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

過去の主要業績

山口 雄輝

Identification of a primary target of thalidomide teratogenicity. Ito T, Ando H, Suzuki T, Ogura T, Hotta K, Imamura Y, Yamaguchi Y, Handa H. Science 327, 1345-1350 (2010).
DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation. Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H. Genes Dev. 23, 2765-2777 (2009).
NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs. Narita T, Yung T M, Yamamoto J, Tsuboi Y, Tanabe H, Tanaka K, Yamaguchi Y, Handa H. Mol. Cell 26, 349-365 (2007).
P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Yamada T, Yamaguchi Y, Inukai N, Okamoto S, Mura T, Handa H . Mol. Cell 21, 227-237 (2006).
Mediator requirement for both recruitment and postrecruitment steps in transcription initiation. Wang G, Balamotis M A, Stevens J L, Yamaguchi Y, Handa H, Berk A J. Mol. Cell 17, 683-694 (2005).
Attenuation of estrogen receptor alpha-mediated transcription through estrogen-stimulated recruitment of a negative elongation factor. Aiyar S E, Sun J L, Blair A L, Moskaluk C A, Lu Y Z, Ye Q N, Yamaguchi Y, Mukherjee A, Ren D M, Handa H, Li R. Genes Dev. 18, 2134-2146 (2004).
NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Wu C H, Yamaguchi Y, Benjamin L R, Horvat-Gordon M, Washinsky J, Enerly E, Larsson J, Lambertsson A, Handa H, Gilmour D. Genes Dev. 17, 1402-1414 (2003).
Stimulation of RNA polymerase II elongation by hepatitis delta antigen. Yamaguchi Y, Filipovska J, Yano K, Furuya A, Inukai N, Narita T, Wada T, Sugimoto S, Konarska M M, Handa H. Science 293, 124-127 (2001).
A regulator of transcriptional elongation controls vertebrate neuronal development. Guo S, Yamaguchi Y, Schilbach S, Wada T, Lee J, Goddard A, French D, Handa H, Rosenthal A. Nature 408, 366-369 (2000).
NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. Cell 97, 41-51 (1999).

田村 智彦

Contribution of IRF5 in B cells to the development of murine SLE-like disease through its transcriptional control of the IgG2a locus. Savitsky D A, Yanai H, Tamura T, Taniguchi T, Honda K. Proc. Natl. Acad. Sci. U. S. A. 107, 10154-10159 (2010).
HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses. Yanai H, Ban T, Wang Z, Choi M K, Kawamura T, Negishi H, Nakasato M, Lu Y, Hangai S, Koshiba R, Savitsky D, Ronfani L, Akira S, Bianchi M E, Honda K, Tamura T, Kodama T, Taniguchi T. Nature 462, 99-103 (2009).
Inducible deposition of the histone variant H3.3 in interferon-stimulated genes. Tamura T, Smith M, Kanno T, Dasenbrock H, Nishiyama A, Ozato K. J. Biol. Chem. 284, 12217-1 2225 (2009).
Cell type-dependent proapoptotic role of Bcl2L12 revealed by a mutation concomitant with the disruption of the juxtaposed Irf3 gene. Nakajima A, Nishimura K, Nakaima Y, Oh T, Noguchi S, Taniguchi T, Tamura T. Proc. Natl. Acad. Sci. U. S. A. 106, 12448-12452 (2009).
The IRF family transcription factors in immunity and oncogenesis. Tamura T, Yanai H, Savitsky D, Taniguchi T. Annu. Rev. Immunol. 26, 535-584 (2008).
A cell-type-specific requirement for IFN regulatory factor 5 (IRF5) in Fas-induced apoptosis. Couzinet A, Tamura K, Chen H M, Nishimura K, Wang Z, Morishita Y, Takeda K, Yagita H, Yanai H, Taniguchi T, Tamura T. Proc. Natl. Acad. Sci. U. S. A. 105, 2556-2561 (2008).
Identification of target genes and a unique cis element regulated by IRF-8 in developing macrophages. Tamura T, Thotakura P, Tanaka T S, Ko M S, Ozato K. Blood 106, 1938-1947 (2005).
ICSBP directs bipotential myeloid progenitor cells to differentiate into mature macrophages. Tamura T, Nagamura-Inoue T, Shmeltzer Z, Kuwata T, Ozato K. Immunity 13, 155 -165 (2000).

川内 潤也

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 (2011).
Co-transcriptional RNA cleavage provides a failsafe termination mechanism for yeast RNA polymerase I. Braglia P, Kawauchi J, Proudfoot N J. Nucleic Acids Res. 39, 1439-1448 (2010).
Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Rondon A G, Mischo H E, Kawauchi J, Proudfoot N J. Mol. Cell 36, 88-98 (2009).
Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Kawauchi J, Mischo H, Braglia P, Rondon A, Proudfoot N J. Genes Dev. 1082-1092 (2008).
RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Jones H S, Kawauchi J, Braglia P, Alen C M, Kent N A, Proudfoot N J. Nature Struct. Mol. Biol. 14, 123-130 ( 2007).
Stress response gene ATF3 is a target of c-myc in serum-induced cell proliferation. Tamura K, Hua B, Adachi S, Guney I, Kawauchi J, Morioka M, Tamamori-Adachi M, Tanaka Y, Nakabeppu Y, Sunamori M, Sedivy J M, Kitajima S. EMBO J. 24, 2590-2601 (2005).

伊藤 敬

Methionine adenosyltransferase II serves as a transcriptional corepressor of Maf oncoprotein. Katoh Y, Ikura T, Hoshikawa Y, Tashiro S, Ito T, Ohta M, Kera Y, Noda T, Igarashi K. Mol. Cell 41, 554-566 (2011).
A histone chaperone, DEK, transcriptionally coactivates a nuclear receptor. Sawatsubashi S, Murata T, Lim J, Fujiki R, Ito S, Suzuki E, Tanabe M, Zhao Y, Kimura S, Fujiyama S, Ueda T, Umetsu D, Ito T, Takeyama K, Kato S. Genes Dev. 24, 159-170 (2010).
Transcriptional activation of polycomb-repressed genes by ZRF1. Richly H, Rocha-Viegas L, Ribeiro J D, Demajo S, Gundem G, Lopez-Bigas N, Nakagawa T, Rospert S, Ito T, Di Croce L. Nature 468, 1124-1128 (2010).
Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation. Nakagawa T, Kajitani T, Togo S, Masuko N , Ohdan H, Hishikawa Y, Koji T, Matsuyama T, Ikura T, Muramatsu M, Ito T. Genes Dev. 22, 37-49 (2008).
Regulation of histone acetylation and nucleosome assembly by transcription factor JDP2. Jin C, Kato K, Chimura T, Yamasaki T, Nakade K, Murata T, Li H, Pan J, Zhao M, Sun K , Chiu R, Ito T, Nagata K, Horikoshi M, Yokoyama K K. Nature Struct. Mol. Biol. 13, 331-338 (2006).
A histone code in meiosis: the histone kinase, NHK-1, is required for proper chromosomal architecture in Drosophila oocytes. Ivanovska I, Khandan T, Ito T, Orr-Weaver T L. Genes Dev. 19, 2571-2582 (2005).
Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo. Aihara H, Nakagawa T, Yasui K, Ohta T, Hirose S, Dhomae N, Takio K, Kaneko M, Takeshima Y, Muramatsu M, Ito T. Genes Dev. 18, 877-888 (2004).
The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome. Kitagawa H, Fujiki R, Yoshimura K, Mezaki Y, Uematsu Y, Matsui D, Ogawa S, Unno K, Okubo M, Tokita A, Nakagawa T, Ito T, Ishimi Y, Nagasawa H , Matsumoto T, Yanagisawa J, Kato S. Cell 113, 905-917 (2003).
p300-mediated acetylation facilitates the transfer of histone H2A-H2B dimers from nucleosomes to a histone chaperone. Ito T, Ikehara T, Nakagawa T, Kraus W L, Muramatsu M. Genes Dev. 14, 1899-1907 (2000).
ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-de pendent catalysis of chromatin assembly. Ito T, Levenstein M E, Fyodorov D V, Kutach A K, Kobayashi R, Kadonaga J T. Genes Dev. 13, 1529-1539 (1999).
ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Ito T, Bulger M, Pazin M J, Kobayashi R, Kadonaga J T. Cell 90, 145-155 (1997).

大熊 芳明

The HIRA complex subunit Hip3 plays important roles in the silencing of meiosis-specific genes in Schizosaccharomyces pombe. Mizuki F, Tanaka A, Hirose Y, Ohkuma Y. PLoS ONE 6, e19442 (2011).
Prolyl isomerase Pin1 shares functional similarity with phosphorylated CTD interacting factor PCIF1 in vertebrate cells. Yunokuchi I, Fan H, Iwamoto Y, Araki C, Yuda M, Umemura H, Harada F, Ohkuma Y, Hirose Y. Genes Cells 14, 1105-1118 (2009).
Central forkhead domain of human TFIIE beta plays a primary role in binding double-stranded DNA at transcription initiation. Tanaka A, Watanabe T, Iida Y, Hanaoka F, Ohkuma Y. Genes Cells 14, 395-405 (2009).
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. Okuda M, Tanaka A, Satoh M, Mizuta S, Takazawa M, Ohkuma Y, Nishimura Y. EMBO J. 27, 1161-1171 (2008).
A kinase subunit of the human mediator complex, CDK8, positively regulates transcriptional activation. Furumoto T, Tanaka A, Ito M, Malik S, Hirose Y, Hanaoka F, Ohkuma Y. Genes Cells 12, 119-132 (2007).
Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface. Okuda M, Watanabe Y, Okamura H, Hanaoka F, Ohkuma Y, Nishimura Y. EMBO J. 19, 1346-1356 (2000).
Regulation of TFIIH ATPase and kinase activities by TFIIE during active initiation complex formation. Ohkuma Y, Roeder R G. Nature 368, 160-163 (1994).

高橋 陽介

Alteration of substrate specificity: the variable N-terminal domain of tobacco Ca(2+)- dependent protein kinase is important for substrate recognition. Ito T, Nakata M, Fukazawa J, Ishida S, Takahashi Y. Plant Cell 22, 1592-1604 (2010).
The transcription factor RSG regulates negative feedback of NtGA20ox1 encoding GA 20-oxidase. Fukazawa J, Nakata M, Ito T, Yamaguchi S, Takahashi Y. Plant J. 62, 1035-1045 (2010).
CDPK1, a calcium-dependent protein kinase, regulates transcriptional activator RSG in response to gibberellins. Nakata M, Yuasa T, Takahashi Y, Ishida S. Plant Signal Behav. 4, 372-374 (2009).
Identification of negative cis-acting elements in response to copper in the chloroplastic iron superoxide dismutase gene of the moss Barbula unguiculata. Nagae M, Nakata M, Takahashi Y. Plant Physiol. 146, 1687-1696 (2008).
A tobacco calcium-dependent protein kinase, CDPK1, regulates the transcription factor REPRESSION OF SHOOT GROWTH in response to gibberellins. Ishida S, Yuasa T, Nakata M, Takahashi Y. Plant Cell 20, 3273-3288 (2008).
AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase. Matsushita A, Furumoto T, Ishida S, Takahashi Y. Plant Physiol. 143, 1152-1162 (2007).
Involvement of 14-3-3 signaling protein binding in the functional regulation of the transcriptional activator REPRESSION OF SHOOT GROWTH by gibberellins. Ishida S, Fukazawa J, Yuasa T, Takahashi Y. Plant Cell 16, 2641-2651 (2004).
14-3-3 proteins regulate intracellular localization of the bZIP transcriptional activator RSG. Igarashi D, Ishida S, Fukazawa J, Takahashi Y. Plant Cell 13, 2483-2497 (2001).
Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. Fukazawa J, Sakai T, Ishida S, Yamaguchi I , Kamiya Y, Takahashi Y. Plant Cell 12, 901-915 (2000).

緒方一博

Structural basis of Ets1 cooperative binding to palindromic sequences on stromelysin-1 promoter DNA. Babayeva N D, Wilder P J, Shiina M, Mino K, Desler M, Ogata K, Rizzino A, Tahirov T H. Cell Cycle 9, 3054-3062 (2010).
De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early infantile epileptic encephalopathy. Saitsu H, Kato M, Mizuguchi T, Hamada K, Osaka H, Tohyama J, Uruno K, Kumada S, Nishiyama K, Nishimura A, Okada I, Yoshimura Y, Hirai S, Kumada T, Hayasaka K, Fukuda A, Ogata K, Matsumoto N. Nature Genet. 40, 782-788 (2008).
Distant N- and C-terminal domains are required for intrinsic kinase activity of SMG-1, a critical component of nonsense-mediated mRNA decay. Morita T, Yamashita A, Kashima I, Ogata K, Ishiura S, Ohno S. J. Biol. Chem. 282, 7799-7808 (2007).
Cyclin-dependent kinase (CDK) phosphorylation destabilizes somatic Wee1 via multiple pathways. Watanabe N, Arai H, Iwasaki J, Shiina M, Ogata K, Hunter T, Osada H. Proc. Natl. Acad. Sci. U. S. A. 102, 11663-11668 (2005).
Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Ogata K, Sato K, Tahirov T H. Curr. Opin. Struct. Biol. 13, 40-48 (2003).
Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter. Tahirov T H, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K. Cell 108, 57-70 (2002).
Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta. Tahirov T H, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K. Cell 104, 755-767 (2001).
The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Ogata K, Kanei-Ishii C, Sasaki M, Hatanaka H, Nagadoi A, Enari M, Nakamura H, Nishimura Y, Ishii S, Sarai A. Nature Struct. Biol. 3, 178-187 (1996).
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb. Ogata K, Morikawa S, Nakamura H, Hojo H, Yoshimura S, Zhang R, Aimoto S, Ametani Y, Hirata Z, Sarai A, Ishii S, Nishimura Y. Nature Struct. Biol. 2, 309-320 (1995).
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y. Cell 79, 639-648 (1994).

松本 直通

Exome sequencing reveals a homozygous SYT14 mutation in adult-onset autosomal recessive spinocerebellar ataxia with psychomotor retardation. Doi H, Miyake N, Matsumoto N, et al. Am. J. Hum. Genet. 89, 320-327 (2011).
Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Ng S B, Matsumoto N, Bamshad M J, Shendure J, et al. Nature Genet. 42, 790-793 (2010).
Dominant-negative mutations in alpha-II spectrin cause West syndrome with severe cerebral hypomyelination, spastic quadriplegia, and developmental delay. Saitsu H, Miyake N , Matsumoto N, et al. Am. J. Hum. Genet. 86, 881-891 (2010).
Loss-of-function mutations of CHST14 in a new type of Ehlers-Danlos syndrome. Miyake N , Matsumoto N, et al. Hum. Mutat. 31, 966-974 (2010).
De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early infantile epileptic encephalopathy. Saitsu H, Matsumoto N, et al. Nature Genet. 40, 782-788 (2008).
Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome. Niihori T, Matsumoto N, Matsubara Y, et al. Nature Genet. 38, 294-296 (2006).
Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Visser R, Shimokawa O, Harada N, Kinoshita A , Ohta T, Niikawa N, Matsumoto N. Am. J. Hum. Genet. 76, 52-67 (2005).
Heterozygous TGFBR2 mutations in Marfan syndrome. Mizuguchi T, Matsumoto N, et al. Nature Genet. 36, 855-860 (2004).
Heterozygous mutations of the kinesin KIF21A in congenital fibrosis of the extraocular muscles type 1 (CFEOM1). Yamada K, Matsumoto N, Engle E C, et al. Nature Genet. 35, 318-321 (2003).
Haploinsufficiency of NSD1 causes Sotos syndrome. Kurotaki N, Matsumoto N, et al. Nature Genet. 30, 365-366 (2002).

三宅 紀子

Rapid detection of a mutation causing X-linked leukoencephalopathy by exome sequencing. Tsurusaki Y, Osaka H, Hamanoue H, Shimbo H, Tsuji M, Doi H, Saitsu H, Matsumoto N, Miyake N. J. Med. Genet. 48, 606-609 (2011).
CHN1 mutations are not a common cause of sporadic Duane's retraction syndrome. Miyake N, Andrews C, Fan W, He W, Chan W M, Engle E C. Am. J. Med. Genet. A 152A, 215-217 (2010).
Human CHN1 mutations hyperactivate alpha2-chimaerin and cause Duane's retraction syndrome. Miyake N, Engle E C, et al. Science 321, 839-843 (2008).
No detectable genomic aberrations by BAC array CGH in Kabuki make-up syndrome patients. Miyake N, Matsumoto N, et al. Am. J. Med. Genet. A 140, 291-293 (2006).
Four novel NIPBL mutations in Japanese patients with Cornelia de Lange syndrome. Miyake N, Visser R, Kinoshita A, Yoshiura K, Niikawa N, Kondoh T, Matsumoto N, Harada N, Okamoto N, Sonoda T, Naritomi K, Kaname T, Chinen Y, Tonoki H, Kurosawa K. Am. J. Med. Genet. A 135, 103-105 (2005).
Phenotype-genotype correlation in two patients with 12q proximal deletion. Miyake N, Tonoki H, Gallego M, Harada N, Shimokawa O, Yoshiura K, Ohta T, Kishino T, Niikawa N, Matsumoto N. J. Hum. Genet. 49, 282-284 (2004).
Preferential paternal origin of microdeletions caused by prezygotic chromosome or chromatid rearrangements in Sotos syndrome. Miyake N, Matsumoto N, et al. Am. J. Hum. Genet. 72, 1331-1337 (2003).

中村 春木

A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. Higo J, Nishimura Y, Nakamura H. J. Am. Chem. Soc. 133, 10448-10458 (2011).
Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle. Fukuda I, Yonezawa Y, Nakamura H. J. Chem. Phys. 134, 164107 (2011).
Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Ikebe J, Standley DM, Nakamura H, Higo H. Protein Science 20, 187-196 (2011).
HitPredict: a database of quality assessed protein-protein interactions in nine species. Patil A, Nakai K, Nakamura H. Nucleic Acids Res. 39, D744-D749 (2011).
Structure determination of a protein assembly by amino acid selective cross-saturation. Kanamori E, Igarashi S, Osawa M, Fukunishi Y, Shimada I, Nakamura H. Proteins 79, 179-190 (2011).
Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a. Takano Y, Nakamura H. J. Comput. Chem. 31, 954-962 (2010).
Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. Kinjo A R, Nakamura H. J. Mol. Biol. 399, 526-540 (2010).
Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water. Yonezawa Y, Nakata K, Sakakura K, Takada T, Nakamura H. J. Am. Chem. Soc. 131, 4535-4540 (2009).
Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Matsushita K, Takeuchi O, Standley D M, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S. Nature 458, 1185-1190 (2009).
Membrane attachment facilitates ligand access to the active site in monoamine oxidase A. Apostolov R, Yonezawa Y, Standley D M, Kikugawa G, Takano Y, Nakamura H. Biochemistry 48, 5864-5873 (2009).

皿井 明倫

Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. Ahmad S, Sarai A. BMC Struct. Biol. 11, 8 (2011).
Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines. Fernandez M, Ahmad S, Sarai A. J. Chem. Inf. Model 50, 1179-1188 (2010).
A generalized conformational energy function of DNA derived from molecular dynamics simulations. Yamasaki S, Terada T, Shimizu K, Kono H, Sarai A. Nucleic Acids Res. 37, e135 (2009).
Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast. Fernandez M, Fujii S, Kono H, Sarai A. Genome Inform. 23, 13-20 (2009).
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Arauzo-Bravo M J, Sarai A. Nucleic Acids Res. 36, 376-386 (2008).
Sequence-dependent DNA deformability studied using molecular dynamics simulations. Fujii S, Kono H, Takenaka S, Go N, Sarai A. Nucleic Acids Res. 35, 6063-6074 (2007).
Classification of protein-DNA complexes based on structural descriptors. Prabakaran P, Siebers J G, Ahmad S, Gromiha M M, Singarayan M G, Sarai A. Structure 14, 1355-1367 (2006).
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Ahmad S, Kono H, Arauzo-Bravo M J, Sarai A. Nucleic Acids Res. 34, W124-127 (2006).
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. Arauzo-Bravo M J, Fujii S, Kono H, Ahmad S, Sarai A. J. Am. Chem. Soc. 127, 16074-16089 (2005).
Protein-DNA recognition patterns and predictions. Sarai A, Kono H. Annu. Rev. Biophys. Biomol. Struct. 34, 379-398 (2005).

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.