Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

作     者：QianWu, Jia Du, Jiang Rozowsky, Joel Zhang, Zhengdong Urban, Alexander E. Euskirchen, Ghia Weissman, Sherman Gerstein, Mark Snyder, Michael 

作者机构：Yale Univ Mol Cellular & Dev Biol Dept New Haven CT 06511 USA Yale Univ Dept Comp Sci New Haven CT 06511 USA Yale Univ Dept Biochem & Mol Biophys New Haven CT 06511 USA Yale Univ Dept Genet New Haven CT 06511 USA 

出 版 物：《GENOME BIOLOGY》 (基因组生物学)

年 卷 期：2008年第9卷第1期

页      面：R3-R3页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

基　　金：NIGMS NIH HHS [F32 GM078822] Funding Source: Medline 

主　　题：Additional Data File Antisense Transcript Tiling Array Antisense Transcription Encode Region 

摘      要：Background: Recent studies of the mammalian transcriptome have revealed a large number of additional transcribed regions and extraordinary complexity in transcript diversity. However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced. Results: We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing. We analyzed annotated known gene regions, but primarily we focused on novel transcriptionally active regions (TARs), which were previously identified by high-density oligonucleotide tiling arrays and on random regions that were not believed to be transcribed. We found RACE sequencing to be very sensitive and were able to detect low levels of transcripts in specific cell types that were not detectable by microarrays. We also observed many instances of sense-antisense transcripts;further analysis suggests that many of the antisense transcripts (but not all) may be artifacts generated from the reverse transcription reaction. Our results show that the majority of the novel TARs analyzed (60%) are connected to other novel TARs or known exons. Of previously unannotated random regions, 17% were shown to produce overlapping transcripts. Furthermore, it is estimated that 9% of the novel transcripts encode proteins. Conclusion: We conclude that RACE sequencing is an efficient, sensitive, and highly accurate method for characterization of the transcriptome of specific cell/tissue types. Using this method, it appears that much of the genome is represented in polyA+ RNA. Moreover, a fraction of the novel RNAs can encode protein and are likely to be functional.