ilkka Julkunen, Hideo Namiki, Mitsutoshi Yoneyama, Takashi Fujita
PLoS Pathogens 2010 Jul 22;6(7):e1001012 (doi:10.1371/journal.ppat.1001012)
- Translational repression by the oocyte-specific protein P100 in Xenopus
Yoriko Nakamura, Kimio J Tanaka, Maki Miyauchi, Lin Huang, Masafumi Tsujimoto and Ken Matsumoto
Developmental Biology 2010 Aug 1;344(1):272-83. Epub 2010 May 21
- The transDSL ligase ribozyme can utilize various forms of modules to clamp its substrate and enzyme units
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- Hsc70/Hsp90 Chaperone Machinery Mediates ATP-Dependent RISC Loading of Small RNA Duplexes
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Molecular Cell, Volume 39, Issue 2, 292-299, 03 June 2010
- In Vitro Assembly of Plant RNA-induced Silencing Complexes Facilitated by Molecular Chaperone HSP90
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Molecular Cell, Volume 39, Issue 2, 282-291, 03 June 2010
- MVH in piRNA Processing and Gene Silencing of Retrotransposons
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- AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay.
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- Self-assembly of Zn(II) Porphyrin1,2,3-Triazole Conjugate with Alcohol Glue
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- Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
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Nature Chemical Biology 6, 277–282 (2010)
- Enhanced Antitumor Effects of an Engineered Measles Virus Edmonston Strain Expressing the Wild-type N, P, L Genes on Human Renal Cell Carcinoma
Xin Meng, Takafumi Nakamura, Toshihiko Okazaki, Hiroyuki Inoue, Atsushi Takahashi, Shohei Miyamoto, Gaku Sakaguchi, Masatoshi Eto, Seiji Naito, Makoto Takeda, Yusuke Yanagi and Kenzaburo Tani
Molecular Therapy (2010) 18 3, 544–551
- Amino Acid Homochirality and the RNA World: Necessities for Life on Earth
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Journal of Cosmology, Vol. 5, 883-889, 2010
- Functional characterization of human Nucleosome Assembly Protein 1-like proteins as histone chaperones
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Genes to Cells, Volume 15 Issue 1, Pages 13 - 27
- Evolutionary optimization of a modular ligase ribozyme: a small catalytic unit and a hairpin motif masking an element that could form an inactive structure
Fujita, Y., Furuta. H., & Ikawa, Y.
Nucl. Acids Res. (2010) 38 (10): 3328-3339
- Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana
Hisataka Numa, Jong-Myong Kim, Akihiro Matsui, Yukio Kurihara, Taeko Morosawa, Junko Ishida,Yoshiki Mochizuki, Hiroshi Kimura, Kazuo Shinozaki, Tetsuro Toyoda, Motoaki Seki, Manabu Yoshikawa, and Yoshiki Habu
EMBO Journal Volume 29 Number 2 20 January 2010 p352 - 362
- A novel application of metabolomics in vertebrate development .
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- Molecular handedness of life: significance of RNA aminoacylation
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Journal of Biosciences, Vol. 34, 991-994, 2009
- Endogenous non-retroviral RNA virus elements in mammalian genomes
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Nature 463:84-87 (2010)
- The ELAV protein HuD stimulates cap-dependent translation in a poly(A)- and eIF4A-dependent manner
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Molecular Cell, Volume 36, Issue 6, 1007-1017, 24 December 2009
- ATP-dependent human RISC assembly pathways.
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Nature Structural & Molecular Biology 17, 17 - 23 (2010)
- Associations between PIWI Proteins and TDRD1/MTR-1 Are Critical for Integrated Subcellular Localization in Murine Male Germ Cells
Kanako Kojima, Satomi Kuramochi-Miyagawa, Shinichiro Chuma, Takashi Tanaka, Norio Nakatsuji, Tohru Kimura and Toru Nakano
Genes to Cells (2009) 14, 1155-1165. doi:10.1111/j.1365-2443.2009.01342
- Autogenous translational regulation of the Borna disease virus negative control factor X from polycistronic mRNA using host RNA helicases
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- Molecular chaperone BiP interacts with Borna disease virus glycoprotein at cell surface
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Journal of Virology, December 2009, p. 12622-12625, Vol. 83, No. 23
- Designed RNAs with Two Peptide-Binding Units as Artificial Templates for Native Chemical Ligation of RNABinding Peptides
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ChemBioChem 10, 2745-2752 (2009)
- Xtr, a plural tudor domain-containing protein, coexists with FRGY2 both in cytoplasmic mRNP particle and germ plasm in Xenopus embryo: Its possible role in translational regulation of maternal mRNAs
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Development, Growth and Differentiation 51, 595-605, 2009
- The Hsp90 inhibitor geldanamycin abrogates colocalization of eIF4E and 4E-T into stress granules and association of eIF4E with eIF4G.
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The Journal of Biological Chemistry, 284, 35597-35604, December 18, 2009
- A dominant mutation of TWISTED DWARF 1 encoding an α-tubulin protein causes severe dwarfism and right helical growth in rice
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Genes & Genetic Systems Vol. 84 (2009) , No. 3 p.209-218
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EMBO Journal 28, 3353 - 3365 (04 November 2009)
- Loss of the Brm-type SWI/SNF chromatin remodeling complex is a strong barrier to the Tat-independent transcriptional elongation of HIV-1 transcripts
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- Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules
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Nature Structural & Molecular Biology 16, 953 - 960 (2009)
- Structural insights into eRF3 and stop codon recognition by eRF1
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Genes & Development 2009 23: 1106-1118
- MG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay.
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- Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction
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FEBS Letters Volume 583, Issue 17, Pages 2819-2826 (3 September 2009)
- Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units
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Genes and Development 23:963-974, April 15, 2009
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Bioorganic & Medicinal Chemistry Letters Volume 19, Issue 9, 1 May 2009, Pages 2448-2452
- Drosophila Argonaute1 and Argonaute2 Employ Distinct Mechanisms for Translational Repression
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Molecular Cell Volume 34, Issue 1, 10 April 2009, Pages 58-67
→論文紹介(PDF:151KB)
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- Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts
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Molecular and Biochemical Parasitology 2008 Nov; 162(1): 40-51
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Nucleic Acids Sympo. Ser., 503-504 (2008)
- Synthesis and silencing properties of siRNA possessing lipophilic groups at their 3′-termini
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Bioorganic & Medicinal Chemistry Letters 18 (2008) 6394-6397
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Organic & Biomolecular Chemistry, 2008, 6, 4157-4166
- WDR55 is a nucleolar modulator of ribosomal RNAsynthesis, cell cycle progression, and teleost organ development
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- Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme
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EMBO Journal 27(14), 1944-1952, 2008
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- Distribution of U3 small nucleolar RNA and fibrillarin during early embryogenesis in Caenorhabditis elegans
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Biochimie 90(6), 898-907, 2008
- Lilliputians get into the limelight - novel class of small peptide genes in morphogenesis
Yoshiko Hashimoto, Takefumi Kondo and Yuji Kageyama
Development, Growth & Differentiation 50, S269-276, 2008
- Selection of a novel class of RNA RNA interaction motifs based on the ligase ribozyme with defined modular architecture
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Nucleic Acids Res. 36:3600-3607, 2008.
- Facile syntheses of BODIPY derivatives for fluorescent labeling of the 30 and 50 ends of RNAs
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Analytical Biochemistry 378 (2008) 166-170
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- Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein, in BT-type cytoplasmic male sterile rice
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The Plant Journal 55, 619-628 (2008)
- MLE activates transcription via the minimal transactivation domain in Drosophila.
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- Epidermal Growth Factor Receptor (EGFR)-Retargeted Measles Virus Strains Effectively Target EGFR- or EGFRvIII Expressing Gliomas
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Molecular Therapy 2007 Apr;15(4):677-86
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- Characterization of a Borna disease virus field isolate which shows efficient viral propagation and transmissibility.
Yohei Watanabe, Madiha S. Ibrahim, Katsuro Hagiwara, Minoru Okamoto, Wataru Kamitani, Hideyuki Yanai, Naohiro Ohtaki, Yohei Hayashi, Hiroyuki Taniyama, Kazuyoshi Ikuta1 and Keizo Tomonaga
Microbes and Infection 9, 417-427, 2007
- Synthesis and properties of double-stranded antisense oligonucleotides connected with a pentaerythritol linker
A. Shibata, Y. Ueno, A. Matsuda, and Y. Kitade
Nucleic Acids Sympo. Ser., 73-74 (2006).
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