The Necessity of Using Strand-Specific cDNA for Achieving Accurate Transcriptome Analysis Result.

Abstract

The importance of transcriptome analysis results due to their critical roles in genome annotation and subsequently progression in prevention, prognosis, diagnosis, and treatment of disease, led us on sharing our concern about the accuracy level of these existent data and meta‐analysis on them. Transcriptome analysis, especially RNA sequencing (RNA‐seq), has increasingly provided new insights for understanding gene structure, expression, and regulation and has been developed in some methodology.[1,2] There are regions in the genome (nearly 10% of the human genome loci) that produce both coding and noncoding isoforms that are called bifunctional RNAs and were confirmed and annotated by NCBI. The balance between noncoding and coding RNAs levels are affected by both physiologic process like development stages and differentiation and also environmental factors such as drug, physical or chemical agent or viral, bacterial or fungal pathogens.[3] Moreover, information in antisense transcripts plays important role in transcriptome profiling according to their critical roles in biological functions, as well as, by affecting accurately quantifying sense gene expression, particularly for genes with the overlapping loci and opposite direction of transcription. Therefore, discrimination between coding and noncoding isoforms is crucial to prevent misinterpretation of RNA‐Seq data.