|Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site|
|Wang, Pingzhang1,2,3; Yu, Peng1; Gao, Peng1; Shi, Taiping1,2,3; Ma, Dalong1,2,3|
|WOS标题词||Science & Technology|
|类目[WOS]||Biotechnology & Applied Microbiology ; Genetics & Heredity|
|研究领域[WOS]||Biotechnology & Applied Microbiology ; Genetics & Heredity|
|关键词[WOS]||MESSENGER-RNA POLYADENYLATION ; NECROSIS-FACTOR RECEPTORS ; ACTIVATED PROTEIN-KINASE ; GENOME BROWSER DATABASE ; NF-KAPPA-B ; ALTERNATIVE POLYADENYLATION ; HUMAN-DISEASE ; HUMAN TISSUES ; SOLUBLE FORM ; 2008 UPDATE|
Background: 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.
Results: 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.
Conclusion: 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.
|项目编号||30600549 ; 2006AA02A305 ; 2009ZX09503-004|
|资助机构||National Natural Science Foundation of China ; National High Technology Research and Development Program of China ; Key National S& ; T Program--"Major New Drug Development"|
|作者单位||1.Chinese Natl Human Genome Ctr, Beijing 100176, Peoples R China|
2.Peking Univ, Hlth Sci Ctr, Sch Basic Med Sci, Lab Med Immunol, Beijing 100083, Peoples R China
3.Peking Univ, Ctr Human Dis Genom, Beijing 100083, Peoples R China
|Wang, Pingzhang,Yu, Peng,Gao, Peng,et al. Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site[J]. BMC GENOMICS,2009,10(0).|
|APA||Wang, Pingzhang,Yu, Peng,Gao, Peng,Shi, Taiping,&Ma, Dalong.(2009).Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.BMC GENOMICS,10(0).|
|MLA||Wang, Pingzhang,et al."Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site".BMC GENOMICS 10.0(2009).|
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