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 tran-scription has been identified in bacteria, fungi, protozoa, plants, invertebrates and mammals. It seems that antisense tran-scriptional ‘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 ori-gin 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 in-formation surrounding the transcriptome, this cutting edge technology may hold the key to developing a greater under-standing of the transcriptome.
Highlights
As sequencing techniques become more sophisticated and our understanding of molecular biology increases, it has become apparent that the pathway from gene to protein is an intricate and multifaceted process
One trend that does exist amongst higher eukaryotes and humans is an increase in alternative splicing events and the addition of a variety of non-coding RNAs [5]
Any aligned read that contains a stretch of adenines at the end of the transcript must be a transcript that originated from the DNA antisense strand, while any reads that align with a stretch of thymines at the front must be a transcript from the DNA sense strand (Fig. 1A) [54]
Summary
As sequencing techniques become more sophisticated and our understanding of molecular biology increases, it has become apparent that the pathway from gene to protein is an intricate and multifaceted process. While the use of RNA-seq is becoming more common throughout molecular biology, one significant short-coming of the standard RNA-seq protocol is that it loses the strand of origin information for each transcript. This is of particular concern due to the possible regulatory role carried out by antisense transcripts. Due to the increase in the time and knowledge required or lack of awareness, this method is severely underutilized in research This could be leading to vital elements of the transcriptome being overlooked. Through the use of strand-specific RNA-Seq a more complete understanding of the transcriptome could be achieved, this has the potential to identify new levels of regulation of gene expression
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