Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

被引:47
作者
Boivin, Vincent [1 ]
Deschamps-Francoeur, Gabrielle [1 ]
Couture, Sonia [2 ]
Nottingham, Ryan M. [3 ,4 ]
Bouchard-Bourelle, Philia [1 ]
Lambowitz, Alan M. [3 ,4 ]
Scott, Michelle S. [1 ]
Abou-Elela, Sherif [2 ]
机构
[1] Univ Sherbrooke, Fac Med & Sci Sante, Dept Biochim, Sherbrooke, PQ J1E 4K8, Canada
[2] Univ Sherbrooke, Fac Med & Sci Sante, Dept Microbiol & Infectiol, Sherbrooke, PQ J1E 4K8, Canada
[3] Univ Texas Austin, Inst Cellular & Mol Biol, Austin, TX 78712 USA
[4] Univ Texas Austin, Dept Mol Biosci, Austin, TX 78712 USA
基金
美国国家卫生研究院; 加拿大健康研究院; 加拿大自然科学与工程研究理事会;
关键词
high-throughput sequencing; noncoding RNA; snoRNA; RNA detection; thermostable group II intron reverse transcriptase; transcriptome analysis; SIGNAL RECOGNITION PARTICLE; INTRON REVERSE-TRANSCRIPTASE; TIME QUANTITATIVE PCR; SMALL NUCLEOLAR RNAS; DROPLET DIGITAL PCR; RIBOSOMAL-RNA; OVARIAN-CARCINOMA; CANCER; SEQ; DATABASE;
D O I
10.1261/rna.064493.117
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. Structured noncoding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing.
引用
收藏
页码:950 / 965
页数:16
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