Experts and Doctors on molecular sequence data in Mishima, Shizuoka, Japan


Locale: Mishima, Shizuoka, Japan
Topic: molecular sequence data

Top Publications

  1. Jishage M, Ishihama A. A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A. 1998;95:4953-8 pubmed
    ..The isolated Rsd inhibited transcription in vitro to various extents depending on the promoters used. We propose that Rsd is a stationary phase E. coli protein with regulatory activity of the sigma70 function...
  2. Kitano T, Saitou N. Evolutionary history of the Rh blood group-related genes in vertebrates. Immunogenetics. 2000;51:856-62 pubmed
    ..Both groups contain genes from three domains (bacteria, archaea, and eukaryota). The Rh blood group and related genes are separated from both amt alpha and beta groups. ..
  3. 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. ..
  4. 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...
  5. Kitano T, Noda R, Takenaka O, Saitou N. Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis. Mol Phylogenet Evol. 2009;51:465-71 pubmed publisher
    ..This establishes the coexistence of divergent allelic lineages of the ABO blood group gene for a long period in the ancestral gibbon species, and strengthens the non-neutral evolution for this gene. ..
  6. Ito Y, Hirochika H, Kurata N. Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice. Gene. 2002;288:41-7 pubmed
    ..These results suggest that the expression of the alternative transcripts is organ-specific, and their products have different degrees of abilities for activation or repression of transcription. ..
  7. Yamamoto K, Ogasawara H, Fujita N, Utsumi R, Ishihama A. Novel mode of transcription regulation of divergently overlapping promoters by PhoP, the regulator of two-component system sensing external magnesium availability. Mol Microbiol. 2002;45:423-38 pubmed
    ..The PhoP box is located between -46 and -30 with respect to treRP3, and the alpha CTD is needed for this repression. ..
  8. Tanaka S, Miura I, Yoshiki A, Kato Y, Yokoyama H, Shinogi A, et al. Mutations in the helix termination motif of mouse type I IRS keratin genes impair the assembly of keratin intermediate filament. Genomics. 2007;90:703-11 pubmed
    ..These results suggest that the helix termination motif is essential for the proper assembly of types I and II IRS keratin protein complexes and the formation of keratin intermediate filaments. ..
  9. Hayakawa E, Takahashi T, Nishimiya Fujisawa C, Fujisawa T. A novel neuropeptide (FRamide) family identified by a peptidomic approach in Hydra magnipapillata. FEBS J. 2007;274:5438-48 pubmed publisher
    ..In contrast, FRamide-2 evoked body column contraction. These results suggest that both of the neuropeptides directly act on epithelial cells as neurotransmitters and regulate body movement in an axial direction...

More Information


  1. Sagai T, Masuya H, Tamura M, Shimizu K, Yada Y, Wakana S, et al. Phylogenetic conservation of a limb-specific, cis-acting regulator of Sonic hedgehog ( Shh). Mamm Genome. 2004;15:23-34 pubmed
    ..Absence of the conserved sequence in limbless reptiles and amphibians and a cis- trans test using the Hx and Shh KO alleles suggest that the sequence is a cis-acting regulator that controls the polarized expression of Shh...
  2. 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. ..
  3. Hirata H, Wen H, Kawakami Y, Naganawa Y, Ogino K, Yamada K, et al. Connexin 39.9 protein is necessary for coordinated activation of slow-twitch muscle and normal behavior in zebrafish. J Biol Chem. 2012;287:1080-9 pubmed publisher
    ..9 facilitates the spreading of neuronal inputs, which is irregular during motor development, beyond the muscle cells and that gap junctions play an essential role in the efficient recruitment of slow muscle fibers. ..
  4. Hara H, Yamamoto Y, Higashitani A, Suzuki H, Nishimura Y. Cloning, mapping, and characterization of the Escherichia coli prc gene, which is involved in C-terminal processing of penicillin-binding protein 3. J Bacteriol. 1991;173:4799-813 pubmed
    ..The mutation resulted in greatly reduced heat shock response at low osmolarity and in leakage of periplasmic proteins. ..
  5. Kubo T, Takashi T, Ashikari M, Yoshimura A, Kurata N. Two Tightly Linked Genes at the hsa1 Locus Cause Both F1 and F2 Hybrid Sterility in Rice. Mol Plant. 2016;9:221-232 pubmed publisher
    ..We propose a simple genetic model to explain how a single causal mechanism can drive both F1 and F2 hybrid sterility. ..
  6. Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K. Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection. Genetics. 2013;195:1027-35 pubmed publisher
    ..Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome. ..
  7. 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...
  8. Take uchi M, Kobayashi Y, Kimura K, Ishihara T, Katsura I. FLR-4, a novel serine/threonine protein kinase, regulates defecation rhythm in Caenorhabditis elegans. Mol Biol Cell. 2005;16:1355-65 pubmed
    ..Thus, a novel protein kinase with a unique structural feature acts in the intestine to increase the length of defecation cycle periods. ..
  9. Susa M, Kubori T, Shimamoto N. A pathway branching in transcription initiation in Escherichia coli. Mol Microbiol. 2006;59:1807-17 pubmed
    ..Consistently, decrease in the level of the GreA in an anaerobic stationary condition accompanied a decrease in the levels of transcripts of these genes. ..
  10. Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993;12:625-30 pubmed
    ..The katF gene product, a stationary phase-specific sigma factor, was not required for the expression of rmf. Disruption of rmf resulted in loss of ribosome dimers and reduction of cell viability during stationary phase. ..
  11. Seino H, Kishi T, Nishitani H, Yamao F. Two ubiquitin-conjugating enzymes, UbcP1/Ubc4 and UbcP4/Ubc11, have distinct functions for ubiquitination of mitotic cyclin. Mol Cell Biol. 2003;23:3497-505 pubmed
  12. Ozoline O, Fujita N, Ishihama A. Mode of DNA-protein interaction between the C-terminal domain of Escherichia coli RNA polymerase alpha subunit and T7D promoter UP element. Nucleic Acids Res. 2001;29:4909-19 pubmed
  13. Fujimoto R, Kinoshita Y, Kawabe A, Kinoshita T, Takashima K, Nordborg M, et al. Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet. 2008;4:e1000048 pubmed publisher
    ..The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed. ..
  14. Takahashi A, Takahashi K, Ueda R, Takano Shimizu T. Natural variation of ebony gene controlling thoracic pigmentation in Drosophila melanogaster. Genetics. 2007;177:1233-7 pubmed
    ..It was found to be the difference in expression level of ebony, which codes for an enzyme in the melanin-synthesis pathway and has pleiotropic effects on vision and behavior. ..
  15. 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
  16. Kotani T, Nagayoshi S, Urasaki A, Kawakami K. Transposon-mediated gene trapping in zebrafish. Methods. 2006;39:199-206 pubmed
    ..Here, we describe how we performed the gene trap screen and characterized the gene trap insertions and will discuss the outcome of the pilot screen. ..
  17. 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. ..
  18. Shimada M, Hayakawa S, Humle T, Fujita S, Hirata S, Sugiyama Y, et al. Mitochondrial DNA genealogy of chimpanzees in the Nimba mountains and Bossou, West Africa. Am J Primatol. 2004;64:261-75 pubmed
    ..This suggests that the Bossou-Nimba populations derived only recently from the common ancestral population of the West African chimpanzees, and did not pass through a bottleneck. ..
  19. Mitobe J, Mitsuzawa H, Ishihama A. Functional analysis of RNA polymerase II Rpb3 mutants of the fission yeast Schizosaccharomyces pombe. Curr Genet. 2001;39:210-21 pubmed
    ..We propose that both terminal regions (A and D) play important roles in RNA polymerase assembly, while the central portion (regions B and C) is involved in activated transcription. ..
  20. Nonomura K, Nakano M, Murata K, Miyoshi K, Eiguchi M, Miyao A, et al. An insertional mutation in the rice PAIR2 gene, the ortholog of Arabidopsis ASY1, results in a defect in homologous chromosome pairing during meiosis. Mol Genet Genomics. 2004;271:121-9 pubmed publisher
    ..The study also suggested the possibility that a highly homologous copy of the PAIR2 gene located on a different chromosome is in fact a pseudogene...
  21. Kobayashi M, Aita N, Hayashi S, Okada K, Ohta T, Hirose S. DNA supercoiling factor localizes to puffs on polytene chromosomes in Drosophila melanogaster. Mol Cell Biol. 1998;18:6737-44 pubmed
    ..Upon heat treatment of larvae, the staining on the endogenous puffs disappeared, and strong staining appeared on heat shock puffs. These results implicate SCF in gene expression. ..
  22. Shirayoshi Y, Yuasa Y, Suzuki T, Sugaya K, Kawase E, Ikemura T, et al. Proto-oncogene of int-3, a mouse Notch homologue, is expressed in endothelial cells during early embryogenesis. Genes Cells. 1997;2:213-24 pubmed
  23. Mizuno K, Koide T, Sagai T, Moriwaki K, Shiroishi T. Molecular analysis of a recombinational hotspot adjacent to Lmp2 gene in the mouse MHC: fine location and chromatin structure. Mamm Genome. 1996;7:490-6 pubmed
    ..cerevisiae, in which hotspots are always associated with DHSSs. ..
  24. Ishiguro A, Nogi Y, Hisatake K, Muramatsu M, Ishihama A. The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol Cell Biol. 2000;20:1263-70 pubmed
    ..Taken together, the results lead us to propose that Rpb6 plays a role in the interaction between RNA polymerase II and the transcription elongation factor TFIIS. ..
  25. Miyao T, Yasui K, Sakurai H, Yamagishi M, Ishihama A. Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit-subunit contact network involving Rpb5. Genes Cells. 1996;1:843-54 pubmed
    ..Rpb3 and Rpb5, the putative subunits of RNA polymerase II, associate each other to form binary complexes. These two subunits also bind to the two large subunits, Rpb1 and Rpb2, independently. ..
  26. Tak Y, Tanaka Y, Endo S, Kamimura Y, Araki H. A CDK-catalysed regulatory phosphorylation for formation of the DNA replication complex Sld2-Dpb11. EMBO J. 2006;25:1987-96 pubmed
    ..Finally, we argue that this novel mechanism sets a threshold of CDK activity for formation of the essential Sld2 to Dpb11 complex and therefore prevents premature DNA replication. ..
  27. Osaka F, Seino H, Seno T, Yamao F. A ubiquitin-conjugating enzyme in fission yeast that is essential for the onset of anaphase in mitosis. Mol Cell Biol. 1997;17:3388-97 pubmed
  28. 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...
  29. Oginuma M, Hirata T, Saga Y. Identification of presomitic mesoderm (PSM)-specific Mesp1 enhancer and generation of a PSM-specific Mesp1/Mesp2-null mouse using BAC-based rescue technology. Mech Dev. 2008;125:432-40 pubmed publisher
    ..This successfully rescued gastrulation defects due to the lack of the early mesoderm in the dKO mouse and we thereby obtained a PSM-specific Mesp1/Mesp2-null mouse showing a lack of segmented somites. ..
  30. Fujiwara M, Ishihara T, Katsura I. A novel WD40 protein, CHE-2, acts cell-autonomously in the formation of C. elegans sensory cilia. Development. 1999;126:4839-48 pubmed
    ..Expression of che-2 in a che-2 mutant under a heat shock promoter showed that the extension of cilia, surprisingly, can occur even at the adult stage, and that such cilia can function apparently normally in behavior. ..
  31. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008;453:539-43 pubmed publisher
    ..Our results reveal a role for endogenous siRNAs in mammalian oocytes and show that organisms lacking RdRP activity can produce functional endogenous siRNAs from naturally occurring dsRNAs. ..
  32. Urasaki A, Asakawa K, Kawakami K. Efficient transposition of the Tol2 transposable element from a single-copy donor in zebrafish. Proc Natl Acad Sci U S A. 2008;105:19827-32 pubmed publisher
    ..Our present study demonstrates that the in vivo Tol2 transposition system is useful for creating genome-wide insertions from a single-copy donor and should facilitate functional genomics and transposon biology in vertebrates. ..
  33. Uchida K, Koopman P, Mita A, Wakana S, Wright E, Kikkawa Y, et al. Exclusion of Sox9 as a candidate for the mouse mutant tail-short. Mamm Genome. 1996;7:481-5 pubmed
    ..8 +/- 0.011 cM. Six microsatellite markers were co-localized to the Ts locus, providing reagents for positional cloning of Ts. ..
  34. Harafuji N, Takahashi T, Hatta M, Tezuka H, Morishita F, Matsushima O, et al. Enhancement of foot formation in Hydra by a novel epitheliopeptide, Hym-323. Development. 2001;128:437-46 pubmed
    ..Lateral transplantation experiments indicated that the foot activation potential was increased in the peptide-treated tissue. These results suggest that Hym-323 is a peptide involved in a foot-patterning process in Hydra. ..
  35. Azam T, Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem. 1999;274:33105-13 pubmed
  36. Mizuta Y, Harushima Y, Kurata N. Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A. 2010;107:20417-22 pubmed publisher
    ..rufipogon, and that the DPL2 gene defect is specific to japonica cultivars. ..
  37. Sakurai H, Mitsuzawa H, Kimura M, Ishihama A. The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Mol Cell Biol. 1999;19:7511-8 pubmed
    ..However, S. pombe Rpb4 is closer in certain molecular functions to S. cerevisiae RPB4 than the eukaryotic RPB4 homologues. ..
  38. Liu Q, Jindra M, Ueda H, Hiromi Y, Hirose S. Drosophila MBF1 is a co-activator for Tracheae Defective and contributes to the formation of tracheal and nervous systems. Development. 2003;130:719-28 pubmed
    ..These data demonstrate a crucial role of MBF1 in the development of tracheae and central nervous system. ..
  39. Mitobe J, Mitsuzawa H, Yasui K, Ishihama A. Isolation and characterization of temperature-sensitive mutations in the gene (rpb3) for subunit 3 of RNA polymerase II in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet. 1999;262:73-84 pubmed
    ..We conclude that the majority of rpb3 mutations affect the assembly of Rpb3, even though their effects on subunit assembly vary depending on the location of the mutation considered. ..
  40. Kondo S, Ueda R. Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics. 2013;195:715-21 pubmed publisher
    ..3-23%. Our method is readily scalable to high-throughput gene targeting, thereby accelerating comprehensive functional annotation of the Drosophila genome. ..
  41. Higashitani A, Higashitani N, Horiuchi K. A cell division inhibitor SulA of Escherichia coli directly interacts with FtsZ through GTP hydrolysis. Biochem Biophys Res Commun. 1995;209:198-204 pubmed
    ..The complex is formed in a molar ratio of approximately one to one of the two proteins. It is likely that the complex formation represents the in vivo mechanism by which SulA inhibits cell division...
  42. Kanno Y, Tamura M, Chuma S, Sakura T, Machida T, Nakatsuji N. A cystatin-related gene, testatin/cresp, shows male-specific expression in germ and somatic cells from the initial stage of murine gonadal sex-differentiation. Int J Dev Biol. 1999;43:777-84 pubmed
  43. Andachi Y. Caenorhabditis elegans T-box genes tbx-9 and tbx-8 are required for formation of hypodermis and body-wall muscle in embryogenesis. Genes Cells. 2004;9:331-44 pubmed
    ..Together, these data indicate that tbx-9 and tbx-8 do not only contribute individually to formation of the hypodermis and body-wall muscle, but also suggests functional redundancy between tbx-9 and tbx-8 in embryonic morphogenesis. ..
  44. Tanaka S, Nakato R, Katou Y, Shirahige K, Araki H. Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing. Curr Biol. 2011;21:2055-63 pubmed publisher
    ..Additionally, an increased dosage of DDK also allows the late-firing origins to fire earlier. The DDK-dependent limited association between origins and Sld3-Sld7-Cdc45 is a key step for determining the timing of origin firing. ..
  45. Mochizuki K, Sano H, Kobayashi S, Nishimiya Fujisawa C, Fujisawa T. Expression and evolutionary conservation of nanos-related genes in Hydra. Dev Genes Evol. 2000;210:591-602 pubmed
    ..Thus, the function of nanos-related genes in the germline appears to be well conserved from primitive to highly evolved metazoans. ..
  46. Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, et al. A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell. 2007;19:2583-94 pubmed
  47. Mitsuzawa H, Ishihama A. Identification of histone H4-like TAF in Schizosaccharomyces pombe as a protein that interacts with WD repeat-containing TAF. Nucleic Acids Res. 2002;30:1952-8 pubmed
    ..These results indicate that the C-terminal region of spTAF72, which largely consists of WD repeats, interacts with spTAF50 in the TFIID and SAGA-like complexes, suggesting a role for the WD repeat domain in the interaction between TAFs. ..
  48. Oishi A, Gengyo Ando K, Mitani S, Mohri Shiomi A, Kimura K, Ishihara T, et al. FLR-2, the glycoprotein hormone alpha subunit, is involved in the neural control of intestinal functions in Caenorhabditis elegans. Genes Cells. 2009;14:1141-54 pubmed publisher
    ..These results are informative to studies of glycoprotein hormone signaling in higher animals. ..
  49. 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...
  50. Miyoshi K, Ahn B, Kawakatsu T, Ito Y, Itoh J, Nagato Y, et al. PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. Proc Natl Acad Sci U S A. 2004;101:875-80 pubmed publisher
    ..The expression pattern and mutant phenotype suggest that the PLA1 gene acting in developing leaf primordia affects the timing of successive leaf initiation and the termination of vegetative growth...
  51. Miyoshi K, Ito Y, Serizawa A, Kurata N. OsHAP3 genes regulate chloroplast biogenesis in rice. Plant J. 2003;36:532-40 pubmed
    ..These results suggest that one or more OsHAP3 genes regulate the expression of nuclear-encoded chloroplast-targeted genes and normal development of chloroplasts...
  52. Nonomura K, Nakano M, Fukuda T, Eiguchi M, Miyao A, Hirochika H, et al. The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in meiosis. Plant Cell. 2004;16:1008-20 pubmed publisher
    ..These observations clarify that the PAIR1 protein plays an essential role in establishment of homologous chromosome pairing in rice meiosis...
  53. Mitsuzawa H, Kanda E, Ishihama A. Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res. 2003;31:4696-701 pubmed
    ..The role for Rpb7 is consistent with its location in the pol II complex determined by recent structural studies. ..
  54. Kawakami K, Takeda H, Kawakami N, Kobayashi M, Matsuda N, Mishina M. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev Cell. 2004;7:133-44 pubmed
    ..We propose our gene trap approach should facilitate studies of vertebrate development and organogenesis. ..
  55. Tabara H, Hill R, Mello C, Priess J, Kohara Y. pos-1 encodes a cytoplasmic zinc-finger protein essential for germline specification in C. elegans. Development. 1999;126:1-11 pubmed
  56. Tsuda K, Ito Y, Sato Y, Kurata N. Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice. Plant Cell. 2011;23:4368-81 pubmed publisher
    ..Thus, the maintenance of the indeterminate state mediated by positive autoregulation of a KNOX gene is an indispensable mechanism of self-maintenance of the SAM. ..
  57. Jishage M, Dasgupta D, Ishihama A. Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase. J Bacteriol. 2001;183:2952-6 pubmed
  58. Shang W, Hori T, Toyoda A, Kato J, Popendorf K, Sakakibara Y, et al. Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences. Genome Res. 2010;20:1219-28 pubmed publisher
  59. Saze H, Kakutani T. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. 2007;26:3641-52 pubmed
    ..We discuss possible molecular mechanisms and the evolutionary implications of transposon-mediated epigenetic changes in the BNS locus. ..
  60. Sadaie Y, Takamatsu H, Nakamura K, Yamane K. Sequencing reveals similarity of the wild-type div+ gene of Bacillus subtilis to the Escherichia coli secA gene. Gene. 1991;98:101-5 pubmed
    ..subtilis. Since both genes are similar in their functions and deduced aa sequences, we propose that the div+ gene is the counterpart of the secA gene of E. coli. ..
  61. Watanabe T, Honda A, Iwata A, Ueda S, Hibi T, Ishihama A. Isolation from tobacco mosaic virus-infected tobacco of a solubilized template-specific RNA-dependent RNA polymerase containing a 126K/183K protein heterodimer. J Virol. 1999;73:2633-40 pubmed
    ..We propose that the TMV RNA polymerase for minus-strand RNA synthesis is composed of one molecule each of the 183- and 126-kDa proteins, possibly together with two or more host proteins. ..
  62. Makino S, Masuya H, Ishijima J, Yada Y, Shiroishi T. A spontaneous mouse mutation, mesenchymal dysplasia (mes), is caused by a deletion of the most C-terminal cytoplasmic domain of patched (ptc). Dev Biol. 2001;239:95-106 pubmed
  63. Ito Y, Chujo A, Eiguchi M, Kurata N. Radial axis differentiation in a globular embryo is marked by HAZ1, a PHD-finger homeobox gene of rice. Gene. 2004;331:9-15 pubmed
    ..Radial axis differentiation marked by HAZ1 is then collapsed dynamically along with embryo morphogenesis, and HAZ1 later marks the ventral surface of the embryo. ..
  64. Satta Y, Takahata N. Evolution of Drosophila mitochondrial DNA and the history of the melanogaster subgroup. Proc Natl Acad Sci U S A. 1990;87:9558-62 pubmed
    ..simulans. Yet geographic isolation is so weak as to show no evidence for further speciation. Moreover, one type of mtDNA shared by D. simulans and D. mauritiana suggests either recent divergence or ongoing introgression. ..
  65. 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. ..
  66. Fukami Kobayashi K, Tateno Y, Nishikawa K. Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol. 2003;20:267-77 pubmed
  67. 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. ..
  68. Matakatsu H, Tadokoro R, Gamo S, Hayashi S. Repression of the wing vein development in Drosophila by the nuclear matrix protein plexus. Development. 1999;126:5207-16 pubmed
    ..Plexus may regulate transcription of vein-and intervein-specific genes by tethering transcriptional regulators to specific locations in the nucleus. ..
  69. Fujita N, Endo S, Ishihama A. Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase. Biochemistry. 2000;39:6243-9 pubmed
  70. Takahashi K, Tanaka K, Itoh M, Takano Shimizu T. Reduced X-linked rare polymorphism in males in comparison to females of Drosophila melanogaster. J Hered. 2009;100:97-105 pubmed publisher
    ..These results suggest that some rare polymorphisms on the X chromosome from females are recessively deleterious and are removed by stronger purifying selection when transferred to hemizygous males. ..
  71. Ohkura K, Suzuki N, Ishihara T, Katsura I. SDF-9, a protein tyrosine phosphatase-like molecule, regulates the L3/dauer developmental decision through hormonal signaling in C. elegans. Development. 2003;130:3237-48 pubmed
  72. Tsuda M, Sasaoka Y, Kiso M, Abe K, Haraguchi S, Kobayashi S, et al. Conserved role of nanos proteins in germ cell development. Science. 2003;301:1239-41 pubmed
    ..Hence, although mice and flies differ in their mechanisms for germ cell specification, there seems to be conserved function for nanos proteins among invertebrates and vertebrates. ..
  73. Takahashi A, Takano Shimizu T. A high-frequency null mutant of an odorant-binding protein gene, Obp57e, in Drosophila melanogaster. Genetics. 2005;170:709-18 pubmed
    ..In addition, the Obp57d gene region showed an excess of high-frequency-derived mutants that is consistent with a pattern predicted under positive natural selection. ..
  74. Ito Y, Takaya K, Kurata N. Expression of SERK family receptor-like protein kinase genes in rice. Biochim Biophys Acta. 2005;1730:253-8 pubmed publisher
    ..This promoter activity suggests that OsSERK1 may have roles in non-embryonic tissues rather than in the embryo...
  75. Ohta T, Kobayashi M, Hirose S. Cloning of a cDNA for DNA supercoiling factor reveals a distinctive Ca(2+)-binding protein. J Biol Chem. 1995;270:15571-5 pubmed
    ..The factor contains three other potential EF-hand domains and actually binds Ca2+. Moreover, the supercoiling reaction has been shown to be activated by Ca2+. These results implicate Ca2+ in the control of the superhelical state of DNA. ..
  76. Ohta T. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc Natl Acad Sci U S A. 1993;90:4548-51 pubmed
    ..These observations suggest that amino acid substitutions are facilitated by small population size. The result is in accord with the nearly neutral theory of molecular evolution...
  77. 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. ..
  78. Ueda H, Hirose S. Identification and purification of a Bombyx mori homologue of FTZ-F1. Nucleic Acids Res. 1990;18:7229-34 pubmed
    ..The mobility of the factor-DNA complex formed in the silk gland extract changes depending on the developmental stages. Purification of BmFTZF1 to an almost homogeneous state reveals that the factor is a 73 kd protein. ..
  79. Nakajima Y, Morimoto M, Takahashi Y, Koseki H, Saga Y. Identification of Epha4 enhancer required for segmental expression and the regulation by Mesp2. Development. 2006;133:2517-25 pubmed
    ..In addition, ectopic Mesp2 expression induces abnormally epithelialized structures, which support to the idea that Mesp2 induces the formation of segmental borders by activating genes that play roles in cellular epithelialization. ..
  80. 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. ..
  81. Mochizuki K, Nishimiya Fujisawa C, Fujisawa T. Universal occurrence of the vasa-related genes among metazoans and their germline expression in Hydra. Dev Genes Evol. 2001;211:299-308 pubmed
    ..These results suggest that the vas-related genes occur universally among metazoans and that their expression in germline cells was established at least before cnidarian evolution...
  82. Takayama Y, Kamimura Y, Okawa M, Muramatsu S, Sugino A, Araki H. GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. Genes Dev. 2003;17:1153-65 pubmed
    ..Moreover, genetic and two-hybrid interactions suggest that GINS interacts with Sld3 and Dpb11. Therefore, Dpb11, Sld3, Cdc45, and GINS assemble in a mutually dependent manner on replication origins to initiate DNA synthesis. ..
  83. Nonomura K, Miyoshi K, Eiguchi M, Suzuki T, Miyao A, Hirochika H, et al. The MSP1 gene is necessary to restrict the number of cells entering into male and female sporogenesis and to initiate anther wall formation in rice. Plant Cell. 2003;15:1728-39 pubmed
    ..These results suggest that the MSP1 product plays crucial roles in restricting the number of cells entering into male and female sporogenesis and in initiating anther wall formation in rice. ..
  84. 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. ..
  85. Goto S, Taniguchi M, Muraoka M, Toyoda H, Sado Y, Kawakita M, et al. UDP-sugar transporter implicated in glycosylation and processing of Notch. Nat Cell Biol. 2001;3:816-22 pubmed
    ..The results suggest that changes in nucleotide-sugar levels can differently affect Wingless and two distinct aspects of Notch signalling. ..
  86. Kimura M, Suzuki H, Ishihama A. Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II. Mol Cell Biol. 2002;22:1577-88 pubmed
    ..This result indicates the importance of Fcp1-Rpb4 interaction for formation of the Fcp1/TFIIF/pol II complex in vivo. ..
  87. Torayama I, Ishihara T, Katsura I. Caenorhabditis elegans integrates the signals of butanone and food to enhance chemotaxis to butanone. J Neurosci. 2007;27:741-50 pubmed