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Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing

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Gene Expression Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1783))

Abstract

The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach. However, due to inherent limitations of this approach in de novo transcriptome assembly and isoform quantification, long-read RNA-Seq approaches, which also happen to be single molecule sequencing approaches, are increasingly becoming the standard for de novo transcriptome assembly and isoform quantification. In this chapter, we review the technical aspects of the current methods of RNA-Seq, both short and long-read approaches, and data analysis methods available. We discuss recent advances in single-cell RNA-Seq and direct RNA-Seq approaches, which perhaps will dominate the future of RNA-Seq.

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Authors and Affiliations

  1. McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada

    Anthony Bayega, Spyros Oikonomopoulos & Jiannis Ragoussis

  2. Research Institute of McGill University Health Centre, Montréal, QC, Canada

    Somayyeh Fahiminiya

  3. Department of Bioengineering, McGill University, Montréal, QC, Canada

    Jiannis Ragoussis

  4. Cancer and Mutagen Unit, Department of Biochemistry, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Jiannis Ragoussis

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  1. Anthony Bayega
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  2. Somayyeh Fahiminiya
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  3. Spyros Oikonomopoulos
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  4. Jiannis Ragoussis
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Correspondence to Jiannis Ragoussis .

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Editors and Affiliations

  1. Division of Geriatrics and Clinical Gerontology, National Institute on Aging, Bethesda, Maryland, USA

    Nalini Raghavachari

  2. Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi, USA

    Natàlia Garcia-Reyero

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Bayega, A., Fahiminiya, S., Oikonomopoulos, S., Ragoussis, J. (2018). Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing. In: Raghavachari, N., Garcia-Reyero, N. (eds) Gene Expression Analysis. Methods in Molecular Biology, vol 1783. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7834-2_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7834-2_11

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