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  1. Article: Co-precipitation molecules hemopexin and transferrin may be key molecules for fibrillogenesis in TTR V30M amyloidogenesis

    Ohta, Mika / Aki Sugano / Naoya Hatano / Hirotaka Sato / Hirofumi Shimada / Hitoshi Niwa / Toshiyuki Sakaeda / Hajime Tei / Yoshiyuki Sakaki / Ken-ichi Yamamura / Yutaka Takaoka

    Transgenic research. 2018 Feb., v. 27, no. 1

    2018  

    Abstract: The disease model of familial amyloidotic polyneuropathy—7.2-hMet30 mice—manifests amyloid deposition that consists of a human amyloidogenic mutant transthyretin (TTR) (TTR V30M). Our previous study found amyloid deposits in 14 of 27 7.2-hMet30 mice at ... ...

    Abstract The disease model of familial amyloidotic polyneuropathy—7.2-hMet30 mice—manifests amyloid deposition that consists of a human amyloidogenic mutant transthyretin (TTR) (TTR V30M). Our previous study found amyloid deposits in 14 of 27 7.2-hMet30 mice at 21–24 months of age. In addition, non-fibrillar TTR deposits were found in amyloid-negative 7.2hMet30 mice. These results suggested that TTR amyloidogenesis required not only mutant TTR but also an additional factor (or factors) as an etiologic molecule. To determine the differences in serum proteome in amyloid-positive and amyloid-negative mice in the 7.2-hMet30 model, we used proteomic analyses and studied serum samples obtained from these mice. Hemopexin (HPX) and transferrin (Tf) were detected in the serum samples from amyloid-positive mice and were also found in amyloid deposits via immunohistochemistry, but serum samples from amyloid-negative mice did not contain HPX and Tf. These two proteins were also not detected in non-fibrillar TTR deposits. In addition, in silico analyses suggested that HPX and Tf facilitate destabilization of TTR secondary structures and misfolding of TTR. These results suggest that HPX and Tf may be associated with TTR amyloidogenesis after fibrillogenesis in vivo.
    Keywords amyloid ; blood serum ; coprecipitation ; disease models ; etiology ; genetic engineering ; humans ; immunohistochemistry ; mice ; mutants ; prealbumin ; proteome ; transferrin
    Language English
    Dates of publication 2018-02
    Size p. 15-23.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 31620-9
    ISSN 1573-9368 ; 0962-8819
    ISSN (online) 1573-9368
    ISSN 0962-8819
    DOI 10.1007/s11248-017-0054-x
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Identification of an imprinted gene cluster in the X-inactivation center.

    Shin Kobayashi / Yasushi Totoki / Miki Soma / Kazuya Matsumoto / Yoshitaka Fujihara / Atsushi Toyoda / Yoshiyuki Sakaki / Masaru Okabe / Fumitoshi Ishino

    PLoS ONE, Vol 8, Iss 8, p e

    2013  Volume 71222

    Abstract: Mammalian development is strongly influenced by the epigenetic phenomenon called genomic imprinting, in which either the paternal or the maternal allele of imprinted genes is expressed. Paternally expressed Xist, an imprinted gene, has been considered as ...

    Abstract Mammalian development is strongly influenced by the epigenetic phenomenon called genomic imprinting, in which either the paternal or the maternal allele of imprinted genes is expressed. Paternally expressed Xist, an imprinted gene, has been considered as a single cis-acting factor to inactivate the paternally inherited X chromosome (Xp) in preimplantation mouse embryos. This means that X-chromosome inactivation also entails gene imprinting at a very early developmental stage. However, the precise mechanism of imprinted X-chromosome inactivation remains unknown and there is little information about imprinted genes on X chromosomes. In this study, we examined whether there are other imprinted genes than Xist expressed from the inactive paternal X chromosome and expressed in female embryos at the preimplantation stage. We focused on small RNAs and compared their expression patterns between sexes by tagging the female X chromosome with green fluorescent protein. As a result, we identified two micro (mi)RNAs-miR-374-5p and miR-421-3p-mapped adjacent to Xist that were predominantly expressed in female blastocysts. Allelic expression analysis revealed that these miRNAs were indeed imprinted and expressed from the Xp. Further analysis of the imprinting status of adjacent locus led to the discovery of a large cluster of imprinted genes expressed from the Xp: Jpx, Ftx and Zcchc13. To our knowledge, this is the first identified cluster of imprinted genes in the cis-acting regulatory region termed the X-inactivation center. This finding may help in understanding the molecular mechanisms regulating imprinted X-chromosome inactivation during early mammalian development.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: ATP13A2 deficiency induces a decrease in cathepsin D activity, fingerprint-like inclusion body formation, and selective degeneration of dopaminergic neurons

    Matsui, Hideaki / Fumiaki Sato / Shigeto Sato / Masato Koike / Yosuke Taruno / Shinji Saiki / Manabu Funayama / Hidefumi Ito / Yoshihito Taniguchi / Norihito Uemura / Atsushi Toyoda / Yoshiyuki Sakaki / Shunichi Takeda / Yasuo Uchiyama / Nobutaka Hattori / Ryosuke Takahashi

    Federation of European Biochemical Societies FEBS letters. 2013 May 02, v. 587, no. 9

    2013  

    Abstract: Kufor-Rakeb syndrome (KRS) was originally described as an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia. ATP13A2 was identified as the causative gene in KRS. ATP13A2 encodes the ATP13A2 protein, which is a ... ...

    Abstract Kufor-Rakeb syndrome (KRS) was originally described as an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia. ATP13A2 was identified as the causative gene in KRS. ATP13A2 encodes the ATP13A2 protein, which is a lysosomal type5 P-type ATPase, and ATP13A2 mutations are linked to autosomal recessive familial parkinsonism.Here, we report that normal ATP13A2 localizes in the lysosome, whereas disease-associated variants remain in the endoplasmic reticulum. Cathepsin D activity was decreased in ATP13A2-knockdown cells that displayed lysosome-like bodies characterized by fingerprint-like structures. Furthermore, an atp13a2 mutation in medaka fish resulted in dopaminergic neuronal death, decreased cathepsin D activity, and fingerprint-like structures in the brain. Based on these results, lysosome abnormality is very likely to be the primary cause of KRS/PARK9.
    Keywords Parkinson disease ; adenosinetriphosphatase ; brain ; cathepsin D ; death ; dementia ; endoplasmic reticulum ; fish ; genes ; lysosomes ; mutation ; neurons
    Language English
    Dates of publication 2013-0502
    Size p. 1316-1325.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1016/j.febslet.2013.02.046
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  4. Article: Coupling Deep Transcriptome Analysis with Untargeted Metabolic Profiling in Ophiorrhiza pumila to Further the Understanding of the Biosynthesis of the Anti-Cancer Alkaloid Camptothecin and Anthraquinones

    Yamazaki, Mami / Atsushi Toyoda / C. Robin Buell / Dayan B. Goodenowe / Elsa Góngora-Castillo / Kazuki Saito / Keiichi Mochida / Motoaki Chiba / Nirin Udomson / Ryo Nakabayashi / Takashi Asano / Takuhiro Yoshida / Tetsuya Sakurai / Ushio Sankawa / Yasushi Totoki / Yasuyo Yamazaki / Yoshiyuki Sakaki

    Plant & cell physiology. 2013 May, v. 54, no. 5

    2013  

    Abstract: The Rubiaceae species, Ophiorrhiza pumila , accumulates camptothecin, an anti-cancer alkaloid with a potent DNA topoisomerase I inhibitory activity, as well as anthraquinones that are derived from the combination of the isochorismate and hemiterpenoid ... ...

    Abstract The Rubiaceae species, Ophiorrhiza pumila , accumulates camptothecin, an anti-cancer alkaloid with a potent DNA topoisomerase I inhibitory activity, as well as anthraquinones that are derived from the combination of the isochorismate and hemiterpenoid pathways. The biosynthesis of these secondary products is active in O. pumila hairy roots yet very low in cell suspension culture. Deep transcriptome analysis was conducted in O. pumila hairy roots and cell suspension cultures using the Illumina platform, yielding a total of 2 Gb of sequence for each sample. We generated a hybrid transcriptome assembly of O. pumila using the Illumina-derived short read sequences and conventional Sanger-derived expressed sequence tag clones derived from a full-length cDNA library constructed using RNA from hairy roots. Among 35,608 non-redundant unigenes, 3,649 were preferentially expressed in hairy roots compared with cell suspension culture. Candidate genes involved in the biosynthetic pathway for the monoterpenoid indole alkaloid camptothecin were identified; specifically, genes involved in post-strictosamide biosynthetic events and genes involved in the biosynthesis of anthraquinones and chlorogenic acid. Untargeted metabolomic analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated that most of the proposed intermediates in the camptothecin biosynthetic pathway accumulated in hairy roots in a preferential manner compared with cell suspension culture. In addition, a number of anthraquinones and chlorogenic acid preferentially accumulated in hairy roots compared with cell suspension culture. These results suggest that deep transcriptome and metabolome data sets can facilitate the identification of genes and intermediates involved in the biosynthesis of secondary products including camptothecin in O. pumila .
    Keywords anthraquinones ; biochemical pathways ; biosynthesis ; cDNA libraries ; cell suspension culture ; chlorogenic acid ; clones ; complementary DNA ; data collection ; DNA topoisomerase ; expressed sequence tags ; indole alkaloids ; mass spectrometry ; metabolome ; metabolomics ; monoterpenoids ; Ophiorrhiza pumila ; RNA ; roots ; transcriptome ; transcriptomics ; unigenes
    Language English
    Dates of publication 2013-05
    Size p. 686-696.
    Publishing place Japanese Society of Plant Physiologists.
    Document type Article
    ZDB-ID 208907-5
    ISSN 1471-9053 ; 0032-0781
    ISSN (online) 1471-9053
    ISSN 0032-0781
    DOI 10.1093/pcp/pct040
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

    Ohshima, Kazuhiko / Masahira Hattori / Norihiro Okada / Takashi Gojobori / Tetsusi Yada / Yoshiyuki Sakaki

    Genome biology. 2003 Nov., v. 4, no. 11

    2003  

    Abstract: BACKGROUND: Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been ... ...

    Abstract BACKGROUND: Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first comprehensive analysis of human PPs using all known human genes as queries. RESULTS: The human genome was queried and 3,664 candidate PPs were identified. The most abundant were copies of genes encoding keratin 18, glyceraldehyde-3-phosphate dehydrogenase and ribosomal protein L21. A simple method was developed to estimate the level of nucleotide substitutions (and therefore the age) of PPs. A Poisson-like age distribution was obtained with a mean age close to that of the Alu repeats, the predominant human short interspersed elements. These data suggest a nearly simultaneous burst of PP and Alu formation in the genomes of ancestral primates. The peak period of amplification of these two distinct retrotransposons was estimated to be 40-50 million years ago. Concordant amplification of certain L1 subfamilies with PPs and Alus was observed. CONCLUSIONS: We suggest that a burst of formation of PPs and Alus occurred in the genome of ancestral primates. One possible mechanism is that proteins encoded by members of particular L1 subfamilies acquired an enhanced ability to recognize cytosolic RNAs in trans.
    Keywords glyceraldehyde-3-phosphate dehydrogenase ; humans ; keratin ; messenger RNA ; Primates ; pseudogenes ; retrotransposons ; reverse transcription ; screening ; transcription (genetics)
    Language English
    Dates of publication 2003-11
    Size p. 583.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2003-4-11-r74
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  6. Article ; Online: Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells.

    Takeshi Nagashima / Takahiro Suzuki / Shinji Kondo / Yoko Kuroki / Kaoru Takahashi / Kaori Ide / Noriko Yumoto / Aki Hasegawa / Tetsuro Toyoda / Toshio Kojima / Akihiko Konagaya / Harukazu Suzuki / Yoshihide Hayashizaki / Yoshiyuki Sakaki / Mariko Hatakeyama

    PLoS ONE, Vol 3, Iss 3, p e

    2008  Volume 1803

    Abstract: Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen ...

    Abstract Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570 ; 572
    Language English
    Publishing date 2008-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Generation of medaka gene knockout models by target-selected mutagenesis

    Taniguchi, Yoshihito / Atsushi Toyoda / Edwin Cuppen / Hiroshi Mitani / Hisato Kondoh / Josine Mudde / Makoto Furutani-Seiki / Masayuki Hidaka / Mitsuyoshi Yamazoe / Ronald HA Plasterk / Shunichi Takeda / Takao Sasado / Takeshi Todo / Tomonori Deguchi / Yasuhiro Kamei / Yoshiyuki Sakaki

    Genome biology. 2006 Dec., v. 7, no. 12

    2006  

    Abstract: We have established a reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts. A cryopreserved library of N-ethyl-N-nitrosourea (ENU) mutagenized fish was screened by high-throughput resequencing for induced point ... ...

    Abstract We have established a reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts. A cryopreserved library of N-ethyl-N-nitrosourea (ENU) mutagenized fish was screened by high-throughput resequencing for induced point mutations. Nonsense and splice site mutations were retrieved for the Blm, Sirt1, Parkin and p53 genes and functional characterization of p53 mutants indicated a complete knockout of p53 function. The current cryopreserved resource is expected to contain knockouts for most medaka genes.
    Keywords cryopreservation ; fish ; gene targeting ; genes ; models ; mutagenesis ; mutants ; N-ethyl-N-nitrosourea ; Oryzias latipes ; point mutation
    Language English
    Dates of publication 2006-12
    Size p. 1384.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2006-7-12-r116
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

    Renfree, Marilyn B / Allison Hall / Amber Stephens / Amir Mohammadi / Andrew Cree / Andrew J Pask / Annette McGrath / Anthony T Papenfuss / Artem Men / Arthur Hsu / Asao Fujiyama / Atsushi Toyoda / Benjamin G Cocks / Benjamin Lansdell / Brandon R Menzies / Carmen Troon / Chen Wu / Chenwei Wang / Christie L Kovar /
    Christophe M Lefèvre / Chyn Jing / Daniel Thomas / Danielle Hickford / David Wood / Dawn M Carone / Desmond W Cooper / Donna M Muzny / Elizabeth A Pharo / Elizabeth Kuczek / Emily SW Wong / Frank W Nicholas / Fremiet Lara / Geoff Shaw / Geoffrey O Okwuonu / George Weinstock / Gerald Fowler / Hannah V Siddle / Hongshi Yu / Huyen H Dinh / Ion Mandiou / James Lindsay / Janette Edson / Janine E Deakin / Javier Herrero / Jennifer A M Graves / Jessica M Stringer / Jianghui Wang / Jireh Santibanez / Jixin Deng / John Davis / Joshua Y Shen / Kaighin A McColl / Katherine Belov / Kathryn Beal / Keng Yih Chew / Kevin R Nicholas / Kim C Worley / Kirsty R Short / Kyall R Zenger / Lankesha Yapa / Lei Chen / Lora R Lewis / Lynne Nazareth / Malcolm Ferguson-Smith / Margaret B Morgan / Margaret L Delbridge / Matthew J Wakefield / Mehlika Hazar-Rethinam / Nanette Y Schneider / Paul D Waters / Paul Flicek / Peter Wilson / Rachel J O’Neill / Rebecca Thornton / Richard A Gibbs / San Juana Ruiz / Sarah Williams / Shafagh Al Nadaf / Shalini N Jhangiani / Shinji Kondo / Shoji Tatsumoto / Shunsuke Suzuki / Stephen MJ Searle / Stephen R Frankenberg / Sumio Sugano / Susan Fairley / Susan M Forrest / Tanya Levchenko / Terence P Speed / Thomas Heider / Timothy A Hore / Vandita Joshi / Willem Rens / William O’Hara / Xing-Zhi Song / Yanqiu Hu / Yogi Sundaravadanam / Yoko Kuroki / Yoshiyuki Sakaki / Yue Liu / Yuichiro Nishida / Yutaka Suzuki / Zhi-Ping Feng

    Genome biology. 2011 Aug., v. 12, no. 8

    2011  

    Abstract: BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual ... ...

    Abstract BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
    Keywords breeding ; chromosome mapping ; chromosomes ; data analysis ; diapause ; evolution ; genome assembly ; genomics ; germ cells ; high-throughput nucleotide sequencing ; immunity ; lactation ; Macropus eugenii ; major histocompatibility complex ; mammals ; microRNA ; models ; regulatory sequences ; retrotransposons ; transcriptome ; Australia
    Language English
    Dates of publication 2011-08
    Size p. 2659.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2011-12-8-r81
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Tadashi Imanishi / Takeshi Itoh / Yutaka Suzuki / Claire O'Donovan / Satoshi Fukuchi / Kanako O Koyanagi / Roberto A Barrero / Takuro Tamura / Yumi Yamaguchi-Kabata / Motohiko Tanino / Kei Yura / Satoru Miyazaki / Kazuho Ikeo / Keiichi Homma / Arek Kasprzyk / Tetsuo Nishikawa / Mika Hirakawa / Jean Thierry-Mieg / Danielle Thierry-Mieg /
    Jennifer Ashurst / Libin Jia / Mitsuteru Nakao / Michael A Thomas / Nicola Mulder / Youla Karavidopoulou / Lihua Jin / Sangsoo Kim / Tomohiro Yasuda / Boris Lenhard / Eric Eveno / Yoshiyuki Suzuki / Chisato Yamasaki / Jun-ichi Takeda / Craig Gough / Phillip Hilton / Yasuyuki Fujii / Hiroaki Sakai / Susumu Tanaka / Clara Amid / Matthew Bellgard / Maria de Fatima Bonaldo / Hidemasa Bono / Susan K Bromberg / Anthony J Brookes / Elspeth Bruford / Piero Carninci / Claude Chelala / Christine Couillault / Sandro J de Souza / Marie-Anne Debily / Marie-Dominique Devignes / Inna Dubchak / Toshinori Endo / Anne Estreicher / Eduardo Eyras / Kaoru Fukami-Kobayashi / Gopal R Gopinath / Esther Graudens / Yoonsoo Hahn / Michael Han / Ze-Guang Han / Kousuke Hanada / Hideki Hanaoka / Erimi Harada / Katsuyuki Hashimoto / Ursula Hinz / Momoki Hirai / Teruyoshi Hishiki / Ian Hopkinson / Sandrine Imbeaud / Hidetoshi Inoko / Alexander Kanapin / Yayoi Kaneko / Takeya Kasukawa / Janet Kelso / Paul Kersey / Reiko Kikuno / Kouichi Kimura / Bernhard Korn / Vladimir Kuryshev / Izabela Makalowska / Takashi Makino / Shuhei Mano / Regine Mariage-Samson / Jun Mashima / Hideo Matsuda / Hans-Werner Mewes / Shinsei Minoshima / Keiichi Nagai / Hideki Nagasaki / Naoki Nagata / Rajni Nigam / Osamu Ogasawara / Osamu Ohara / Masafumi Ohtsubo / Norihiro Okada / Toshihisa Okido / Satoshi Oota / Motonori Ota / Toshio Ota / Tetsuji Otsuki / Dominique Piatier-Tonneau / Annemarie Poustka / Shuang-Xi Ren / Naruya Saitou / Katsunaga Sakai / Shigetaka Sakamoto / Ryuichi Sakate / Ingo Schupp / Florence Servant / Stephen Sherry / Rie Shiba / Nobuyoshi Shimizu / Mary Shimoyama / Andrew J Simpson / Bento Soares / Charles Steward / Makiko Suwa / Mami Suzuki / Aiko Takahashi / Gen Tamiya / Hiroshi Tanaka / Todd Taylor / Joseph D Terwilliger / Per Unneberg / Vamsi Veeramachaneni / Shinya Watanabe / Laurens Wilming / Norikazu Yasuda / Hyang-Sook Yoo / Marvin Stodolsky / Wojciech Makalowski / Mitiko Go / Kenta Nakai / Toshihisa Takagi / Minoru Kanehisa / Yoshiyuki Sakaki / John Quackenbush / Yasushi Okazaki / Yoshihide Hayashizaki / Winston Hide / Ranajit Chakraborty / Ken Nishikawa / Hideaki Sugawara / Yoshio Tateno / Zhu Chen / Michio Oishi / Peter Tonellato / Rolf Apweiler / Kousaku Okubo / Lukas Wagner / Stefan Wiemann / Robert L Strausberg / Takao Isogai / Charles Auffray / Nobuo Nomura / Takashi Gojobori / Sumio Sugano

    PLoS Biology, Vol 2, Iss 6, p e

    2004  Volume 162

    Abstract: The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation ... ...

    Abstract The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
    Keywords Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2004-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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