Deciphering the RNA landscape by RNAome sequencing

Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence...

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Bibliographic Details
Published in:RNA biology 2015-01, Vol.12 (1), p.30-42
Main Authors: Derks, Kasper WJ, Misovic, Branislav, van den Hout, Mirjam CGN, Kockx, Christel EM, Payan Gomez, Cesar, Brouwer, Rutger WW, Vrieling, Harry, Hoeijmakers, Jan HJ, van IJcken, Wilfred FJ, Pothof, Joris
Format: Article
Language:English
Subjects:
Animals
High-Throughput Nucleotide Sequencing - methods
Humans
Mice
non-coding RNA
RNA - metabolism
RNA abundance
RNA expression
RNAome
Sequence Analysis, RNA - methods
strand-specific RNA-sequencing
Technical Paper
Transcriptome
whole transcriptome
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Summary:Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.
ISSN:1547-6286
1555-8584
DOI:10.1080/15476286.2015.1017202