Complete sequencing and characterization of 21,243 full-length human cDNAs

Ota, Toshio; Suzuki, Yutaka; Nishikawa, Tetsuo; Otsuki, Tetsuji; Sugiyama, Tomoyasu; Irie, Ryotaro; Wakamatsu, Ai; Hayashi, Koji; Sato, Hiroyuki; Nagai, Keiichi; Kimura, Kouichi; Makita, Hiroshi; Sekine, Mitsuo; Obayashi, Masaya; Nishi, Tatsunari; Shibahara, Toshikazu; Tanaka, Toshihiro; Ishii, Shizuko; Yamamoto, Junichi; Saito, Kaoru; Kawai, Yuri; Isono, Yuko; Nakamura, Yoshitaka; Nagahari, Kenji; Murakami, Katsuhiko; Yasuda, Tomohiro; Iwayanagi, Takao; Wagatsuma, Masako; Shiratori, Akiko; Sudo, Hiroaki; Hosoiri, Takehiko; Kaku, Yoshiko; Kodaira, Hiroyo; Kondo, Hiroshi; Sugawara, Masanori; Takahashi, M.; Kanda, Katsuhiro; Yokoi, Takeshi; Furuya, Tetsuo; Kikkawa, Emiko; Omura, Yoko; Abe, Kuniyoshi; Kamihara, Kumiko; Katsuta, Naoko; Sato, Koma; Tanikawa, M.; Yamazaki, Makoto; Ninomiya, Ken; Ishibashi, Tadashi; Yamashita, Hiromichi; Murakawa, Katsuji; Fujimori, Kiyoshi; Tanai, Hiroyuki; Kimata, Manabu; Watanabe, Motoji; Hiraoka, Susumu; Chiba, Yoshiyuki; Ishida, Shinichi; Ono, Yukio; Takiguchi, Sumiyo; Watanabe, Susumu; Yosida, Makoto; Hotuta, Tomoko; Kusano, Junko; Kanehori, Keiichi; Takahashi-Fujii, Asako; Hara, Hiroto; Tanase, Tomo-o; Nomura, Yasuo; Togiya, Sakae; Komai, Fukuyo; Hara, Reiko; Takeuchi, Kazuha; Arita, Miho; Imose, Nobuyuki; Musashino, Kaoru; Yuuki, Hisatsugu; Oshima, Akira; Sasaki, Naokazu; Aotsuka, Satoshi; Yoshikawa, Yoko; Matsunawa, Hiroshi; Ichihara, Tatsuo; Shiohata, Namiko; Sano, Sanae; Moriya, Shogo; Momiyama, Hiroko; Satoh, Noriko; Takami, Sachiko; Terashima, Yuko; Сузукі, Осаму; Nakagawa, Satoshi; Senoh, Akihiro; Mizoguchi, Hiroshi; Goto, Yoshihiro; Shimizu, Fumio; Wakebe, Hirokazu; Hishigaki, Haretsugu; Watanabe, Takeshi; Sugiyama, Akio; Takemoto, Makoto; Kawakami, Bunsei; Yamazaki, Masaaki; Watanabe, Kôji; Kumagai, Akira; Itakura, Shoko; Fukuzumi, Yasuhito; Fujimori, Yoshifumi; Komiyama, Megumi; Tashiro, Hiroyuki; Tanigami, Akira; Fujiwara, Tsutomu; Ono, Toshihide; Yamada, Katsue; Fujii, Yuka; Ozaki, Kouichi; Hirao, Maasa; Ohmori, Yuki; Kawabata, Ayako; Hikiji, Takeshi; Kobatake, Naoko; Inagaki, Hiromi; Ikema, Yasuko; Okamoto, Sachiko; Okitani, Rie; Kawakami, Takuma; Noguchi, Satoko; Itoh, Tomoko; Shigeta, Keiko; Senba, Tadashi; Matsumura, Kyoka; Nakajima, Yoshie; Mizuno, Takae; Morinaga, Misato; Sasaki, Masahide; Togashi, Takushi; Oyama, Masaaki; Hata, Hiroko; Watanabe, Masao; Komatsu, Takami; Mizushima‐Sugano, Junko; Satoh, Tadashi; Shirai, Yuko; Takahashi, Yukiko; Nakagawa, K.; Okumura, Koji; Nagase, Takahiro; Nomura, Nobuo; Kikuchi, Hisashi; Masuho, Yasuhiko; Yamashita, Riu; Nakai, Kenta; Yada, Tetsushi; Nakamura, Yusuke; Ohara, Osamu; Isogai, Takao; Sugano, Sumio

doi:10.1038/ng1285

Cited by 814 publications

(602 citation statements)

References 29 publications

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“…28 The predicted truncated transcript was based on evidence derived from a study characterizing all human cDNAs in a brain cDNA library. 29 Depending on the annotation considered, the variant, g.22879A > G, is in exon 6 of the short transcript, or in intron 5 of the long transcript. We sought to validate the existence of the predicted truncated TPH 2 transcript isoform experimentally by RT-PCR.…”

Section: Resultsmentioning

confidence: 99%

Genetic architecture of the human tryptophan hydroxylase 2 Gene: existence of neural isoforms and relevance for major depression

et al. 2008

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Impaired brain serotonin neurotransmission is a potential component of the diathesis of major depression. Tryptophan hydroxylase-2 (TPH2), is the rate limiting biosynthetic isoenzyme for serotonin that is preferentially expressed in the brain and a cause of impaired serotonin transmission. Here, we identify a novel TPH2 short isoform with truncated catalytic domain expressed in human brainstem, prefrontal cortex, hippocampus and amygdala. An exploratory study of 166 Caucasian subjects revealed association with major depression or suicide of a novel single nucleotide polymorphism (SNP) g.22879A > G located in exon 6 of this short isoform. This SNP and additional SNPs were discovered through a systematic characterization of the genetic architecture of the TPH2 gene for further genetic and functional investigations of its relationship to major depression and other psychopathology.

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Section: Resultsmentioning

confidence: 99%

Genetic architecture of the human tryptophan hydroxylase 2 Gene: existence of neural isoforms and relevance for major depression

et al. 2008

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“…B) CGI 1060 (bold font) overlaps with exon 9 (underlined) and promoter GXP_168256 (dashed line) of a non-coding transcript AK024830. The curved arrow indicates the transcription start site (TSS), 'T', for transcript AK024830 (1687 bp), first reported by Ota et al [40]. CGI 1060 harbours seventeen CpGs (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) and seven SNPs indicated with IUB redundancy codes (R: A/G, Y: Methylation levels were determined with bisulphite pyrosequencing and significance of differences between populations, with Mann-Whitney U. Boxplots show location and dispersion of Venda control (n = 28, white) and Venda TB (n = 32, grey) methylation levels.…”

Section: Discussionmentioning

confidence: 99%

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism

et al. 2011

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The Vitamin D Receptor (VDR) gene encodes a transcription factor which, on activation by vitamin D, modulates diverse biological processes including calcium homeostasis and immune function. Genetic variation involving VDR shows striking differences in allele frequency between populations and has been associated with disease susceptibility including tuberculosis and autoimmunity, although results have often been conflicting. We hypothesized that methylation of VDR may be population specific and that the combination of differential methylation and genetic variation may characterise TB predisposition. We use bisulphite conversion and/or pyrosequencing to analyse the methylation status of 17 CpGs of VDR and to genotype 7 SNPs in the 3′ CpG Island (CGI 1060), including the commonly studied SNPs ApaI (rs7975232) and TaqI (rs731236). We show that for lymphoblastoid cell lines from two ethnically diverse populations (Yoruba from HapMap, n=30 and Caucasians, n=30) together with TB cases (n=32) and controls (n=29) from the Venda population of South Africa there are methylation variable positions (MVPs) in the 3′ end that significantly distinguish ethnicity (9/17 CpGs) and TB status (3/17 CpGs). Moreover methylation status shows complex association with TaqI genotype highlighting the need to consider both genetic and epigenetic variants in genetic studies of VDR association with disease.

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“…15). We searched the completely sequenced full-length cDNAs that corresponded to these TSCs and found seven overlapping cDNAs from the FLJ (Ota et al 2004) and MGC (Gerhard et al 2004) cDNA collections in DLD-1 and TIG-3 cells (Supplementary Table 6a). All of the corresponding full-length cDNAs lacked clear open reading frames.…”

Section: Hif-1a Binding Sites In Intergenic Regionsmentioning

confidence: 99%

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Tanimoto

Tsuchihara

Kanai

et al. 2010

HUGO J

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We identified 531 and 616 putative HIF-1a target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1a binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1a target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1a binding sites, but this event occurred prior to the actual binding of HIF1a. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock.

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Complete sequencing and characterization of 21,243 full-length human cDNAs

Cited by 814 publications

References 29 publications

Genetic architecture of the human tryptophan hydroxylase 2 Gene: existence of neural isoforms and relevance for major depression

Genetic architecture of the human tryptophan hydroxylase 2 Gene: existence of neural isoforms and relevance for major depression

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

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