Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.
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通过分析具有聚腺苷酸化位点的内含子单块 EST 发现新的人类转录物变体
DOI：
10.1186/1471-2164-10-518
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发表时间：
2009-11-12
期刊：
影响因子：
4.4
通讯作者：
Ma D
中科院分区：
文献类型：
--
作者：
Wang P;Yu P;Gao P;Shi T;Ma D
基因内不同的聚腺苷化位点可导致不同的转录物变异。尽管利用公共数据库中的核酸序列（EST/mRNA）进行生物信息学分析以检测聚腺苷化位点，但一种特殊类型的单片段EST却很少受到重视。这种偏见为发现新的转录变体留下了很大的空间。在本研究中，我们通过检测内含子聚腺苷酸化位点在人类基因组中发现了新的转录变体。从单块ESTs中获得Poly(A/T)-tailed ESTs，聚类成10,844组，代表5,670个基因。大多数位点未在其他备选剪接数据库中找到。为了验证这些位点来自于表达的转录本，我们分析了每个位点的支持EST数量，对已知的mRNA序列进行了代表性EST的blast，从cDNA克隆中追踪了末端序列，并与Affymetrix平铺阵列的数据进行了比较。这些分析证实了约84%（9,118/10,844）的新替代转录本，特别是来自2,704个基因的33%（3,575/10,844）的转录本被认为是高可靠性的。此外，RT-PCR证实了38%（10/26）预测的新转录物变异。我们的研究结果为含有内含子多聚(A)位点的新型转录物变体提供了证据。这些新变异的表达通过计算和实验工具得到了证实。我们的数据为鉴定具有内含子多腺苷化位点的新型人类转录物变体提供了全基因组资源，并为人类转录组之谜提供了新的视角。
Alternative polyadenylation sites within a gene can lead to alternative transcript variants. Although bioinformatic analysis has been conducted to detect polyadenylation sites using nucleic acid sequences (EST/mRNA) in the public databases, one special type, single-block EST is much less emphasized. This bias leaves a large space to discover novel transcript variants. In the present study, we identified novel transcript variants in the human genome by detecting intronic polyadenylation sites. Poly(A/T)-tailed ESTs were obtained from single-block ESTs and clustered into 10,844 groups standing for 5,670 genes. Most sites were not found in other alternative splicing databases. To verify that these sites are from expressed transcripts, we analyzed the supporting EST number of each site, blasted representative ESTs against known mRNA sequences, traced terminal sequences from cDNA clones, and compared with the data of Affymetrix tiling array. These analyses confirmed about 84% (9,118/10,844) of the novel alternative transcripts, especially, 33% (3,575/10,844) of the transcripts from 2,704 genes were taken as high-reliability. Additionally, RT-PCR confirmed 38% (10/26) of predicted novel transcript variants. Our results provide evidence for novel transcript variants with intronic poly(A) sites. The expression of these novel variants was confirmed with computational and experimental tools. Our data provide a genome-wide resource for identification of novel human transcript variants with intronic polyadenylation sites, and offer a new view into the mystery of the human transcriptome.
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AltTrans：针对替代剪接和替代聚腺苷酸化的转录本模式变体。
影响因子：
3
作者：
Le Texier, V;Riethoven, JJ;Kumanduri, V;Gopalakrishnan, C;Lopez, F;Gautheret, D;Thanaraj, TA
通讯作者：
Thanaraj, TA
影响因子：
14.9
作者：
Castrignanò T;Rizzi R;Talamo IG;De Meo PD;Anselmo A;Bonizzoni P;Pesole G
通讯作者：
Pesole G
影响因子：
4.4
作者：
Iwami, K;Matsuguchi, T;Yoshikai, Y
通讯作者：
Yoshikai, Y
影响因子：
7
作者：
Beaudoing, E;Gautheret, D
通讯作者：
Gautheret, D
影响因子：
56.9
作者：
Kapranov, Philipp;Cheng, Jill;Gingeras, Thomas R.
通讯作者：
Gingeras, Thomas R.