Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling

James      Dominic Mills; Yoshihiro      Kawahara; Michael      Janitz

doi:10.2174/1389202911314030003

Abstract

RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for unique insights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternative splicing events and the presence of non-coding RNAs. It has been realised non-coding RNAs are more then just artefacts of erroneous transcription and play vital regulatory roles at the genomic, transcriptional and translational level. Transcription of the DNA sense strand produces antisense transcripts. This is known as antisense transcription and often results in the production of non-coding RNAs that are complementary to their associated sense transcripts. Antisense transcription has been identified in bacteria, fungi, protozoa, plants, invertebrates and mammals. It seems that antisense transcriptional ‘hot spots’ are located around nucleosome-free regions such as those associated with promoters, indicating that it is likely that antisense transcripts carry out important regulatory functions. This underlines the importance of identifying the presence and understanding the function of these antisense non-coding RNAs. The information concerning strand origin is often lost during conventional RNA-Seq; capturing this information would substantially increase the worth of any RNA-Seq experiment. By manipulating the input cDNA during the template preparation stage it is possible to retain this vital information. This forms the basis of strand-specific RNA-Seq. With an ability to unlock immense portions of new information surrounding the transcriptome, this cutting edge technology may hold the key to developing a greater understanding of the transcriptome.

Keywords: Antisense RNA, Next-generation sequencing, Non-coding, RNA, Transcriptome, Pervasive transcription.

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