Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Zhihua Jiang; Xiang Zhou; Rui Li; Jennifer J Michal; Shuwen Zhang; Michael V Dodson; Zhiwu Zhang; Richard M Harland

doi:10.1007/s00018-015-1934-y

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Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Journal article

Open access

Peer reviewed

Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer J Michal, Shuwen Zhang, Michael V Dodson, Zhiwu Zhang and Richard M Harland

Cellular and molecular life sciences : CMLS, Vol.72(18), pp.3425-3439

09/2015

DOI: https://doi.org/10.1007/s00018-015-1934-y

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https://hdl.handle.net/2376/100901

PMCID: PMC6233721

PMID: 26018601

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Abstract

5′ ends and 3′ ends

PolyA+ RNAs

Next generation sequencing

PolyA− RNAs

Circular RNAs

RNA methylation

Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5′ and 3′ ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.

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Title: Whole transcriptome analysis with sequencing: methods, challenges and potential solutions
Creators: Zhihua Jiang - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Xiang Zhou - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Rui Li - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Jennifer J Michal - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Shuwen Zhang - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Michael V Dodson - Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
Zhiwu Zhang - Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA
Richard M Harland - Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
Publication Details: Cellular and molecular life sciences : CMLS, Vol.72(18), pp.3425-3439
Academic Unit: Animal Sciences, Department of; Crop and Soil Sciences, Department of
Identifiers: 99900546686601842
Language: English
Resource Type: Journal article