Genomes and Genes
Experts and Doctors on humans in Mishima, Shizuoka, Japan
Locale: Mishima, Shizuoka, Japan
- Ohno M, Fukagawa T, Lee J, Ikemura T. Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies. Chromosoma. 2002;111:201-13 pubmed..Triplexes visualized differentially with distinct PuPy tract probes were associated spatially with centromeric sequences in the interphase nucleus in a sequence-specific manner. ..
- Itoh K, Kawasaki S, Kawamoto S, Seishima M, Chiba H, Michibata H, et al. Identification of differentially expressed genes in psoriasis using expression profiling approaches. Exp Dermatol. 2005;14:667-74 pubmed..These seven genes, which were reported to be related to apoptosis or antiproliferation, might have causal roles in pathophysiology in psoriasis. ..
- Yokomine T, Shirohzu H, Purbowasito W, Toyoda A, Iwama H, Ikeo K, et al. Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. Genome Res. 2005;15:154-65 pubmed..Our findings show that the imprinted genes were clustered before the emergence of imprinting and that the elements associated with imprinting probably evolved after the divergence of mammals and birds. ..
- Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 2009;37:D16-8 pubmed publisher..To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa sequencer. ..
- Yokomine T, Hata K, Tsudzuki M, Sasaki H. Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet Genome Res. 2006;113:75-80 pubmed..The acquisition of DNMT3L by a common ancestor of eutherians and marsupials might have been closely related to the evolution of imprinting...
- Fukagawa T, Mikami Y, Nishihashi A, Regnier V, Haraguchi T, Hiraoka Y, et al. CENP-H, a constitutive centromere component, is required for centromere targeting of CENP-C in vertebrate cells. EMBO J. 2001;20:4603-17 pubmed..These findings indicate that centromere assembly in vertebrate cells proceeds in a hierarchical manner in which localization of the centromere-specific histone CENP-A is an early event that occurs independently of CENP-C and CENP-H. ..
- Sumiyama K, Saitou N. Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1. Mol Biol Evol. 2011;28:3005-7 pubmed publisher..This result infers that loss of function in the HACNS1 81-bp region, possibly via a BGC, played an important role in human-specific evolution. ..
- Saga Y. The mechanism of somite formation in mice. Curr Opin Genet Dev. 2012;22:331-8 pubmed publisher..Particular attention is paid to the interplay between two the distinct signaling pathways of Notch and FGF and the Mesp2 transcription factor acting as an effector molecule during mouse somitogenesis. ..
- Shiina N, Tokunaga M. RNA granule protein 140 (RNG140), a paralog of RNG105 localized to distinct RNA granules in neuronal dendrites in the adult vertebrate brain. J Biol Chem. 2010;285:24260-9 pubmed publisher..These results suggest that RNG140 has roles in the maintenance of the dendritic structure in the adult vertebrate brain through localizing to a kind of RNA granules that are distinct from RNG105-containing granules...
- Nonomura K, Eiguchi M, Nakano M, Takashima K, Komeda N, Fukuchi S, et al. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L.). PLoS Genet. 2011;7:e1001265 pubmed publisher..This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species...
- Takata H, Nishijima H, Maeshima K, Shibahara K. The integrator complex is required for integrity of Cajal bodies. J Cell Sci. 2012;125:166-75 pubmed publisher..SMN and Sm proteins formed striking cytoplasmic granules. These findings demonstrate that the integrator complex is essential for snRNA maturation and Cajal body homeostasis. ..
- Nishino T, Takeuchi K, Gascoigne K, Suzuki A, Hori T, Oyama T, et al. CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Cell. 2012;148:487-501 pubmed publisher..These data suggest that the CENP-T-W-S-X complex forms a unique nucleosome-like structure to generate contacts with DNA, extending the "histone code" beyond canonical nucleosome proteins...
- Hirata H, Nanda I, van Riesen A, McMichael G, Hu H, Hambrock M, et al. ZC4H2 mutations are associated with arthrogryposis multiplex congenita and intellectual disability through impairment of central and peripheral synaptic plasticity. Am J Hum Genet. 2013;92:681-95 pubmed publisher..Our results highlight the importance of ZC4H2 for genetic testing of individuals presenting with ID plus muscle weakness and minor or major forms of AMC...
- Morita Y, Andersen P, Hotta A, Tsukahara Y, Sasagawa N, Hayashida N, et al. Sall1 transiently marks undifferentiated heart precursors and regulates their fate. J Mol Cell Cardiol. 2016;92:158-62 pubmed publisher..These findings provide fundamental insights into CPC maintenance, which can be instrumental for CPC-based regenerative medicine. ..
- Komiyama H, Aoki A, Tanaka S, Maekawa H, Kato Y, Wada R, et al. Alu-derived cis-element regulates tumorigenesis-dependent gastric expression of GASDERMIN B (GSDMB). Genes Genet Syst. 2010;85:75-83 pubmed..Reporter assays using intact, deleted, and mutated Alu elements clearly showed that this Alu element positively regulates GSDMB expression and that a putative IKZF binding motif in this element is crucial to upregulate GSDMB expression. ..
- Hara Y, Kimura A. Cell-size-dependent control of organelle sizes during development. Results Probl Cell Differ. 2011;53:93-108 pubmed publisher..Understanding the cell-size dependency of organelle sizes is expected to impact not only on the morphogenesis of the individual organelle, but also on cell homeostasis, cell cycle progression, and cell differentiation. ..
- Ayusawa D, Kaneda S, Itoh Y, Yasuda H, Murakami Y, Sugasawa K, et al. Complementation by a cloned human ubiquitin-activating enzyme E1 of the S-phase-arrested mouse FM3A cell mutant with thermolabile E1. Cell Struct Funct. 1992;17:113-22 pubmed..Relevance of the unusually high incidence of the temperature-sensitive E1 mutation was discussed in terms of the E1 as a determinant of heat tolerance of cells. ..
- Amano M, Suzuki A, Hori T, Backer C, Okawa K, Cheeseman I, et al. The CENP-S complex is essential for the stable assembly of outer kinetochore structure. J Cell Biol. 2009;186:173-82 pubmed publisher..In addition, we found that intrakinetochore distance was increased in CENP-S- and CENP-X-deficient cells. These results suggest that the CENP-S complex is essential for the stable assembly of the outer kinetochore. ..
- Hori T, Amano M, Suzuki A, Backer C, Welburn J, Dong Y, et al. CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell. 2008;135:1039-52 pubmed publisher..In total, our results suggest that the CENP-T/CENP-W complex is directly involved in establishment of centromere chromatin structure coordinately with CENP-A. ..
- Ito K, Kawasaki T, Takashima S, Matsuda I, Aiba A, Hirata T. Semaphorin 3F confines ventral tangential migration of lateral olfactory tract neurons onto the telencephalon surface. J Neurosci. 2008;28:4414-22 pubmed publisher..These results reveal that semaphorin 3F is an important regulator of the ventral tangential migration stream, confining the migrating neurons on the telencephalon surface by repelling from the deeper domain. ..
- Nozaki T, Imai R, Tanbo M, Nagashima R, Tamura S, Tani T, et al. Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. Mol Cell. 2017;67:282-293.e7 pubmed publisher..Notably, we observed the domains during mitosis, suggesting that they act as building blocks of chromosomes and may serve as information units throughout the cell cycle. ..
- Kagoshima H, Nimmo R, Saad N, Tanaka J, Miwa Y, Mitani S, et al. The C. elegans CBFbeta homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal. Development. 2007;134:3905-15 pubmed..These studies provide new insights into the function and regulation of this important cancer-associated DNA-binding complex in stem cells and support the view that Runx/CBFbeta factors have oncogenic potential. ..
- Tsunoyama K, Gojobori T. Evolution of nicotinic acetylcholine receptor subunits. Mol Biol Evol. 1998;15:518-27 pubmed..Thus, the window analysis of the f values is useful for evaluating the degree of functional constraints in not only the entire gene region, but also the within-gene subregion. ..
- Sumiyama K, Kitano T, Noda R, Ferrell R, Saitou N. Gene diversity of chimpanzee ABO blood group genes elucidated from exon 7 sequences. Gene. 2000;259:75-9 pubmed..We also estimated nucleotide diversities for common chimpanzee and bonobo ABO blood group genes, and these values were 0.4% and 0.2%, respectively. These values are higher than that of most human genes...
- Kitano T, Liu Y, Ueda S, Saitou N. Human-specific amino acid changes found in 103 protein-coding genes. Mol Biol Evol. 2004;21:936-44 pubmed publisher..These results suggest that a small proportion of protein-coding genes started to evolve differently in the human lineage after it diverged from the ape lineage...
- Hihara S, Pack C, Kaizu K, Tani T, Hanafusa T, Nozaki T, et al. Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell Rep. 2012;2:1645-56 pubmed publisher..Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information. ..
- Sumiyama K, Saitou N, Ueda S. Adaptive evolution of the IgA hinge region in primates. Mol Biol Evol. 2002;19:1093-9 pubmed
- ..This review presents discussion of the latest structural and functional data on CENP-A and CENPs from the CCAN as well as their interaction with the KMN network. ..
- Ohta T. Evolution of gene families. Gene. 2000;259:45-52 pubmed..Positive selection is necessary for the evolution of novel functions. However, many examples of current gene families suggest that both drift and selection are at work on their evolution. ..
- Shiina N, Shinkura K, Tokunaga M. A novel RNA-binding protein in neuronal RNA granules: regulatory machinery for local translation. J Neurosci. 2005;25:4420-34 pubmed..These findings suggest that RNG105 is a translational repressor in the RNA granules and provide insight into the link between RNG105 dynamics and local translational regulation. ..
- Ogawa Y, Ono T, Wakata Y, Okawa K, Tagami H, Shibahara K. Histone variant macroH2A1.2 is mono-ubiquitinated at its histone domain. Biochem Biophys Res Commun. 2005;336:204-9 pubmed..2 and histone H2A has similar or synergistic implications, but that the multiple ubiquitination sites in macroH2A1.2 might confer a variety of functions upon macroH2A1.2 to modulate chromatin states. ..
- Rodriguez Bravo V, Maciejowski J, Corona J, Buch H, Collin P, Kanemaki M, et al. Nuclear pores protect genome integrity by assembling a premitotic and Mad1-dependent anaphase inhibitor. Cell. 2014;156:1017-31 pubmed publisher..A heterologous Mad1-NPC tether restored Cdc20 inhibitor production and normal MÂ phase control. We conclude that nuclear pores and kinetochores both emit "wait anaphase" signals that preserve genome integrity. ..
- Tamura M, Tanaka S, Fujii T, Aoki A, Komiyama H, Ezawa K, et al. Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. Genomics. 2007;89:618-29 pubmed..Further database searching revealed the presence of other related genes with a similar N-terminal motif. These results suggest that the Gsdm family and related genes have evolved divergent epithelial expression profiles. ..
- Kitano T, Sumiyama K, Shiroishi T, Saitou N. Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene. Biochem Biophys Res Commun. 1998;249:78-85 pubmed..Some peaks where nonsynonymous substitutions are higher than synonymous ones were located on outer membrane regions. This suggests the existence of positive Darwinian selection on Rh and Rh50 genes through host-parasite interactions. ..
- Natsume T, Kiyomitsu T, Saga Y, Kanemaki M. Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors. Cell Rep. 2016;15:210-218 pubmed publisher..This approach should greatly facilitate the functional analysis of essential proteins, particularly those of previously unknown function. ..
- Natsume T, Nishimura K, Minocherhomji S, Bhowmick R, Hickson I, Kanemaki M. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis. Genes Dev. 2017;31:816-829 pubmed publisher..We propose that stalled replication forks can be restarted in S phase via homologous recombination using MCM8-9 as an alternative replicative helicase. ..
- Ishihara K, Sasaki H. An evolutionarily conserved putative insulator element near the 3' boundary of the imprinted Igf2/H19 domain. Hum Mol Genet. 2002;11:1627-36 pubmed..Together with the findings on the differentially methylated CTCF sites 5' to H19, CTCF-dependent insulators may not only regulate but also delimit the imprinted domain. ..
- Osada N, Akashi H. Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex. Mol Biol Evol. 2012;29:337-46 pubmed publisher..This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution. ..
- Ogino K, Ramsden S, Keib N, Schwarz G, Harvey R, Hirata H. Duplicated gephyrin genes showing distinct tissue distribution and alternative splicing patterns mediate molybdenum cofactor biosynthesis, glycine receptor clustering, and escape behavior in zebrafish. J Biol Chem. 2011;286:806-17 pubmed publisher..These data indicate that duplicated gephyrin genes mediate Moco biosynthesis and control postsynaptic clustering of GlyRs, thereby mediating key escape behaviors in zebrafish. ..
- Jinam T, Saitou N, Edo J, Mahmood A, Phipps M. Molecular analysis of HLA Class I and Class II genes in four indigenous Malaysian populations. Tissue Antigens. 2010;75:151-8 pubmed publisher..These results showed the scope of HLA diversity in these indigenous minority groups and may prove beneficial for future disease association, anthropological and forensic studies. ..
- Kokubo H, Miyagawa Tomita S, Johnson R. Hesr, a mediator of the Notch signaling, functions in heart and vessel development. Trends Cardiovasc Med. 2005;15:190-4 pubmed..This review highlights the many functions of the hesr gene family in heart and vessel development. ..
- Minoshima Y, Hori T, Okada M, Kimura H, Haraguchi T, Hiraoka Y, et al. The constitutive centromere component CENP-50 is required for recovery from spindle damage. Mol Cell Biol. 2005;25:10315-28 pubmed..We also observed severe mitotic defects in CENP-50-deficient cells with apparent premature sister chromatid separation when the mitotic checkpoint was activated, indicating that CENP-50 is required for recovery from spindle damage. ..
- Okada M, Cheeseman I, Hori T, Okawa K, McLeod I, Yates J, et al. The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol. 2006;8:446-57 pubmed
- Shirohzu H, Kubota T, Kumazawa A, Sado T, Chijiwa T, Inagaki K, et al. Three novel DNMT3B mutations in Japanese patients with ICF syndrome. Am J Med Genet. 2002;112:31-7 pubmed..This is the first missense mutation mapped to the N-terminal half of the protein, suggesting that the region plays an important role in the regulation of the DNMT3B enzyme. ..
- Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol. 2004;6:784-91 pubmed..We conclude that Dicer-related RNA interference machinery is involved in the formation of the heterochromatin structure in higher vertebrate cells. ..
- Ishihara K, Hatano N, Furuumi H, Kato R, Iwaki T, Miura K, et al. Comparative genomic sequencing identifies novel tissue-specific enhancers and sequence elements for methylation-sensitive factors implicated in Igf2/H19 imprinting. Genome Res. 2000;10:664-71 pubmed..Our results demonstrate that comparative genomic sequencing is highly efficient in identifying regulatory elements. ..
- Takemaru K, Harashima S, Ueda H, Hirose S. Yeast coactivator MBF1 mediates GCN4-dependent transcriptional activation. Mol Cell Biol. 1998;18:4971-6 pubmed..These findings indicate that the coactivator MBF1 functions by recruiting TBP to promoters where DNA-binding regulators are bound. ..
- Yabe T, Suzuki N, Furukawa T, Ishihara T, Katsura I. Multidrug resistance-associated protein MRP-1 regulates dauer diapause by its export activity in Caenorhabditis elegans. Development. 2005;132:3197-207 pubmed..Thus, MRP-1, through its export activity, supports the induction of the normal (non-dauer) life cycle by the insulin signaling pathway. ..
- Koike Kumagai M, Yasunaga K, Morikawa R, Kanamori T, Emoto K. The target of rapamycin complex 2 controls dendritic tiling of Drosophila sensory neurons through the Tricornered kinase signalling pathway. EMBO J. 2009;28:3879-92 pubmed publisher..These findings suggest that TORC2 likely acts together with the Trc signalling pathway to regulate the dendritic tiling of class IV da neurons, and thus uncover the first neuronal function of TORC2 in vivo. ..
- Sagai T, Koide T, Endo M, Tanoue K, Kikkawa Y, Yonekawa H, et al. rim2 (recombination-induced mutation 2) is a new allele of pearl and a mouse model of human Hermansky-Pudlak syndrome (HPS): genetic and physical mapping. Mamm Genome. 1998;9:2-7 pubmed..Thus, rim2 appeared to be a new allele of the pe locus and serves as a mouse model for human HPS. We have made a YAC contig covering the rim2/pe locus toward positional cloning of the causative gene. ..
- Kagoshima H, Shigesada K, Kohara Y. RUNX regulates stem cell proliferation and differentiation: insights from studies of C. elegans. J Cell Biochem. 2007;100:1119-30 pubmed..In this review, we will outline these new findings and discuss their general implications in the mechanism of coordination between proliferation and differentiation of stem cells. ..
- Li F, Takemaru K, Goto M, Ueda H, Handa H, Hirose S. Transcriptional activation through interaction of MBF2 with TFIIA. Genes Cells. 1997;2:143-53 pubmed..MBF2 activates transcription through its interaction with TFIIA. Selective transcriptional activation occurs when MBF2 is recruited to a promoter carrying the FTZ-F1 binding site by FTZ-F1 and MBF1. ..