Synthetic Genomics Research Team

Papers

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2021

Hisayuki Kudo, Mitsuhiro Matsuo, Soichirou Satoh, Takayuki Hata, Rei Hachisu, Masayuki Nakamura, Yoshiharu Y Yamamoto, Hiroshi Kimura, Minami Matsui, Junichi Obokata
Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome
The Plant journal : for cell and molecular biology 2021 Jul 12. doi: 10.1111/tpj.15420.

Yuko Makita, Shigekatsu Suzuki, Keiji Fushimi, Setsuko Shimada, Aya Suehisa, Manami Hirata, Tomoko Kuriyama, Yukio Kurihara, Hidefumi Hamasaki, Emiko Okubo-Kurihara, Kazutoshi Yoshitake, Tsuyoshi Watanabe, Masaaki Sakuta, Takashi Gojobori, Tomoko Sakami, Rei Narikawa, Haruyo Yamaguchi, Masanobu Kawachi, Minami Matsui
Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton
Nature Communications 2021 Jun 16;12(1):3593.

Ye Zhang, Nobutaka Mitsuda, Takeshi Yoshizumi, Yoko Horii, Yoshimi Oshima, Masaru Ohme-Takagi, Minami Matsui & Tatsuo Kakimoto
Two types of bHLH transcription factor determine the competence of the pericycle for lateral root initiation
Nature Plants 2021 May;7(5):633-643.

Emiko Okubo-Kurihara,Wen-Dee Ong,Yukio Kurihara,Natsumaro Kutsuna,Minami Matsui
Method for Phenotypic Chemical Screening to Identify Cryptochrome Inhibitors
Methods in Molecular Biology(Clifton, N.J.) 2021;2213:17-27.

2020

Hidefumi Hamasaki, Madoka Ayano, Ayako Nakamura, Shozo Fujioka, Tadao Asami, Suguru Takatsuto, Shigeo Yoshida, Yoshito Oka, Minami Matsui, Yukihisa Shimada
Light Activates Brassinosteroid Biosynthesis to Promote Hook Opening and Petiole Development in Arabidopsis thaliana
Plant and Cell Physiology 2020 Jul 1;61(7):1239-1251.

Tomoko Yamaguchi,Yukio Kurihara,Yuko Makita,Emiko Okubo-Kurihara,Ami Kageyama,Emi Osada,Setsuko Shimada,Hiroko Tsuchida,Hiroaki Shimada and Minami Matsui(2020)
Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis
Plants 2020,9,674

Yukio Kurihara, Yuko Makita, Haruka Shimohira, Minami Matsui(2020)
Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in Arabidopsis.
International journal of molecular sciences 21(6) 3 14, 2020

Davide Marzi, Patrizia Brunetti, Giovanni Mele, Nadia Napoli, Lorenzo Calò, Erica Spaziani, Minami Matsui, Simone De Panfilis, Paolo Costantino, Giovanna Serino, Maura Cardarelli(2020)
Light controls stamen elongation via cryptochromes, phytochromes and COP1 through HY5 and HYH.
The Plant journal : for cell and molecular biology 3 6, 2020

Yukio Kurihara, Yuko Makita, Haruka Shimohira, Tomoya Fujita, Shintaro Iwasaki, Minami Matsui(2020)
Translational Landscape of Protein-Coding and Non-Protein-Coding RNAs upon Light Exposure in Arabidopsis.
Plant & cell physiology 61(3) 536 - 545 3 1, 2020

2019

Miku Ishizawa, Kayo Hashimoto, Misato Ohtani, Ryosuke Sano, Yukio Kurihara, Hiroaki Kusano, Taku Demura, Minami Matsui, Kumi Sato-Nara(2019)
Inhibition of Pre-mRNA Splicing Promotes Root Hair Development in Arabidopsis thaliana
Plant and Cell Physiology 60(9) 1974 - 1985 9 1, 2019

Ayaka Hieno, Hushna Ara Naznin, Keiko Inaba-Hasegawa, Tomoko Yokogawa, Natsuki Hayami, Mika Nomoto, Yasuomi Tada, Takashi Yokogawa, Mieko Higuchi-Takeuchi, Kosuke Hanada, Minami Matsui, Yoko Ikeda, Yuko Hojo, Takashi Hirayama, Kazutaka Kusunoki, Hiroyuki Koyama, Nobutaka Mitsuda, Yoshiharu Y. Yamamoto(2019)
Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H2O2
Plant Physiology 180(3) 1629 - 1646 7 2019

Hamasaki H, Kurihara Y, Kuromori T, Kusano H, Nagata N, Yamamoto YY, Shimada H, Matsui M(2019)
SnRK1 Kinase and the NAC Transcription Factor SOG1 Are Components of a Novel Signaling Pathway Mediating the Low Energy Response Triggered by ATP Depletion.
Frontiers in plant science 10 503 5 10, 2019

Kuriyama T, Shimada S, Matsui M(2019)
Improvement of Agrobacterium-mediated transformation for tannin-producing sorghum.
Plant biotechnology (Tokyo, Japan) 36(1) 43 - 48 3 2019

Maeda S, Dubouzet JG, Kondou Y, Jikumaru Y, Seo S, Oda K, Matsui M, Hirochika H, Mori M(2019)
The rice CYP78A gene BSR2 confers resistance to Rhizoctonia solani and affects seed size and growth in Arabidopsis and rice.
Scientific reports 9(1) 587 1 24, 2019

2018

Nadia Napoli, Roberta Ghelli, Patrizia Brunetti, Angelo De Paolis, Valentina Cecchetti, Tomohiko Tsuge, Giovanna Serino, Minami Matsui, Giovanni Mele, Gianmarco Rinaldi, Gianna Aurora Palumbo, Fabrizio Barozzi, Paolo Costantino, Maura Cardarelli(2018)
A Newly Identified Flower-Specific Splice Variant of AUXIN RESPONSE FACTOR8 Regulates Stamen Elongation and Endothecium Lignification in Arabidopsis
The Plant Cell Vol. 30: 620–637, Mar 2018

Yukio Kurihara, Yuko Makita, Mika Kawashima, Tomoya Fujita, Shintaro Iwasaki, Minami Matsui(2018)
Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7831-7836.

Saito Y, Tsuchida H, Matsumoto T, Makita Y, Kawashima M, Kikuchi J, Matsui M.(2018)
Screening of fungi for decomposition of lignin-derived products from Japanese cedar.
J Biosci Bioeng. 2018 Nov;126(5):573-579.

Nakaminami Kentaro, Okamoto Masanori, Higuchi-Takeuchi Mieko, Yoshizumi Takeshi, Yamaguchi Yube, Fukao Yoichiro, Shimizu Minami, Ohashi Chihiro, Tanaka Maho, Matsui Minami, Shinozaki Kazuo, Seki Motoaki, Hanada Kousuke
AtPep3 is a hormone-like peptide that plays a role in the salinity stress tolerance of plants
PNAS May 29, 2018, 115(22) 5810-5815

Ogita Nobuo, Okushima Yoko, Tokizawa Mutsutomo, Yamamoto Yoshiharu Y., Tanaka Maho, Seki Motoaki, Makita Yuko, Matsui Minami, Okamoto-Yoshiyama Kaoru, Sakamoto Tomoaki, Kurata Tetsuya, Hiruma Kei, Saijo Yusuke, Takahashi Naoki, Umeda Masaaki
Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis
PLANT JOURNAL 2018 May, 94(3) 439-453

Kiba Takatoshi, Inaba Jun, Kudo Toru, Ueda Nanae, Konishi Mineko, Mitsuda Nobutaka, Takiguchi Yuko, Kondou Youichi, Yoshizumi Takeshi, Ohme-Takagi Masaru, Matsui Minami, Yano Kentaro, Yanagisawa Shuichi, Sakakibara Hitoshi
Repression of Nitrogen Starvation Responses by Members of the Arabidopsis GARP-Type Transcription Factor NIGT1/HRS1 Subfamily
PLANT CELL 2018 Apr, 30(4) 925-945

Makita Yuko, Kawashima Mika, Lau Nyok Sean, Othman Ahmad Sofiman, Matsui Minami
Construction of Para rubber tree genome and multi-transcriptome database accelerates rubber researches
BMC GENOMICS 2018 Jan, 19;19(Suppl 1):922.

Okubo-Kurihara E, Matsui M(2018)
Phenotype-Based Screening of Small Molecules to Modify Plant Cell Walls Using BY-2 Cells.
Methods in molecular biology (Clifton, N.J.) 1795 85 - 92 2018

2017

Wen-Dee Ong, Emiko Okubo-Kurihara, Yukio Kurihara, Setsuko Shimada, Yuko Makita, Mika Kawashima, Kaori Honda, Yasumitsu Kondoh, Nobumoto Watanabe, Hiroyuki Osada, Sean R. Cutler, Kumar Sudesh, Minami Matsui (2017)
Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana.
Plant Cell Physiol.58 (1): 95-105

Hong JP, Adams E, Yanagawa Y, Matsui M, Shin R. (2017)
AtSKIP18 and AtSKIP31, F-box subunits of the SCF E3 ubiquitin ligase complex, mediate the degradation of 14-3-3 proteins in Arabidopsis.
Biochem Biophys Res Commun.S0006-291X(17)30314-5

Makita Y.,Ng KK.,Singham V.,Kawashima M., Hirakawa H., Sato S.,Othman AS., Matsui M. (2017)
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis
Dna Research 0(0), 1–9

Kondou, Y., Manickavelu,A., Komatsu K., Arifi M., Kawashima, M., Ishii T., Hattori T., Iwata H., Tsujimoto H., Ban T., Matsui M. (2017)
Analysis of grain elements and identification of best genotypes for Fe and P in Afgan wheat landraces.
Breeding Science 66:676-682

Manickavelu A, Hattori T, Yamaoka S, Yoshimura K, Kondou Y, Onogi A, Matsui M, Iwata H, Ban T. (2017) Genetic Nature of Elemental Contents in Wheat Grains and Its Genomic Prediction: Toward the Effective Use of Wheat Landraces from Afghanistan. PLoS One. 10;12(1)

2016

Ka-Kei Sam, Nyok-Sean Lau, Amirul Al-Ashraf Abdullah, Minami Matsui (2016)
Photoautotrophic Polyhydroxyalkanoate Production in Cyanobacteria.
Cyanobacteria -Omics and Manipulation-235-251

Wang, Q., Zuo, Z., Wang, X., Gu, L., Yoshizumi, T., Yang, Z., Yang, L., Liu, Q., Liu, W., Han, Y. J., Kim, J. I., Liu, B., Wohlschlegel, J. A., Matsui, M., Oka, Y.and Lin, C. (2016)
Photoactivation and inactivation of Arabidopsis cryptochrome 2,
Science 354: 343-347.

Kim, H., Kojima, M., Choi, D., Park, S., Matsui, M., Sakakibara, H.and Hwang, I. (2016)
Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth.
Journal of integrative plant biology 58: 874-889.

Lau, N. S., Makita, Y., Kawashima, M., Taylor, T. D., Kondo, S., Othman, A. S., Shu-Chien, A. C.and Matsui, M. (2016)
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis.
Sci Rep. 6: 28594.

Okubo-Kurihara, E., Ohtani, M., Kurihara, Y., Kakegawa, K., Kobayashi, M., Nagata, N., Komatsu, T., Kikuchi, J., Cutler, S., Demura, T.and Matsui, M. (2016)
Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium.
Sci Rep. 6: 34602.

Sugano, S., Hayashi, N., Kawagoe, Y., Mochizuki, S., Inoue, H., Mori, M., Nishizawa, Y., Jiang, C. J., Matsui, M.and Takatsuji, H. (2016)
Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease,
Plant Mol Biol. 91: 81-95.

Tsuzuki, M., Nishihama, R., Ishizaki, K., Kurihara, Y., Matsui, M., Bowman, J. L., Kohchi, T., Hamada, T.and Watanabe, Y. (2016)
Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants.
Plant Cell Physiol., 57: 359-372.

2015

Shimada S, Makita Y, Kuriyama-Kondou T, Kawashima M, Mochizuki Y, Hirakawa H, Sato S, Toyoda T, Matsui M. (2015)
Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.
DNA Res. 22(6):485-93.

Makita, Y., Shimada, S., Kawashima, M., Kondou-Kuriyama, T., Toyoda, T., Matsui, M.(2015)
MOROKOSHI: Transcriptome Database in Sorghum bicolor
Plant Cell Physiol.56(1):e6. doi: 10.1093/pcp/pcu187

Foong,CP., Lau,NS., Deguchi, S., Toyofuku, T., Taylor, TD., Sudesh S., Matsui, M.(2015)
Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater Manuscript
BMC Microbiology24;14(1):7

Kurihara, Y., Okubo-Kurihara, E., Matsui, M.(2015)
Polycistronic expression of RNA silencing suppressor protects its own mRNA from RNA silencing.(2015)
Plant Biotechnol. 32, 1-7

Shimada,S., Komatsu, T., Yamagami, A., Nakazawa, M., Matsui, M., Kawaide, H., Natsume, M., Osada, H., Asami, T., Nakano, T.(2015)
Formation and dissociation of BSS1 protein complex regulates plant development via brassinosteroid signaling
Plant Cell27(2):375-90

2014

Lau, NS., Foong, CP., Kurihara, Y., Sudesh, K., Matsui, M.(2014)
RNA-seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis sp”  
PLOSONEdoi; 10.1371/journal.pone.0086368

Kurihara, Y., Makita, Y., Kawashima, M., Hamasaki, H., Yamamoto, YY., Matsui, M.(2014)
Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Genes5:1115-1131

Yoshizawa E, Kaizuka M, Yamagami A, Higuchi-Takeuchi M, Matsui M, Kakei Y, Shimada Y, Sakuta M, Osada H, Asami T, Nakano T.(2014)
BPG3 is a novel chloroplast protein that involves the greening of leaves and related to brassinosteroid signaling.
Biosci Biotechnol Biochem.78(3):420-9

Kunihiro S, Kowata H, Kondou Y, Takahashi S, Matsui M, Berberich T, Youssefian S, Hidema J, Kusano T.(2014)
Overexpression of rice OsREX1-S, encoding a putative component of the core general transcription and DNA repair factor IIH, renders plant cells tolerant to cadmium- and UV-induced damage by enhancing DNA excision repair.
Planta.239(5):1101-11

Higuchi-Takeuchi, M, Matsui, M.(2014)
Screening for gene function using the FOX (full-length cDNA overexpressor gene) hunting system.
Methods Mol Biol. 1056:201-210.

Adams,E., Diaz,C., Matsui,M. and Shin, R.(2014)
Overexpression of a Novel Component Induces HAK5 and Enhances Growth in Arabidopsis.
ISRN Botany490252, 9

Matsui, M.(2014)
PHA from sunlight –New route for bioplastics production in cyanobacteria via photosynthesis
Bioplastics Magazine 9 20-21

2013

Hanada K., Higuchi M., Okamoto M., Yoshizumi T., Shimizu M., Nakaminami K., Nishi R., Ohashi C., Iida K., Tanaka M., Horii Y., Kawashima M., Matsui K., Toyoda T., Shinozaki K., Seki M., and Matsui M. (2013)
Small open reading frames associated with morphogen- esis are hidden in plant genomes.
Proc. Natl. Acad. Sci. USA110,No.6, 2395-400

Lyons, R, Iwase, A, Gänsewig, T, Sherstnev, A, Duc, C, Barton, GJ, Hanada, K, Higuchi-Takeuchi, M, Matsui, M, Sugimoto, K, Kazan, K, Simpson, GG, Shirasu, K(2013)
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation.
Sci. Rep. 3:2866

Cox, RS, Nishikata, K, Shimoyama, S, Yoshida, Y, Matsui, M, Makita, Y, Toyoda, T.(2013)
PromoterCAD: Data-driven design of plant regulatory DNA.
Nucleic Acids Res., 41 W569-74

Hong, JP, Takeshi, Y, Kondou, Y, Schachtman, DP, Matsui, M, Shin, R.(2013)
Identification and Characterization of Transcription Factors Regulating Arabidopsis HAK5.
Plant Cell Physiol. 54:1478-1490

Franciosini, A, Lombardi, B, Iafrate, S, Pecce, V, Mele, G, Lupacchini, L, Rinaldi, G, Kondou, Y, Gusmaroli, G, Aki, S, Tsuge, T, Deng, XW, Matsui, M, Vittorioso, P, Costantino, P, Serino, G(2013)
The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation.
Mol. Plant. 6(5):1616-1629

Bekh-Ochir, D, Shimada, S, Yamagami, A, Kanda, S, Ogawa, K, Nakazawa, M, Matsui, M, Sakuta, M, Osada, H, Asami, T, Nakano, T.(2013)
A novel mitochondrial DnaJ/Hsp40 family protein BIL2 promotes plant growth and resistance against environmental stress in brassinosteroid signaling.
Planta237:1509-25

Higuchi-Takeuchi, M, Mori, M, Matsui, M.(2013)
High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system.
Int J Dev Biol.575:17-523

2012

Kim J., Mizoi J., Kidokoro S., Maruyama K., Nakajima J., Nakashima K., Mitsuda N., Takiguchi Y., Takagi-Ohme M., Kondou Y., Matsui M., Shinozaki K., and Shinozaki-Yamaguchi K. (2012)
Arabidopsis GROWTH-REGULATING FACTOR7 functions as a transcrip-tional repressor of abscisic acid- and osmotic stress- responsive genes, including DREB2A
Plant Cell24(8):3393–33405

Utsumi Y., Tanaka M., Morosawa T., Kurotani A., Yoshida T., Mochida K., Matsui A., Umemura Y., Ishitani M., Shinozaki K., Sakurai T., and Seki M (2012)
Transcriptome analysis using a high-density oligomi- croarray under drought stress in various genotypes of cassava: an important tropical crop
DNA Res.19(4):335–345

Kurihara Y., Schmitz R. J., Nery J. R., Schultz M. D., Kurihara E., Morosawa T., Tanaka M., Toyoda T., Seki M., and Ecker J. R. (2012)
Surveillance of 3’ Noncoding Tran- scripts Requires FIERY1 and XRN3 in Arabidopsis
Genes, Genomes, Genetics2(4):487–498

Utsumi Y., Sakurai T., Umemura Y., Ayling S., Ishitani M., Narangajavana J., Sojikul P., Triwitayakorn K., Matsui M., Manabe R., Shinozaki K., and Seki M.
RIKEN Cassava Initiative: Establishment of a Cassava unctional Genomics Platform
Tropical Plant Biol.5:110–116

2011

Higuchi M., Ichikawa T., Kondou Y., Matsui K., Hasegawa Y., Kawashima M., Sonoike K., Mori M., Hirochika H., and Matsui M. (2011)
Functional analysis of two iso- forms of leaf-type ferredoxin-NADP+-oxidoreductase in rice using heterologous expression system of Arabidopsis thaliana
Plant Physiol.157:96–108

Kurihara Y. and Seki M. (2011)
Genome-wide analysis of RNA degradation in Arabidopsis
RNA Technologies79–89

Kondou Y, Higuchi M, Ichikawa T, Matsui M. (2011)
Application of full-length cDNA resources to gain-of-function technology for characterization of plant.
Methods Mol Biol.729:183-97

2010

Kondou Y, Higuchi M, Matsui M. (2010)
High-throughput characterization of plant gene functions by using gain-of-function technology.
Annual review of Plant Biology 61:373-393

Higuchi M, Kondou Y, Ichikawa T, Matsui M. (2010)
Full-length cDNA overexpressor gene hunting system (FOX hunting system).
Plant Reverse Genetics Methods in Molecular Biology 678:77-89


Books

For search our papers

2020

Special Issue "Plant Systems and Application"
Plants ISSN 2223-7747
https://www.mdpi.com/journal/plants/special_issues/plant_systems_application

The Rubber Tree Genome
Springer Nature ISBN 978-3-030-42258-5
https://link.springer.com/book/10.1007/978-3-030-42258-5