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 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. © Kasper WJ Derks, Branislav Misovic, Mirjam CGN van den Hout, Christel EM Kockx, Cesar Payan Gomez, Rutger WW Brouwer, Harry Vrieling, Jan HJ Hoeijmakers, Wilfred FJ van IJcken, and Joris Pothof.

• Fecha de publicación: 2015
• Institución: Universidad del Rosario
• Repositorio: Repositorio EdocUR - U. Rosario
• Idioma: eng
• OAI Identifier: oai:repository.urosario.edu.co:10336/23257
• Acceso en línea: https://doi.org/10.1080/15476286.2015.1017202; https://repository.urosario.edu.co/handle/10336/23257
• Palabra clave: Cisplatin; Long untranslated rna; Messenger rna; Microrna; Polyadenylated rna; Ribosome rna; Rna; Small nucleolar rna; Rna; Transcriptome; Algorithm; Animal cell; Apoptosis; Article; Controlled study; Dna library; Embryo; Embryonic stem cell; Enhancer region; Gene expression; Gene repression; Genetic code; Genetic transcription; Microarray analysis; Mouse; Nonhuman; Quantitative analysis; Rna analysis; Rna isolation; Rna sequence; Rna synthesis; Animal; High throughput sequencing; Human; Metabolism; Procedures; Sequence analysis; Animals; High-throughput nucleotide sequencing; Humans; Mice; Rna; Transcriptome; Non-coding rna; Rna abundance; Rna expression; Rnaome; Strand-specific rna-sequencing; Whole transcriptome; rna; Sequence analysis
• License: Abierto (Texto Completo)