Genomes and Genes
Affiliation: National Institute of Genetics
- Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytesToshiaki Watanabe
Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411 8540, Japan
Nature 453:539-43. 2008..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...
- Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testesToshiaki Watanabe
Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
Genes Dev 20:1732-43. 2006..These features are reminiscent of Tetrahymena approximately 23- to 24-nt small RNAs and Caenorhabditis elegans X-cluster small RNAs. A conserved novel small RNA pathway may be present in diverse animals...
- Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locusToshiaki Watanabe
Division of Human Genetics and Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
Science 332:848-52. 2011..A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1...
- Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factorYu Fu
Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
EMBO J 32:2407-17. 2013..Proteins related to this anti-silencing factor, which we named VANC, are widespread in the non-TIR MULEs and may have contributed to the recent success of these TEs in natural Arabidopsis populations. ..
- MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germlineToshiaki Watanabe
Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
Dev Cell 20:364-75. 2011..Our results indicate a conserved role for MITOPLD/Zuc in the piRNA pathway and link mitochondrial membrane metabolism/signaling to small RNA biogenesis...
- Gene-body chromatin modification dynamics mediate epigenome differentiation in ArabidopsisSoichi Inagaki
National Institute of Genetics, Mishima, Shizuoka, Japan
EMBO J . 2017..Our results uncover an unexpected role of gene-body H3K9me2/H3K4me1 dynamics as a mediator of heterochromatin silencing and epigenome differentiation...
- Dynamics of Dark-Fly Genome Under Environmental SelectionsMinako Izutsu
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
G3 (Bethesda) 6:365-76. 2015..Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly. ..
- Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cellsDaisuke Shiomi
Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411 8540, Japan
Mol Microbiol 87:1029-44. 2013..Thus, we found that mutations in domain IA of MreB and in the periplasmic domain of PBP2 and RodA can restore growth and rod shape to ΔrodZ cells, possibly by changing the requirements of MreB in the process...
- Genome-wide negative feedback drives transgenerational DNA methylation dynamics in ArabidopsisTasuku Ito
Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo ku, Tokyo, Japan
PLoS Genet 11:e1005154. 2015..The global negative feedback, together with local positive feedback, would ensure robust and balanced differentiation of chromatin states within the genome. ..
- The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strainsToyoyuki Takada
Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
Genome Res 23:1329-38. 2013..m. molossinus genome in classical inbred strains and largely contributed to its intersubspecific genome diversity. ..
- Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrataSayuri Tsukahara
Department of Integrated Genetics, National Institute of Genetics, Shizuoka 411 8540, Japan
Genes Dev 26:705-13. 2012..lyrata and A. thaliana. Our results revealed unexpectedly dynamic controls for evolution of the transposon-rich heterochromatic regions...
- Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River WaterRyosuke Nakai
Genetic Strains Research Center, National Institute of Genetics, Mishima, Japan Superlative Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Tokyo, Japan
Genome Announc 4:. 2016..Strain KNC(T) has an extremely small, streamlined genome of 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that strain KNC(T) has an actinorhodopsin-based photometabolism. ..
- A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA librariesYang An
Department of Biophysics, Kyoto University, Kyoto, Kyoto, Japan
PLoS ONE 10:e0116997. 2015..According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements. ..
- Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypesAsano Ishikawa
Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
Evolution . 2017..This article is protected by copyright. All rights reserved...
- Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processesAkira Kikuchi
Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3 5 8 Saiwai cho, Fuchu, Tokyo, 183 8509, Japan
BMC Genomics 18:83. 2017..To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases...
- HJURP is involved in the expansion of centromeric chromatinMarinela Perpelescu
Department of Molecular Genetics, National Institute of Genetics, and Graduate University for Advanced Studies SOKENDAI, Mishima, Shizuoka 411 8540, Japan
Mol Biol Cell 26:2742-54. 2015..We propose that this centromere expansion activity reflects the functional properties of HJURP, which uses this activity to contribute to the plastic establishment of a centromeric chromatin structure. ..
- Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomesMatthew R Shenton
Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411 8540, Japan
Mol Genet Genomics 290:1753-70. 2015..For the CRP proteins, the process of gain/loss by deletion or duplication at gene clusters seems to be an important mechanism in evolution of the gene families, which also contributes to their expression evolution. ..
- Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocalesTakashi Hamaji
Department of Botany, Graduate School of Science, Kyoto University, Oiwake cho, Kita shirakawa, Sakyo ku, Kyoto, Japan
PLoS ONE 8:e57177. 2013..Overall, the G. pectorale organelle genomes raise several interesting questions about the origin of linear mitochondrial chromosomes within the Volvocales and the relationship between multicellularity and organelle genome expansion...
- Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environmentMinako Izutsu
Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan
PLoS ONE 7:e33288. 2012..Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation...
- A 210-kb segment of tandem repeats and retroelements located between imprinted subdomains of mouse distal chromosome 7Hisao Shirohzu
Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411 8540, Japan
DNA Res 11:325-34. 2004..We propose that this repeat segment could serve either as a boundary between the two subdomains or as a target for epigenetic chromatin modifications that regulate imprinting...
- Loss of PINK1 in medaka fish (Oryzias latipes) causes late-onset decrease in spontaneous movementHideaki Matsui
Department of Neurology, Kyoto University, Graduate School of Medicine, 54 Shogoin Kawahara cho, Sakyo ku, Kyoto 606 8507, Japan
Neurosci Res 66:151-61. 2010..Thus, PINK1 contributes to the maintenance of dopamine metabolism, even before the selective death of dopaminergic neurons. Our animal model is therefore a valuable tool to detect pathogenesis in Parkinson's patients in the early stages...
- DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testesSatomi Kuramochi-Miyagawa
Department of Pathology, Medical School, Graduate School of Frontier Biosciences, Research Institute for Microbial Diseases, Osaka University, Yamada oka 2 2 Suita, Osaka 565 0871, Japan
Genes Dev 22:908-17. 2008..Our data strongly suggest that MILI and MIWI2 play essential roles in establishing de novo DNA methylation of retrotransposons in fetal male germ cells...
- Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobiliNorihiro Futamura
Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305 8687, Japan
BMC Genomics 9:383. 2008..japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages...
- Cloning, nucleotide sequence and expression of the gene encoding the cellulose-binding protein A (CBPA) of Eubacterium cellulosolvens 5Atsushi Toyoda
School of Agriculture, Ibaraki University, Ami, 300 0393, Ibaraki, Japan
FEMS Microbiol Lett 207:141-6. 2002..The cloned gene was inserted into an expression vector, pBAD-TOPO, and expressed in Escherichia coli as a fused protein. The fused protein was detected by immunoblotting using antiserum against CBPA...
- Identification of two novel primate-specific genes in DSCRKunihiko Takamatsu
Laboratory of Functional Genomics Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
DNA Res 9:89-97. 2002..These results strongly suggest that DSCR9 and DSCR10 have emerged as a new class of gene in the primate lineage during evolution...
- Genomic organization and promoter analysis of the Dnmt3b geneChisaki Ishida
Division of Gene Therapy Science, Osaka University School of Medicine, 2 2 Yamada oka, Suita, 565 0870, Osaka, Japan
Gene 310:151-9. 2003..9 kb upstream of Dnmt3b downregulated this gene specifically in somatic cells but not in ES cells. These findings provide a basis for future detailed studies of the mechanisms controlling Dnmt3b expression...
- Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysisKuniya Abe
Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305 0074, Japan
Genome Res 14:2439-47. 2004..2% of the genome showed an extremely low SNP rate (percentage identity = 0.9997); these sequences are likely derived from the molossinus genome...
- PCR detection of bovine mitochondrial DNA derived from meat and bone meal in feedAtsushi Toyoda
College of Agriculture, Ibaraki University, Ibaraki 300 0393, Japan
J Food Prot 67:2829-32. 2004..However, the exclusion of this treatment improved the detection limit of bovine MBM in feed. This method appears suitable for the selective detection of bovine MBM in feed...
- Molecular characterization of ENU mouse mutagenesis and archivesYoshiyuki Sakuraba
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
Biochem Biophys Res Commun 336:609-16. 2005..The base-substitution spectra in this study were different from those of the phenotype-based mutagenesis. The ENU-based gene-driven mutagenesis in the mouse now becomes feasible and practical...
- Cloning, sequencing, and expression of a Eubacterium cellulosolvens 5 gene encoding an endoglucanase (Cel5A) with novel carbohydrate-binding modules, and properties of Cel5AKazutoyo Yoda
College of Agriculture, Ibaraki University, Ami, Ibaraki 300 0393, Japan
Appl Environ Microbiol 71:5787-93. 2005..Removal of the CBMs from rCel5A reduced the catalytic activities with various polysaccharides remarkably. These observations show that CBMs play an important role in the catalytic function of the enzyme...
- A large-scale full-length cDNA analysis to explore the budding yeast transcriptomeFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
Proc Natl Acad Sci U S A 103:17846-51. 2006..The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies...
- An oligodendrocyte enhancer in a phylogenetically conserved intron region of the mammalian myelin gene OpalinJun Aruga
Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako Shi, Saitama, Japan
J Neurochem 102:1533-47. 2007..These results suggest that LIF, cAMP signaling cascades and Myt1 play significant roles in the differentiation of oligodendrocytes through their action on the Opalin oligodendrocyte enhancer...
- Functional annotation of 19,841 Populus nigra full-length enriched cDNA clonesTokihiko Nanjo
Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute FFPRI, 1 Matsunosato, Tsukuba, Ibaraki 305 8687 JAPAN
BMC Genomics 8:448. 2007..ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species...
- The Physcomitrella genome reveals evolutionary insights into the conquest of land by plantsStefan A Rensing
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
Science 319:64-9. 2008..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
- Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress responseTetsuya Sakurai
Metabolomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
BMC Plant Biol 7:66. 2007..A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs)...
- An N-ethyl-N-nitrosourea-induced mutation in N-acetyltransferase 1 in miceRobert P Erickson
Department of Pediatrics, University of Arizona, 1501 N Campbell Avenue, P O Box 245073, Tucson, AZ 85724, USA
Biochem Biophys Res Commun 370:285-8. 2008..Analysis of hepatic Nat1 activity with the selective substrate isoniazid showed that there was a significant reduction in enzymatic activity in the homozygous mutants compared to the parental strain...
- Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cellYuichi Hongoh
Environmental Molecular Biology Laboratory, RIKEN, Saitama 351 0198, Japan
Proc Natl Acad Sci U S A 105:5555-60. 2008..Our results provide a breakthrough to clarify the functions of and the interactions among the individual members of this multilayered symbiotic complex...
- Construction and analysis of a human-chimpanzee comparative clone mapAsao Fujiyama
RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Science 295:131-4. 2002..We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes...