Leveraging human genomic information to identify nonhuman primate sequences for expression array development.
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.
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DOI：
10.1186/1471-2164-6-160
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发表时间：
2005-11-15
期刊：
影响因子：
4.4
通讯作者：
Norgren RB Jr
中科院分区：
文献类型：
--
作者：
Spindel ER;Pauley MA;Jia Y;Gravett C;Thompson SL;Boyle NF;Ojeda SR;Norgren RB Jr
由于非人类灵长类动物与人类的相似性，它们对生物医学研究至关重要。基因表达谱等基于基因组学的方法的应用将大大增加NHPs的效用。来自基因3'端的序列信息是创建寡核苷酸表达阵列所需的关键资源。我们已经开发了必要的算法和程序，从人类基因的非人类灵长类动物的3'端快速获取序列信息。为了实现这一目标，我们通过将mRNA序列与基因组序列比对，鉴定了超过15,000个人类基因的末端外显子。我们发现完整的最后外显子的平均长度约为1,400 bp，明显长于先前的估计。我们设计了引物来扩增基因组DNA，其中至少包括300 bp的末端外显子。我们克隆并测序了5500多个恒河猴与人类基因同源的PCR产物。该序列信息已用于选择恒河猴基因表达谱的探针。我们还测试了10组引物的基因组DNA来自Macaca fascicularis（食蟹猴）、Papio hamadryas（狒狒）和Chlorocebus aethiops（非洲绿猴，黑尾猴）。结果表明，本研究开发的引物可用于其他非人灵长类动物基因3′端序列的获取。该研究表明，人类基因组DNA序列可以利用从NHP同源物的3'端获得序列，然后该序列可用于生成NHP寡核苷酸微阵列。Affymetrix和Agilent在设计恒河猴寡核苷酸微阵列时使用了这种方法获得的序列。
Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays. We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. This sequence information has been used to select probes for rhesus gene expression profiling. We have also tested 10 sets of primers with genomic DNA from Macaca fascicularis (Cynomolgus monkey), Papio hamadryas (Baboon), and Chlorocebus aethiops (African green monkey, vervet). The results indicate that the primers developed for this study will be useful for acquiring sequence from the 3' end of genes for other nonhuman primate species. This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays. Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays.
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DOI：
10.1073/pnas.1534744100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Mei, R;Hubbell, E;Webster, TA
通讯作者：
Webster, TA
影响因子：
9.8
作者：
Imanishi T;Itoh T;Suzuki Y;O'Donovan C;Fukuchi S;Koyanagi KO;Barrero RA;Tamura T;Yamaguchi-Kabata Y;Tanino M;Yura K;Miyazaki S;Ikeo K;Homma K;Kasprzyk A;Nishikawa T;Hirakawa M;Thierry-Mieg J;Thierry-Mieg D;Ashurst J;Jia L;Nakao M;Thomas MA;Mulder N;Karavidopoulou Y;Jin L;Kim S;Yasuda T;Lenhard B;Eveno E;Suzuki Y;Yamasaki C;Takeda J;Gough C;Hilton P;Fujii Y;Sakai H;Tanaka S;Amid C;Bellgard M;Bonaldo Mde F;Bono H;Bromberg SK;Brookes AJ;Bruford E;Carninci P;Chelala C;Couillault C;de Souza SJ;Debily MA;Devignes MD;Dubchak I;Endo T;Estreicher A;Eyras E;Fukami-Kobayashi K;Gopinath GR;Graudens E;Hahn Y;Han M;Han ZG;Hanada K;Hanaoka H;Harada E;Hashimoto K;Hinz U;Hirai M;Hishiki T;Hopkinson I;Imbeaud S;Inoko H;Kanapin A;Kaneko Y;Kasukawa T;Kelso J;Kersey P;Kikuno R;Kimura K;Korn B;Kuryshev V;Makalowska I;Makino T;Mano S;Mariage-Samson R;Mashima J;Matsuda H;Mewes HW;Minoshima S;Nagai K;Nagasaki H;Nagata N;Nigam R;Ogasawara O;Ohara O;Ohtsubo M;Okada N;Okido T;Oota S;Ota M;Ota T;Otsuki T;Piatier-Tonneau D;Poustka A;Ren SX;Saitou N;Sakai K;Sakamoto S;Sakate R;Schupp I;Servant F;Sherry S;Shiba R;Shimizu N;Shimoyama M;Simpson AJ;Soares B;Steward C;Suwa M;Suzuki M;Takahashi A;Tamiya G;Tanaka H;Taylor T;Terwilliger JD;Unneberg P;Veeramachaneni V;Watanabe S;Wilming L;Yasuda N;Yoo HS;Stodolsky M;Makalowski W;Go M;Nakai K;Takagi T;Kanehisa M;Sakaki Y;Quackenbush J;Okazaki Y;Hayashizaki Y;Hide W;Chakraborty R;Nishikawa K;Sugawara H;Tateno Y;Chen Z;Oishi M;Tonellato P;Apweiler R;Okubo K;Wagner L;Wiemann S;Strausberg RL;Isogai T;Auffray C;Nomura N;Gojobori T;Sugano S
通讯作者：
Sugano S
DOI：
10.1016/s0097-8485(02)00009-8
发表时间：
2002-07-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Larizza, A;Makalowski, W;Saccone, C
通讯作者：
Saccone, C
DOI：
10.1186/1477-7827-2-40
发表时间：
2004-06-16
期刊：
Reproductive biology and endocrinology : RB&E
影响因子：
--
作者：
Norgren RB Jr
通讯作者：
Norgren RB Jr
DOI：
10.1186/1477-7827-2-41
发表时间：
2004-06-16
期刊：
Reproductive biology and endocrinology : RB&E
影响因子：
--
作者：
Pau, K-Y Francis;Wolf, Don P
通讯作者：
Wolf, Don P