title: Deciphering the RNA landscape by RNAome sequencing.
abstract: 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.
authors.affiliation: a Department of Genetics; Netherlands Toxicogenomics Center; Erasmus University Medical Center ; Rotterdam , The Netherlands.
authors.forename: Kasper W J
authors.initials: KW
authors.lastname: Derks
authors.forename: Branislav
authors.initials: B
authors.lastname: Misovic
authors.forename: Mirjam C G N
authors.initials: MC
authors.lastname: van den Hout
authors.forename: Christel E M
authors.initials: CE
authors.lastname: Kockx
authors.forename: Cesar Payan
authors.initials: CP
authors.lastname: Gomez
authors.forename: Rutger W W
authors.initials: RW
authors.lastname: Brouwer
authors.forename: Harry
authors.initials: H
authors.lastname: Vrieling
authors.forename: Jan H J
authors.initials: JH
authors.lastname: Hoeijmakers
authors.forename: Wilfred F J
authors.initials: WF
authors.lastname: van IJcken
authors.forename: Joris
authors.initials: J
authors.lastname: Pothof
mesh_terms: D000818:Animals; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D012313:RNA / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: DEGs, differentially expressed genes; NGS, next generation sequencing; RNA abundance; RNA expression; RNAome; eRNA, enhancer RNA; isomiRs, microRNA isoforms.; lncRNAs, long non-coding RNA; mRNASeq, mRNA sequencing; non-coding RNA; poly(A), poly-adenylation; rRNA, ribosomal RNA; smallRNASeq, small non-coding RNA sequencing; snoRNAs, small nucleolar RNAs; strand-specific RNA-sequencing; whole transcriptome
references.citation: PLoS One. 2013;8(8):e73870
references.pmid: 23977393
references.citation: Semin Cell Dev Biol. 2011 Jun;22(4):327
references.pmid: 21621631
references.citation: Nature. 2010 Aug 12;466(7308):835-40
references.pmid: 20703300
references.citation: Cell. 2007 Jun 29;129(7):1401-14
references.pmid: 17604727
references.citation: Bioinformatics. 2010 Jan 1;26(1):139-40
references.pmid: 19910308
references.citation: Stat Methods Med Res. 2013 Oct;22(5):519-36
references.pmid: 22127579
references.citation: Nat Rev Cancer. 2012 Sep;12(9):613-26
references.pmid: 22898542
references.citation: Trends Genet. 2012 Nov;28(11):544-9
references.pmid: 22883467
references.citation: Mutat Res. 2007 Apr 1;617(1-2):58-70
references.pmid: 17327130
references.citation: Genomics. 2010 Nov;96(5):259-65
references.pmid: 20688152
references.citation: Nature. 2013 May 16;497(7449):383-7
references.pmid: 23636329
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Genome Res. 2011 Jul;21(7):1160-7
references.pmid: 21543516
references.citation: Brief Bioinform. 2013 Mar;14(2):178-92
references.pmid: 22517427
references.citation: BMC Biol. 2010;8:149
references.pmid: 21176148
references.citation: J Interferon Cytokine Res. 2013 Apr;33(4):189-98
references.pmid: 23570385
references.citation: Cell Death Differ. 2009 Jun;16(6):858-68
references.pmid: 19229243
references.citation: Protein Sci. 2012 Jun;21(6):797-808
references.pmid: 22434730
references.citation: Mol Cell. 2010 Oct 22;40(2):205-15
references.pmid: 20965416
references.citation: Nature. 2012 Feb 16;482(7385):339-46
references.pmid: 22337053
references.citation: Bioinformatics. 2012 Jan 15;28(2):284-5
references.pmid: 22072383
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Nature. 2013 Jun 27;498(7455):516-20
references.pmid: 23728302
references.citation: Nature. 2012 Sep 6;489(7414):101-8
references.pmid: 22955620
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18097-102
references.pmid: 17989215
references.citation: Nature. 2010 May 13;465(7295):182-7
references.pmid: 20393465
references.citation: Wiley Interdiscip Rev RNA. 2013 Nov-Dec;4(6):677-91
references.pmid: 23881603
references.citation: Stat Appl Genet Mol Biol. 2004;3:Article3
references.pmid: 16646809
references.citation: Sci Rep. 2013;3:1689
references.pmid: 23604310
references.citation: Nucleic Acids Res. 2013 Jun;41(11):5604-13
references.pmid: 23605046
references.citation: Nat Rev Cancer. 2011 Sep;11(9):644-56
references.pmid: 21822212
references.citation: Mol Cell. 2013 Feb 7;49(3):524-35
references.pmid: 23273978
references.citation: Genome Biol. 2013;14(4):R31
references.pmid: 23594475
references.citation: Nucleic Acids Res. 2013 Jul;41(12):6300-15
references.pmid: 23630323
references.citation: Nature. 2011 Jun 16;474(7351):390-4
references.pmid: 21572438
references.citation: Cell. 2009 Jan 23;136(2):215-33
references.pmid: 19167326
references.citation: Mol Cell. 2012 Oct 26;48(2):219-30
references.pmid: 22959273
references.citation: EMBO J. 2009 Jul 22;28(14):2090-9
references.pmid: 19536137
references.citation: Genome Biol. 2011;12(2):R16
references.pmid: 21324177
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
references.pmid: 16381832
references.citation: Cell. 2010 Aug 6;142(3):409-19
references.pmid: 20673990
references.citation: Nature. 2011 Sep 15;477(7364):295-300
references.pmid: 21874018
references.citation: Nat Genet. 2007 May;39(5):673-7
references.pmid: 17401365
references.citation: Nat Rev Genet. 2009 Mar;10(3):155-9
references.pmid: 19188922