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

Boivin, Vincent, Deschamps-Francoeur, Gabrielle, Couture, Sonia, Nottingham, Ryan M., Bouchard-Bourelle, Philia, Lambowitz, Alan M., Scott, Michelle S., Abou-Elela, Sherif·2018·RNA
DOI 10.1261/rna.064493.117PMC PMC6004057
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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. S tructured n on c oding 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.

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  • snoRNA and snRNA are believed to yield incomplete recovery in small RNA-seq experiments due to their secondary structure.

    “snoRNA and snRNA are believed to yield incomplete recovery in small RNA-seq experiments due to their secondary structure (32).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [32]

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Cited by

Sorted by citations

Authors
Boivin, V., Deschamps-Francoeur, G., Couture, S., Nottingham, R. M., Bouchard-Bourelle, P., Lambowitz, A. M., Scott, M. S., & Abou-Elela, S.
Venue
RNA
Publisher
Cold Spring Harbor Laboratory
Published
2018-04-27
Volume
24
Issue
7
Pages
950-965
ISSN
  • 1355-8382
  • 1469-9001
DOI
10.1261/rna.064493.117
PMC
PMC6004057
Cited by
86
References
5
Language
en
Funders
  • Canadian Institutes of Health Research (PJT 153171)
  • National Institutes of Health (R01 GM37949)
  • Welch Foundation (F1706)
  • RNA Biology and Cancer Genomics
  • Natural Sciences and Engineering Research Council
  • Fonds de Recherche du Québec - Santé
  • FRQS Research Scholar Junior 2 Career Award

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