RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)

RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. H...

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Veröffentlicht in:Frontiers in genetics Jg. 9; S. 278
Hauptverfasser: Correia, Carolina N., McLoughlin, Kirsten E., Nalpas, Nicolas C., Magee, David A., Browne, John A., Rue-Albrecht, Kevin, Gordon, Stephen V., MacHugh, David E.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Switzerland Frontiers Media S.A 14.08.2018
Schlagworte:
blood
cattle
Genetics
globin
horses
pigs
reticulocyte
pigs
RNA-seq
globin
reticulocyte
transcriptome
cattle
blood
horses
ISSN:1664-8021, 1664-8021
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Zusammenfassung:RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
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Edited by: John Anthony Hammond, Pirbright Institute (BBSRC), United Kingdom
Kevin Rue-Albrecht, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
Reviewed by: Chuanju Dong, Henan Normal University, China; Luiz Lehmann Coutinho, Universidade de São Paulo, Brazil
This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics
Present Address: Nicolas C. Nalpas, Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2018.00278