Author:
Boivin Vincent,Deschamps-Francoeur Gabrielle,Couture Sonia,Nottingham Ryan M.,Bouchard-Bourelle Philia,Lambowitz Alan M.,Scott Michelle S.,Abou-Elela Sherif
Abstract
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.
Funder
Canadian Institutes of Health Research
National Institutes of Health
Welch Foundation
RNA Biology and Cancer Genomics
Natural Sciences and Engineering Research Council
Fonds de Recherche du Québec - Santé
FRQS Research Scholar Junior 2 Career Award
Publisher
Cold Spring Harbor Laboratory
Cited by
60 articles.
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