Sakaki Y

References (9)

Title : Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs - Iida_2009_DNA.Res_16_155
Author(s) : Iida K , Fukami-Kobayashi K , Toyoda A , Sakaki Y , Kobayashi M , Seki M , Shinozaki K
Ref : DNA Research , 16 :155 , 2009
Abstract : Alternative splicing (AS) is a mechanism by which multiple types of mature mRNAs are generated from a single pre-mature mRNA. In this study, we completely sequenced 1800 full-length cDNAs from Arabidopsis thaliana, which had 5' and/or 3' sequences that were previously found to have AS events or alternative transcription start sites. Unexpectedly, these sequences gave us further evidence of AS, as 601 out of 1800 transcripts showed novel AS events. We focused on the combination patterns of multiple AS events within individual genes. Interestingly, some specific AS event combination patterns tended to appear more frequently than expected. The two most common patterns were: (i) alternative donor-0 approximately 12 times of exon skips-alternative acceptor and (ii) several times ( approximately 8) of retained introns. We also found that multiple AS events in a transcript tend to have the same effects concerning the length of the mature mRNA. Our current results are consistent with our previous observations, which showed changes in AS profiles under different conditions, and suggest the involvement of hypothetical cis- and trans-acting factors in the regulation of AS events.
ESTHER : Iida_2009_DNA.Res_16_155
PubMedSearch : Iida_2009_DNA.Res_16_155
PubMedID: 19423640
Gene_locus related to this paper: arath-AT2G42690 , arath-AT5G20060 , arath-eds1 , arath-MES2 , arath-o65713 , arath-pip , arath-Q8LFB7 , arath-q66gm8 , arath-B9DFR3

Title : Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila - Taji_2008_BMC.Plant.Biol_8_115
Author(s) : Taji T , Sakurai T , Mochida K , Ishiwata A , Kurotani A , Totoki Y , Toyoda A , Sakaki Y , Seki M , Ono H , Sakata Y , Tanaka S , Shinozaki K
Ref : BMC Plant Biol , 8 :115 , 2008
Abstract : BACKGROUND: Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, Arabidopsis thaliana. Thellungiella genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance. RESULTS: We constructed a full-length enriched Thellungiella (Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20,000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN Thellungiella Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and Thellungiella genes showing low identity to Arabidopsis genes revealed that the population of Thellungiella transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in Thellungiella. CONCLUSION: As the number of Thellungiella halophila (Thellungiella salsuginea) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the Thellungiella genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of Thellungiella mutants, and the determination of promoter regions in the Thellungiella genome.
ESTHER : Taji_2008_BMC.Plant.Biol_8_115
PubMedSearch : Taji_2008_BMC.Plant.Biol_8_115
PubMedID: 19014467
Gene_locus related to this paper: theha-e4mwi7 , theha-e4mwx5 , theha-e4mxu0 , eutsa-v4kvd3

Title : Human chromosome 11 DNA sequence and analysis including novel gene identification - Taylor_2006_Nature_440_497
Author(s) : Taylor TD , Noguchi H , Totoki Y , Toyoda A , Kuroki Y , Dewar K , Lloyd C , Itoh T , Takeda T , Kim DW , She X , Barlow KF , Bloom T , Bruford E , Chang JL , Cuomo CA , Eichler E , Fitzgerald MG , Jaffe DB , LaButti K , Nicol R , Park HS , Seaman C , Sougnez C , Yang X , Zimmer AR , Zody MC , Birren BW , Nusbaum C , Fujiyama A , Hattori M , Rogers J , Lander ES , Sakaki Y
Ref : Nature , 440 :497 , 2006
Abstract : Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
ESTHER : Taylor_2006_Nature_440_497
PubMedSearch : Taylor_2006_Nature_440_497
PubMedID: 16554811
Gene_locus related to this paper: human-PRCP

Title : DNA sequence and analysis of human chromosome 18 - Nusbaum_2005_Nature_437_551
Author(s) : Nusbaum C , Zody MC , Borowsky ML , Kamal M , Kodira CD , Taylor TD , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Abouelleil A , Allen NR , Anderson S , Bloom T , Bugalter B , Butler J , Cook A , Decaprio D , Engels R , Garber M , Gnirke A , Hafez N , Hall JL , Norman CH , Itoh T , Jaffe DB , Kuroki Y , Lehoczky J , Lui A , Macdonald P , Mauceli E , Mikkelsen TS , Naylor JW , Nicol R , Nguyen C , Noguchi H , O'Leary SB , O'Neill K , Piqani B , Smith CL , Talamas JA , Topham K , Totoki Y , Toyoda A , Wain HM , Young SK , Zeng Q , Zimmer AR , Fujiyama A , Hattori M , Birren BW , Sakaki Y , Lander ES
Ref : Nature , 437 :551 , 2005
Abstract : Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
ESTHER : Nusbaum_2005_Nature_437_551
PubMedSearch : Nusbaum_2005_Nature_437_551
PubMedID: 16177791
Gene_locus related to this paper: human-LIPG

Title : DNA sequence and comparative analysis of chimpanzee chromosome 22 - Watanabe_2004_Nature_429_382
Author(s) : Watanabe H , Fujiyama A , Hattori M , Taylor TD , Toyoda A , Kuroki Y , Noguchi H , BenKahla A , Lehrach H , Sudbrak R , Kube M , Taenzer S , Galgoczy P , Platzer M , Scharfe M , Nordsiek G , Blocker H , Hellmann I , Khaitovich P , Paabo S , Reinhardt R , Zheng HJ , Zhang XL , Zhu GF , Wang BF , Fu G , Ren SX , Zhao GP , Chen Z , Lee YS , Cheong JE , Choi SH , Wu KM , Liu TT , Hsiao KJ , Tsai SF , Kim CG , S OO , Kitano T , Kohara Y , Saitou N , Park HS , Wang SY , Yaspo ML , Sakaki Y
Ref : Nature , 429 :382 , 2004
Abstract : Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
ESTHER : Watanabe_2004_Nature_429_382
PubMedSearch : Watanabe_2004_Nature_429_382
PubMedID: 15164055
Gene_locus related to this paper: pantr-a0a2j8lmv7

Title : Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis - Ikeda_2003_Nat.Biotechnol_21_526
Author(s) : Ikeda H , Ishikawa J , Hanamoto A , Shinose M , Kikuchi H , Shiba T , Sakaki Y , Hattori M , Omura S
Ref : Nat Biotechnol , 21 :526 , 2003
Abstract : Species of the genus Streptomyces are of major pharmaceutical interest because they synthesize a variety of bioactive secondary metabolites. We have determined the complete nucleotide sequence of the linear chromosome of Streptomyces avermitilis. S. avermitilis produces avermectins, a group of antiparasitic agents used in human and veterinary medicine. The genome contains 9,025,608 bases (average GC content, 70.7%) and encodes at least 7,574 potential open reading frames (ORFs). Thirty-five percent of the ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters related to secondary metabolite biosynthesis were identified, corresponding to 6.6% of the genome. Comparison with Streptomyces coelicolor A3(2) revealed that an internal 6.5-Mb region in the S. avermitilis genome was highly conserved with respect to gene order and content, and contained all known essential genes but showed perfectly asymmetric structure at the oriC center. In contrast, the terminal regions were not conserved and preferentially contained nonessential genes.
ESTHER : Ikeda_2003_Nat.Biotechnol_21_526
PubMedSearch : Ikeda_2003_Nat.Biotechnol_21_526
PubMedID: 12692562
Gene_locus related to this paper: strav-cah , strav-GEOB , strav-PCAL , strav-Q93HH8 , strav-SAV38 , strav-SAV141 , strav-SAV154 , strav-SAV297 , strav-SAV298 , strav-SAV433 , strav-SAV469 , strav-SAV512 , strav-SAV519 , strav-SAV541 , strav-SAV569 , strav-SAV620 , strav-SAV819 , strav-SAV875 , strav-SAV888 , strav-SAV906 , strav-SAV923 , strav-SAV974 , strav-SAV1231 , strav-SAV1256 , strav-SAV1457 , strav-SAV1549 , strav-SAV1585 , strav-SAV1746 , strav-SAV1898 , strav-SAV1906 , strav-SAV1959 , strav-SAV1968 , strav-SAV1973 , strav-SAV2099 , strav-SAV2105 , strav-SAV2113 , strav-SAV2604 , strav-SAV2722 , strav-SAV3039 , strav-SAV3080 , strav-SAV3081 , strav-SAV3092 , strav-SAV3099 , strav-SAV3144 , strav-SAV3359 , strav-SAV3461 , strav-SAV3624 , strav-SAV3810 , strav-SAV3854 , strav-SAV4041 , strav-SAV4252 , strav-SAV4410 , strav-SAV4434 , strav-SAV4531 , strav-SAV4564 , strav-SAV4596 , strav-SAV4674 , strav-SAV4779 , strav-SAV4863 , strav-SAV4922 , strav-SAV4968 , strav-SAV5173 , strav-SAV5300 , strav-SAV5344 , strav-SAV5668 , strav-SAV5711 , strav-SAV5844 , strav-SAV5965 , strav-SAV6079 , strav-SAV6138 , strav-SAV6422 , strav-SAV6559 , strav-SAV6609 , strav-SAV7067 , strav-SAV7089 , strav-SAV7110 , strav-SAV7198 , strav-SAV7423 , strav-SAV7455 , strav-SAV7475 , strav-SLPD , straw-AVEG , straw-pepx , straw-q82bb0 , straw-q82en5 , straw-q82et1 , straw-q93hc9 , straw-SAV1543 , straw-SAV2023

Title : Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites - Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
Author(s) : Omura S , Ikeda H , Ishikawa J , Hanamoto A , Takahashi C , Shinose M , Takahashi Y , Horikawa H , Nakazawa H , Osonoe T , Kikuchi H , Shiba T , Sakaki Y , Hattori M
Ref : Proc Natl Acad Sci U S A , 98 :12215 , 2001
Abstract : Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is commercially important in human and veterinary medicine. The major interest in this genus Streptomyces is the diversity of its production of secondary metabolites as an industrial microorganism. A major factor in its prominence as a producer of the variety of secondary metabolites is its possession of several metabolic pathways for biosynthesis. Here we report sequence analysis of S. avermitilis, covering 99% of its genome. At least 8.7 million base pairs exist in the linear chromosome; this is the largest bacterial genome sequence, and it provides insights into the intrinsic diversity of the production of the secondary metabolites of Streptomyces. Twenty-five kinds of secondary metabolite gene clusters were found in the genome of S. avermitilis. Four of them are concerned with the biosyntheses of melanin pigments, in which two clusters encode tyrosinase and its cofactor, another two encode an ochronotic pigment derived from homogentiginic acid, and another polyketide-derived melanin. The gene clusters for carotenoid and siderophore biosyntheses are composed of seven and five genes, respectively. There are eight kinds of gene clusters for type-I polyketide compound biosyntheses, and two clusters are involved in the biosyntheses of type-II polyketide-derived compounds. Furthermore, a polyketide synthase that resembles phloroglucinol synthase was detected. Eight clusters are involved in the biosyntheses of peptide compounds that are synthesized by nonribosomal peptide synthetases. These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome.
ESTHER : Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
PubMedSearch : Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
PubMedID: 11572948
Gene_locus related to this paper: strav-cah , strav-GEOB , strav-OLMA7 , strav-OLMC , strav-PCAL , strav-PTEA5 , strav-PTEH , strav-Q93GY0 , strav-Q93GY7 , strav-Q93H00 , strav-Q93H03 , strav-Q93H41 , strav-Q93H55 , strav-Q93H68 , strav-Q93H73 , strav-Q93HG2 , strav-Q93HH2 , strav-Q93HH8 , strav-Q93HI2 , strav-SAV38 , strav-SAV141 , strav-SAV154 , strav-SAV297 , strav-SAV298 , strav-SAV299 , strav-SAV433 , strav-SAV469 , strav-SAV512 , strav-SAV519 , strav-SAV541 , strav-SAV569 , strav-SAV620 , strav-SAV819 , strav-SAV875 , strav-SAV888 , strav-SAV906 , strav-SAV923 , strav-SAV974 , strav-SAV1231 , strav-SAV1256 , strav-SAV1457 , strav-SAV1549 , strav-SAV1585 , strav-SAV1746 , strav-SAV1898 , strav-SAV1906 , strav-SAV1959 , strav-SAV1968 , strav-SAV1973 , strav-SAV2099 , strav-SAV2105 , strav-SAV2113 , strav-SAV2604 , strav-SAV2722 , strav-SAV3039 , strav-SAV3080 , strav-SAV3081 , strav-SAV3092 , strav-SAV3099 , strav-SAV3144 , strav-SAV3359 , strav-SAV3461 , strav-SAV3624 , strav-SAV3810 , strav-SAV3854 , strav-SAV4041 , strav-SAV4252 , strav-SAV4410 , strav-SAV4434 , strav-SAV4531 , strav-SAV4564 , strav-SAV4596 , strav-SAV4674 , strav-SAV4779 , strav-SAV4863 , strav-SAV4922 , strav-SAV4968 , strav-SAV5173 , strav-SAV5300 , strav-SAV5344 , strav-SAV5668 , strav-SAV5711 , strav-SAV5844 , strav-SAV5965 , strav-SAV6079 , strav-SAV6138 , strav-SAV6422 , strav-SAV6559 , strav-SAV6609 , strav-SAV7067 , strav-SAV7089 , strav-SAV7110 , strav-SAV7198 , strav-SAV7423 , strav-SAV7455 , strav-SAV7475 , strav-SLPD , straw-AVEG , straw-pepx , straw-q82bb0 , straw-q82en5 , straw-q82et1 , straw-q93hc9 , straw-SAV1543 , straw-SAV2023 , strax-Q93H72

Title : Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS - Shigenobu_2000_Nature_407_81
Author(s) : Shigenobu S , Watanabe H , Hattori M , Sakaki Y , Ishikawa H
Ref : Nature , 407 :81 , 2000
Abstract : Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes, within which are round-shaped bacteria that are designated Buchnera. These bacteria are maternally transmitted to eggs and embryos through host generations, and the mutualism between the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell, and its genome size is only a seventh of that of E. coli. Here we report the complete genome sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and two small plasmids. There are genes for the biosyntheses of amino acids essential for the hosts in the genome, but those for non-essential amino acids are missing, indicating complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defence of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacteriocyte.
ESTHER : Shigenobu_2000_Nature_407_81
PubMedSearch : Shigenobu_2000_Nature_407_81
PubMedID: 10993077

Title : The DNA sequence of human chromosome 21 - Hattori_2000_Nature_405_311
Author(s) : Hattori M , Fujiyama A , Taylor TD , Watanabe H , Yada T , Park HS , Toyoda A , Ishii K , Totoki Y , Choi DK , Groner Y , Soeda E , Ohki M , Takagi T , Sakaki Y , Taudien S , Blechschmidt K , Polley A , Menzel U , Delabar J , Kumpf K , Lehmann R , Patterson D , Reichwald K , Rump A , Schillhabel M , Schudy A , Zimmermann W , Rosenthal A , Kudoh J , Schibuya K , Kawasaki K , Asakawa S , Shintani A , Sasaki T , Nagamine K , Mitsuyama S , Antonarakis SE , Minoshima S , Shimizu N , Nordsiek G , Hornischer K , Brant P , Scharfe M , Schon O , Desario A , Reichelt J , Kauer G , Blocker H , Ramser J , Beck A , Klages S , Hennig S , Riesselmann L , Dagand E , Haaf T , Wehrmeyer S , Borzym K , Gardiner K , Nizetic D , Francis F , Lehrach H , Reinhardt R , Yaspo ML
Ref : Nature , 405 :311 , 2000
Abstract : Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ESTHER : Hattori_2000_Nature_405_311
PubMedSearch : Hattori_2000_Nature_405_311
PubMedID: 10830953
Gene_locus related to this paper: human-LIPI