文部科学省 科学研究費補助金「新学術領域研究」平成24年度〜28年度

研究成果

2014年

<計画研究>

・Magnetically promoted rapid immunoreactions using functionalized fluorescent magnetic beads: a proof of principle. Sakamoto S, Omagari K, Kita Y, Mochizuki Y, Naito Y, Kawata S, Matsuda S, Itano O, Jinno H, Takeuchi H, Yamaguchi Y, Kitagawa Y, *Handa H, Clin Chem 60, 610-620.

・Transcription factor IRF5 drives P2X4R(+)-reactive microglia gating neuropathic pain. Masuda T, Iwamoto S, Yoshinaga R, Tozaki-Saitoh H, Nishiyama A, Mak TW, Tamura T, *Tsuda M, *Inoue K, Nature Commun 5, 3771.

・Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Asakawa H, Yang HJ, Yamamoto TG, Ohtsuki C, Chikashige Y, Sakata-Sogawa K, Tokunaga M, Iwamoto M, *Hiraoka Y, *Haraguchi T, Nucleus 5, 149-162.

・A hemizygous GYG2 mutation and Leigh syndrome: a possible link? Imagawa E, Osaka H, Yamashita A, Shiina M, Takahashi E, Sugie H, Nakashima M, Tsurusaki Y, Saitsu H, Ogata K, Matsumoto N, *Miyake N, Hum Genet 133, 225-234.

・De novo SOX11 mutations cause Coffin-Siris syndrome. Tsurusaki Y, Koshimizu E, Ohashi H, Phadke S, Kou I, Shiina M, Suzuki T, Okamoto N, Imamura S, Yamashita M, Watanabe S, Yoshiura KI, Kodera H, Miyatake S, Nakashima M, Saitsu H, Ogata K, Ikegawa S, Miyake N, *Matsumoto N, Nature Commun 5, 4011.

・Expanding the phenotypic spectrum of TUBB4A-associated hypomyelinating leukoencephalopathies. Miyatake S, Osaka H, Shiina M, Sasaki M, Takanashi JI, Haginoya K, Wada T, Morimoto M, Ando N, Ikuta Y, Nakashima M, Tsurusaki Y, Miyake N, Ogata K, *Matsumoto N, *Saitsu H, Neurology 82, 1-8.

・The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: Analysis of the accuracy and application to liquid systems. *Fukuda I, Kamiya N, Nakamura H, J Chem Phys 140, 194307.

<公募研究>

・RESPAC: method to determine partial charges in coarse-grained protein model and its application to DNA-binding proteins. Terakawa T, *Takada S, J Chem Theory Comput 10,711-721.

・MLL fusion proteins link transcriptional coactivators to previously active CpG-rich promoters. Okuda H, Kawaguchi M, Kanai A, Matsui H, Kawamura T, Inaba T, Kitabayashi I, *Yokoyama A, Nucleic Acids Res 42, 4241-4256.

・Molecular dynamics study of the phosphorylation effect on the conformational states of the C-terminal domain of RNA polymerase II.*Yonezawa Y, J Phys Chem B 17, 4471-4478.

・Possible involvement of LKB1-AMPK signaling in non-homologous end joining. Ui A, Ogiwara H, Nakajima S, Kanno S, Watanabe R, Harata M, Okayama H, Harris CC, Yokota J, Yasui A, *Kohno T, Oncogene 33, 1640-1648.

・Comprehensive analysis of mutually exclusive alternative splicing in C. elegans. *Kuroyanagi H, Takei S, Suzuki Y, Worm 3, e28459.

・Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells. Maejima T, Inoue T, Kanki Y, Kohro T, Li G, Ohta Y, Kimura H, Kobayashi M, Taguchi A, Tsutsumi S, Iwanari H, Yamamoto S, Aruga H, Dong S, Stevens JF, Poh HM, Yamamoto K, Kawamura T, Mimura I, Suehiro J, Sugiyama A, Kaneki K, Shibata H, Yoshinaka Y, Doi T, Asanuma A, Tanabe S, Tanaka T, Minami T, Hamakubo T, Sakai J, Nozaki N, Aburatani H, Nangaku M, Ruan X, Tanabe H, Ruan Y, Ihara S, Endo A, Kodama T, *Wada Y, PLoS One 9, e96005.

・Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements. Inoue T, Kohro T, Tanaka T, Kanki Y, Li G, Poh HM, Mimura I, Kobayashi M, Taguchi A, Maejima T, Suehiro JI, Sugiyama A, Kaneki K, Aruga H, Dong S, Stevens JF, Yamamoto S, Tsutsumi S, Fujita T, Ruan X, Aburatani H, Nangaku M, Ruan Y, Kodama T, *Wada Y, Genome Biol 15, R63.

・Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, Kai C, Yada T, Suzuki Y, Yamada T, Ozawa T, Kaneki K, Inoue T, Kobayashi M, Kodama T, Wada Y, Sekimizu K, *Akimitsu N. Molecular Cell 53, 393-406.

2013年

<計画研究>

・Systematic changes to the apparent diffusion tensor of in vivo rat brain measured with an oscillating-gradient spin-echo sequence.*Kershaw J, Leuze C, Aoki I, Obata T, Kanno I, Ito H, Yamaguchi Y, Handa H, NeuroImage 70, 10-20.

・Vitamin K2 covalently binds to Bak and induces Bak-mediated apoptosis. Karasawa S, Azuma M, Kasama T, Sakamoto S, Kabe Y, Imai T, Yamaguchi Y, Miyazawa K, *Handa H, Mol Pharmacol 83, 613-620.

・Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Yamaguchi Y, Shibata H, *Handa H, Biochimica et Biophysica Acta 1829, 98-104. 総説

・Vesnarinone suppresses TNFα mRNA expression by inhibiting valosin-containing protein.Hotta K, Nashimoto A, Yasumura E, Suzuki M, Azuma M, Iizumi Y, Shima D, Nabeshima R, Hiramoto M, Okada A, Sakata-Sogawa K, Tokunaga M, Ito T, Ando H, Sakamoto S, Kabe Y, Aizawa S, Imai T, Yamaguchi Y, Watanabe H, *Handa H, Mol Pharmacol 83, 930-938.

・Viral protein-coating of magnetic nanoparticles using simian virus 40 VP1. Enomoto T, Kawano M, Fukuda H, Sawada W, Inoue T, Haw KC, Kita Y, Sakamoto S, Yamaguchi Y, Imai T, Hatakeyama M, Saito S, Sandhu A, Matsui M, Aoki I, *Handa H, J Biotechnol 167, 8-15.

・Activation-induced cytidine deaminase auto-activates and triggers aberrant gene expression. Isobe T, Song SN, Tiwari P, Ito H, Yamaguchi Y, *Yoshizaki K, FEBS Lett 587, 2487-2492.

・Salicylic acid induces mitochondrial injury by inhibiting ferrochelatase heme biosynthesis activity. Gupta V, Liu S, Ando H, Ishii R, Tateno S, Kaneko Y, Yugami M, Sakamoto S, Yamaguchi Y, Nureki O, *Handa H, Mol Pharmacol 84, 824-833.

・Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation. Kurotaki D, Osato N, Nishiyama A, Yamamoto M, Ban T, Sato H, Nakabayashi J, Umehara M, Miyake N, Matsumoto N, Nakazawa M, Ozato K,* Tamura T, Blood 121, 1839-1849.

・The transcription factor IRF8 counteracts BCR-ABL to rescue dendritic cell development in chronic myelogenous leukemia. Watanabe T, Hotta C, Koizumi S, Miyashita K, Nakabayashi J, Kurotaki D, Sato GR, Yamamoto M, Nakazawa M, Fujita H, Sakai R, Fujisawa S, Nishiyama A, Ikezawa Z, Aihara M, Ishigatsubo Y, * Tamura T, Cancer Res 73, 6642-6653.

・WHSC1 links transcription elongation to HIRA-mediated histone H3.3 deposition. Sarai N, Nimura K, Tamura T, Kanno T, Patel MC, Heightman TD, Ura K, *Ozato K, EMBO J 32, 2392-2406.

・BRD4 coordinates recruitment of pause release factor P-TEFb and the pausing complex NELF/DSIF to regulate transcription elongation of interferon-stimulated genes. Patel MC, Debrosse M, Smith M, Dey A, Huynh W, Sarai N, *Heightman TD, Tamura T, Ozato K, Mol Cell Biol 33, 2497-2507.

・Egr-2 transcription factor is required for Blimp-1-mediated IL-10 production in IL-27-stimulated CD4+ T cells. Iwasaki Y, *Fujio K, Okamura T, Yanai A, Sumitomo S, Shoda H, Tamura T, Yoshida H, Charnay P, Yamamoto K, European J Immunol 43, 1063-1073.

・Transcriptional properties of mammalian elongin A and its role in stress response. Kawauchi J, Inoue M, Fukuda M, Uchida Y, Yasukawa T, Conaway RC, Conaway JW, Aso T, *Kitajima S, J Biol Chem 288, 24302-24315.

・The USP21 short variant (USP21SV) lacking NES, located mostly in the nucleus in vivo, activates transcription by deubiquitylating ubH2A in vitro. Okuda H, Ohdan H, Nakayama M, Koseki H, *Nakagawa T, *Ito T, PLoS One 8, e79813.

・Mediator complex recruits epigenetic regulators via its two cyclin-dependent kinase subunits to repress transcription of immune response genes. Tsutsui T, Fukasawa R, Shinmyouzu K, Nakagawa R, Tobe K, Tanaka A, *Ohkuma Y, J Biol Chem 288, 20955-20965.

・KDM6A point mutations cause Kabuki syndrome. *Miyake N, Mizuno S, Okamoto N, Ohashi H, Shiina M, Ogata K, Tsurusaki Y, Nakashima M, Saitsu H, Niikawa N, Matsumoto N, Hum Mutat 34, 108-110.

・Mitochondrial complex III deficiency caused by a homozygous UQCRC2 mutation presenting with neonatal-onset recurrent metabolic decompensation. * Miyake N, Yano S, Sakai C, Hatakeyama H, Matsushima Y, Shiina M, Watanabe Y, Bartley J, Abdenur JE, Wang RY, Chang R, Tsurusaki Y, Doi H, Nakashima M, Saitsu H, Ogata K, Goto Y, *Matsumoto N, Hum Mutat 34, 446-452.

・Exome sequencing identifies a novel INPPL1 mutation in opsismodysplasia. Iida A, Okamoto N, Miyake N, Nishimura G, Minami S, Sugimoto T, Nakashima M, Tsurusaki Y, Saitsu H, Shiina M, Ogata K, Watanabe S, Ohashi H, Matsumoto N, *Ikegawa S, J Hum Genet 58, 391-394.

・Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene. Nishiguchi KM, Tearle RG, Liu YP, Oh EC, Miyake N, Benaglio P, Harper S, Koskiniemi-Kuendig H, Venturini G, Sharon D, Koenekoop RK, Nakamura M, Kondo M, Ueno S, Yasuma TR, Beckmann JS, Ikegawa S, Matsumoto N, Terasaki H, Berson EL, Katsanis N, *Rivolta C, Proc Natl Acad Sci USA 110, 16139-16144.

・Identification of KLHL41 mutations implicates BTB-Kelch-mediated ubiquitination as an alternate pathway to myofibrillar disruption in nemaline myopathy. Gupta VA, Ravenscroft G, Shaheen R, Todd EJ, Swanson LC, Shiina M, Ogata K, Hsu C, Clarke NF, Darras BT, Farrar MA, Hashem A, Manton ND, Muntoni F, North KN, Sandaradura SA, Nishino I, Hayashi YK, Sewry CA, Thompson EM, Yau KS, Brownstein CA, Yu TW, Allcock RJ, Davis MR, Wallgren-Pettersson C, Matsumoto N, Alkuraya FS, Laing NG, *Beggs AH, Am J Hum Genet 93, 1108-1117.

・Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. Ravenscroft G, Miyatake S, Lehtokari VL, Todd EJ, Vornanen P, Yau KS, Hayashi YK, Miyake N, Tsurusaki Y, Doi H, Saitsu H, Osaka H, Yamashita S, Ohya T, Sakamoto Y, Koshimizu E, Imamura S, Yamashita M, Ogata K, Shiina M, Bryson-Richardson RJ, Vaz R, Ceyhan O, Brownstein CA, Swanson LC, Monnot S, Romero NB, Amthor H, Kresoje N, Sivadorai P, Kiraly-Borri C, Haliloglu G, Talim B, Orhan D, Kale G, Charles AK, Fabian VA, Davis MR, Lammens M, Sewry CA, Manzur A, Muntoni F, Clarke NF, North KN, Bertini E, Nevo Y, Willichowski E, Silberg IE, Topaloglu H, Beggs AH, Allcock RJ, Nishino I, Wallgren-Pettersson C, *Matsumoto N, *Laing NG, Am J Hum Genet 93, 6-18.

・De novo mutations in GNAO1, encoding a Gαo subunit of heterotrimeric G proteins, cause epileptic encephalopathy. Nakamura K, Kodera H, Akita T, Shiina M, Kato M, Hoshino H, Terashima H, Osaka H, Nakamura S, Tohyama J, Kumada T, Furukawa T, Iwata S, Shiihara T, Kubota M, Miyatake S, Koshimizu E, Nishiyama K, Nakashima M, Tsurusaki Y, Miyake N, Hayasaka K, Ogata K, Fukuda A, *Matsumoto N, *Saitsu H, Am J Hum Genet 93, 496-505.

・De novo mutations in the autophagy gene WDR45 cause static encephalopathy of childhood with neurodegeneration in adulthood. *Saitsu H, Nishimura T, Muramatsu K, Kodera H, Kumada S, Sugai K, Kasai-Yoshida E, Sawaura N, Nishida H, Hoshino A, Ryujin F, Yoshioka S, Nishiyama K, Kondo Y, Tsurusaki Y, Nakashima M, Miyake N, Arakawa H, Kato M, *Mizushima N, *Matsumoto N, Nature Genet 45, 445-449.

・Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders. Nakajima M, Mizumoto S, Miyake N, Kogawa R, Iida A, Ito H, Kitoh H, Hirayama A, Mitsubuchi H, Miyazaki O, Kosaki R, Horikawa R, Lai A, Mendoza-Londono R, Dupuis L, Chitayat D, Howard A, Leal GF, Cavalcanti D, Tsurusaki Y, Saitsu H, Watanabe S, Lausch E, Unger S, Bonafé L, Ohashi H, Superti-Furga A, Matsumoto N, Sugahara K, Nishimura G,* Ikegawa S, Am J Hum Genet 92, 927-934.

・Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. Ravenscroft G, Miyatake S, Lehtokari VL, Todd EJ, Vornanen P, Yau KS, Hayashi YK, Miyake N, Tsurusaki Y, Doi H, Saitsu H, Osaka H, Yamashita S, Ohya T, Sakamoto Y, Koshimizu E, Imamura S, Yamashita M, Ogata K, Shiina M, Bryson-Richardson RJ, Vaz R, Ceyhan O, Brownstein CA, Swanson LC, Monnot S, Romero NB, Amthor H, Kresoje N, Sivadorai P, Kiraly-Borri C, Haliloglu G, Talim B, Orhan D, Kale G, Charles AK, Fabian VA, Davis MR, Lammens M, Sewry CA, Manzur A, Muntoni F, Clarke NF, North KN, Bertini E, Nevo Y, Willichowski E, Silberg IE, Topaloglu H, Beggs AH, Allcock RJ, Nishino I, Wallgren-Pettersson C, *Matsumoto N, *Laing NG, Am J Hum Genet 93, 6-18.

・MLL2 and KDM6A mutations in patients with Kabuki syndrome. *Miyake N, Koshimizu E, Okamoto N, Mizuno S, Ogata T, Nagai T, Kosho T, Ohashi H, Kato M, Sasaki G, Mabe H, Watanabe Y, Yoshino M, Matsuishi T, Takanashi J, Shotelersuk V, Tekin M, Ochi N, Kubota M, Ito N, Ihara K, Hara T, Tonoki H, Ohta T, Saito K, Matsuo M, Urano M, Enokizono T, Sato A, Tanaka H, Ogawa A, Fujita T, Hiraki Y, Kitanaka S, Matsubara Y, Makita T, Taguri M, Nakashima M, Tsurusaki Y, Saitsu H, Yoshiura K, *Matsumoto N, Niikawa N, Am J Med Genet A 161, 2234-2243.

・FOXC2 mutations in familial and sporadic spinal extradural arachnoid cyst. Ogura Y, Yabuki S, Iida A, Kou I, Nakajima M, Kano H, Shiina M, Kikuchi S, Toyama Y, Ogata K, Nakamura M, Matsumoto M, *Ikegawa S, PLoS One 22, e80548.

・A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent. *Higo J, Umezawa K, Nakamura H, J Chem Phys 138, 184106.

・LigandBox: a database for 3D structures of chemical compounds. Kawabata T, Sugihara Y, Fukunishi,Y, *Nakamura H, Biophysics 9, 113-121.

・Exhaustive comparison and classification of ligand-binding surfaces in proteins. *Murakami Y, Kinoshita K, Kinjo AR, Nakamura H, Protein Sci 22, 1379-1391.

・Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method. Arakawa T, *Kamiya N, Nakamura H, Fukuda I, PLoS One 8, e76606.

・Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions. Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I,*Nakamura H, J Chem Theory Comput 9, 5599-5609.

・NF-E2 p45 is important for establishing normal function of platelets. Fujita R, Takayama-Tsujimoto M, Satoh H, Gutiérrez L, Aburatani H, Fujii S, Sarai A, Bresnick EH, *Yamamoto M, *Motohashi H, Mol Cell Biol 33, 2659-2670.

<公募研究>

・Nonmuscle myosin II folds into a 10S form via two portions of tail for dynamic subcellular localization. Kiboku T, Katoh T, Nakamura A, Kitamura A, Kinjo M, Murakami Y, *Takahashi M, Genes Cells 2, 90-109.

・Mediator directs co-transcriptional heterochromatin assembly by RNA interference-dependent and -independent pathways. Oya E, Kato H, Chikashige Y, Tsutsumi C, Hiraoka Y, *Murakami Y, PLoS Genet 9, e1003677.

・Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3. *Kato H, Okazaki K, Iida T, Nakayama J, Murakami Y, Urano T, Sci Rep 3, 2186.

・Histone deacetylases govern heterochromatin in every phase. *Murakami Y, EMBO J 32, 2301-2303. 総説

・Multiple signaling pathways coordinate to induce a threshold response in a chordate embryo. Ohta N, *Satou Y, PLoS Genet 9, e1003818.

・Bayesian parameter inference by Markov chain Monte Carlo with hybrid fitness measures: theory and test in apoptosis signal transduction network. *Murakami Y, Takada S, PLoS One 27, e74178.

・Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations. *McGrath MJ, Kuo IF, Hayashi S, *Takada S, J Am Chem Soc 135, 8908-8919.

・Drug uptake pathways of multidrug transporter AcrB studied by molecular simulations and site-directed mutagenesis experiments. Yao XQ, Kimura N, Murakami S, *Takada S, J Am Chem Soc 135, 7474-7485.

・A time delay gene circuit is required for palp formation in the ascidian embryo. Ikeda T, Matsuoka T, *Satou Y, Development 140, 4703-4708.

・MLL becomes functional through intra-molecular interaction not by proteolytic processing. *Yokoyama A, Ficara F, Murphy MJ, Meisel C, Hatanaka C, Kitabayashi I, Cleary ML, PLoS One 8, e73649.

・Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP). Fujita T, Asano Y, Ohtsuka J, Takada Y, Saito K, Ohki R, *Fujii H, Sci Rep 3, 3171.

・Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Fujita T, *Fujii H, Biochem Biophys Res Commun 439, 132-136.

・Nano-analysis of DNA conformation changes induced by transcription factor complex binding using plasmonic nanodimers. Morimura H, Tanaka S, Ishitobi H, Mikami T, Kamachi Y, Kondoh H, *Inouye Y. ACS Nano 7, 10733-10740.

・Quantifying transcription factor kinetics: at work or at play? Mueller F, Stasevich TJ, Mazza D, *McNally JG. Crit Rev Biochem Mol Biol 48, 492-514.

・Genetically encoded system to track histone modification in vivo. Sato Y, Mukai M, Ueda J, Muraki M, Stasevich TJ, Horikoshi N, Kujirai T, Kita H, Kimura T, Hira S, Okada Y, Hayashi-Takanaka Y, Obuse C, Kurumizaka H, Kawahara A, Yamagata K, Nozaki N, *Kimura H, Sci Rep 3,2436.

・Convergence of chromatin binding estimates in live cells. Mazza D, Mueller F, Stasevich TJ, *McNally JG, Nature Methods 10, 691-692.

・High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation. Anandapadamanaban M, Andresen C, Helander S, Ohyama Y, Siponen MI, Lundström P, Kokubo T, Ikura M, Moche M, *Sunnerhagen M, Nature Struct Mol Biol 20, 1008-1014.

・Macrophage migration inhibitory factor and stearoyl-CoA desaturase 1: potential prognostic markers for soft tissue sarcomas based on bioinformatics analyses. *Takahashi H, Nakayama R, Hayashi S, Nemoto T, Murase Y, Nomura K, Takahashi T, Kubo K, Marui S, Yasuhara K, Nakamura T, Sueo T, Takahashi A, Tsutsumiuchi K, Ohta T, Kawai A, Sugita S, Yamamoto S, Kobayashi T, Honda H, Yoshida T, Hasegawa T. PLoS One 8, e78250.

・Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2. Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, *Kurumizaka H, Acta Crystallogr D Biol Crystallogr 69, 2431-2439.

・Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans. Kuroyanagi H, Watanabe Y, Suzuki Y, Hagiwara M, Nucleic Acids Res 41, 4015-4025.

・Switch-like regulation of tissue-specific alternative pre-mRNA processing patterns revealed by customized fluorescence reporters. Kuroyanagi H, Worm 2, e23834. 総説

2012年度

<計画研究>

・Identification of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel target of bisphenol A. Ito Y, Ito T, Karasawa S, Enomoto T, Nashimoto A, Hase Y, Sakamoto S, Mimori T, Matsumoto Y, Yamaguchi Y, *Handa H, PLoS One 7, e50481.

・Transcriptional elongation factor elongin A regulates retinoic acid-induced gene expression during neuronal differentiation. Yasukawa T, Bhatt S, Takeuchi T, Kawauchi J, Takahashi H, Tsutsui A, Muraoka T, Inoue M, Tsuda M, Kitajima S, Conaway RC, Conaway JW, Trainor PA, *Aso T, Cell Reports 2, 1129-1136.

・DSIF restricts NF-κB signaling by coordinating elongation with mRNA processing of negative feedback genes. Diamant G, Amir-Zilberstein L, Yamaguchi Y, Handa H, *Dikstein R, Cell Reports 2, 722-731.

・Activation of JNK triggers release of Brd4 from mitotic chromosomes and mediates protection from drug-induced mitotic stress. Nishiyama A, Dey A, Tamura T, Ko M, *Ozato K, PLoS One 7, e34719.

・Key role of ATF3 in p53-dependent DR5 induction upon DNA damage of human colon cancer cells. Taketani K, Kawauchi J, Tanaka-Okamoto M, Ishizaki H, Tanaka Y, Sakai T, Miyoshi J, Maehara Y, *Kitajima S, Oncogene 31, 2210-2221.

・IRF8 is a critical transcription factor for transforming microglia into a reactive phenotype. Masuda T, Tsuda M, Yoshinaga R, Tozaki-Saitoh H, Ozato K, Tamura T,*Inoue K, Cell Reports 1, 334-340.

・Mediator CDK subunits are platforms for interactions with various chromatin regulatory complexes. Fukasawa R, Tsutsui T, Hirose Y, Tanaka A, * Ohkuma Y, J Biochem 152, 241-249.

・Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, *Koseki H, PLoS Genet 8, e1002774.

・Histone monoubiquitylation position determines specificity and direction of enzymatic cross-talk with histone methyltransferases Dot1L and PRC2. Whitcomb SJ, Fierz B, McGinty RK, Holt M, Ito T, Muir TW, *Allis CD, J Biol Chem 287, 23718-23725.

・A DYNC1H1 mutation causes a dominant spinal muscular atrophy with lower extremity predominance. Tsurusaki Y, Saitoh S, Tomizawa K, Sudo A, Asahina N, Shiraishi H, Ito J, Tanaka H, Doi H, Saitsu H, Miyake N, *Matsumoto N, Neurogenetics 13, 327-332.

・Diffuse central hypomyelination presenting as 4H syndrome caused by compound heterozygous mutations in POLR3A encoding the catalytic subunit of polymerase III. *Terao Y, Saitsu H, Segawa M, Kondo Y, Sakamoto K, Matsumoto N, Tsuji S, Nomura Y, J Neuro Sci 320, 102-105.

・A novel SACS mutation in an atypical case with autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), Miyatake S, Miyake N, Doi H, Saitsu H, Ogata K, Kawai M,* Matsumoto N, Intern Med 51, 2221-2226.

・Whole exome sequencing identifies KCNQ2 mutations in Ohtahara syndrome. Saitsu H, Kato M, Koide A, Goto T, Fujita T, Nishiyama K, Tsurusaki Y, Doi H, Miyake N, Hayasaka K, *Matsumoto N, Ann Neurol 72, 298-300.

・PAPSS2 mutations cause autosomal recessive brachyolmia. Miyake N, Elcioglu NH, Iida A, Isguven P, Dai J, Murakami N, Takamura K, Cho TJ, Kim OH, Hasegawa T, Nagai T, Ohashi H, Nishimura G, Matsumoto N, *Ikegawa S, J Med Genet 49, 533-538.

・CASK aberrations in male patients with Ohtahara syndrome and cerebellar hypoplasia. *Saitsu H, Kato M, Osaka H, Moriyama N, Horita H, Nishiyama K, Yoneda Y, Kondo Y, Tsurusaki Y, Doi H, Miyake N, Hayasaka K, Matsumoto N, Epilepsia 53, 1441-1449.

・Identification of a novel in-frame de novo mutation in SPTAN1 in intellectual disability and pontocerebellar atrophy. Hamdan FF, Saitsu H, Nishiyama K, Gauthier J, Dobrzeniecka S, Spiegelman D, Lacaille JC, Décarie JC, Matsumoto N, Rouleau GA, *Michaud JL, Eur J Hum Genet 20, 796-800.

・Early onset West syndrome with severe hypomyelination and coloboma-like optic discs in a girl with SPTAN1 mutation. *Writzl K, Primec ZR, Stražišar BG, Osredkar D, Pečarič-Meglič N, Kranjc BS, Nishiyama K, Matsumoto N, Saitsu H, Epilepsia 53, e106-110.

・Contiguous deletion of SLC6A8 and BAP31 in a patient with severe dystonia and sensorineural deafness. *Osaka H, Takagi A, Tsuyusaki Y, Wada T, Iai M, Yamashita S, Shimbo H, Saitsu H, Salomons GS, Jakobs C, Aida N, Toshihiro S, Kuhara T, Matsumoto N, Mol Genet Metab 106, 43-47.

・A girl with early-onset epileptic encephalopathy associated with microdeletion involving CDKL5. *Saitsu H, Osaka H, Nishiyama K, Tsurusaki Y, Doi H, Miyake N, Matsumoto N, Brain Dev 34, 364-367.

・Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, Kato M, Hiraki Y, Yamagata T, Yano S, Mizuno S, Sakazume S, Ishii T, Nagai T, Shiina M, Ogata K , Ohta T, Niikawa N, Miyatake S, Okada I, Mizuguchi T, Doi H, Saitsu H, *Miyake N, *Matsumoto N, Nature Genet 44, 376-378.

・Neurodevelopmental features in 2q23.1 microdeletion syndrome: report of a new patient with intractable seizures and review of literature. Motobayashi M, Nishimura-Tadaki A, Inaba Y, Kosho T, Miyatake S, Niimi T, Nishimura T, Wakui K, Fukushima Y, Matsumoto N, Koike K, Am J Med Genet A 158A, 861-868.

・Association of genomic deletions in the STXBP1 gene with Ohtahara syndrome. *Saitsu H, Kato M, Shimono M, Senju A, Tanabe S, Kimura T, Nishiyama K, Yoneda Y, Kondo Y, Tsurusaki Y, Doi H, Miyake N, Hayasaka K, Matsumoto N, Clin Genet 81, 399-402.

・Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing. Sakai H, Suzuki S, Mizuguchi T, Imoto K, Yamashita Y, Doi H, Kikuchi M, Tsurusaki Y, Saitsu H, Miyake N, Masuda M,* Matsumoto N, Hum Genet 131, 591-599.

・Homozygous c.14576G>A variant of RNF213 predicts early-onset and severe form of moyamoya disease. Miyatake S, Miyake N, Touho H, Nishimura-Tadaki A, Kondo Y, Okada I, Tsurusaki Y, Doi H, Sakai H, Saitsu H, Shimojima K, Yamamoto T, Higurashi M, Kawahara N, Kawauchi H, Nagasaka K, Okamoto N, Mori T, Koyano S, Kuroiwa Y, Taguri M, Morita S, Matsubara Y, Kure S, *Matsumoto N, Neurology 78, 803-810.

・Missense mutations in the DNA-binding/dimerization domain of NFIX cause Sotos-like features. Yoneda Y, Saitsu H, Touyama M, Makita Y, Miyamoto A, Hamada K, Kurotaki N, Tomita H, Nishiyama K, Tsurusaki Y, Doi H, Miyake N, Ogata K, Naritomi K, *Matsumoto N, J Hum Genet 57, 207-211.

・A family of oculofaciocardiodental syndrome (OFCD). with a novel BCOR mutation and genomic rearrangements involving NHS. Kondo Y, Saitsu H, Miyamoto T, Nishiyama K, Tsurusaki Y, Doi H, Miyake N, Ryoo NK, Kim JH, Yu YS, Matsumoto N, J Hum Genet 57, 197-201.

・De novo and inherited mutations in COL4A2, encoding the type IV collagen α2 chain cause porencephaly. Yoneda Y, Haginoya K, Arai H, Yamaoka S, Tsurusaki Y, Doi H, Miyake N, Yokochi K, Osaka H, Kato M, Matsumoto N, *Saitsu H, Am J Hum Genet 90, 86-90.

・Non-Ewald methods: theory and applications to molecular systems. *Fukuda I, Nakamura H, Biophys Rev 4, 161-170.

・Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water. Fukuda I, Kamiya N, Yonezawa Y, *Nakamura H, J Chem Phys 137, 054314.