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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Deciphering the RNA landscape by RNAome sequencing.

Kasper W J Derks1, Branislav Misovic, Mirjam C G N van den Hout

  • 1a Department of Genetics; Netherlands Toxicogenomics Center; Erasmus University Medical Center ; Rotterdam , The Netherlands.

RNA Biology
|April 1, 2015
PubMed
Summary
This summary is machine-generated.

RNAome sequencing offers a comprehensive method for analyzing all RNA types simultaneously, overcoming limitations of traditional RNA expression profiling. This novel approach reveals previously undetectable RNA species and their expression patterns, advancing RNA biology research.

Keywords:
DEGs, differentially expressed genesNGS, next generation sequencingRNA abundanceRNA expressionRNAomeeRNA, enhancer RNAisomiRs, microRNA isoforms.lncRNAs, long non-coding RNAmRNASeq, mRNA sequencingnon-coding RNApoly(A), poly-adenylationrRNA, ribosomal RNAsmallRNASeq, small non-coding RNA sequencingsnoRNAs, small nucleolar RNAsstrand-specific RNA-sequencingwhole transcriptome

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Current RNA expression profiling methods often require enrichment for specific RNA classes, limiting comprehensive analysis.
  • Existing analysis pipelines struggle to simultaneously analyze both small and large RNA species.
  • Unbiased detection of all RNA species is crucial for a complete understanding of RNA biology.

Purpose of the Study:

  • To develop and validate a strand-specific RNAome sequencing method for simultaneous expression profiling of all RNA classes.
  • To introduce the Total RNA Analysis Pipeline (TRAP) for robust analysis of small and large RNAs.
  • To demonstrate the utility of RNAome sequencing in identifying novel RNA species and their expression changes.

Main Methods:

  • Strand-specific RNAome sequencing of rRNA-depleted total RNA.
  • Development of the Total RNA Analysis Pipeline (TRAP) for simultaneous small and large RNA analysis.
  • Application of RNAome sequencing to mouse embryonic stem cells treated with cisplatin.

Main Results:

  • RNAome sequencing quantitatively preserved all RNA classes, enabling cross-class comparisons.
  • High correlation of microRNA and mRNA expression with existing methods and arrays.
  • Detection of novel RNA species, including enhancer RNAs and anti-sense RNAs, undetectable by other methods.
  • Identification of cisplatin-induced global repression of microRNA and microRNA isoforms.

Conclusions:

  • RNAome sequencing provides a comprehensive and unperturbed view of the entire transcriptome.
  • The TRAP pipeline facilitates robust analysis of diverse RNA classes.
  • This method significantly enhances RNA expression analysis and RNA biology studies, revealing insights not accessible with current techniques.