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