Puromycin Selection Confounds the RNA-Seq Profiles of Primary Human Erythroblasts
Guo RL, Lee YT, Byrnes C, and Miller JL*
Molecular Genomics and Therapeutics Section, Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
- *Corresponding Author:
- Jeffery L Miller
Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health, 10 Center Drive, Building 10, Room 9N311, Bethesda, Maryland 20892. USA
E-mail: [email protected]
Received Date: April 01, 2017; Accepted Date: April 27, 2017; Published Date: May 01, 2017
Citation: Guo RL, Lee YT, Byrnes C, Miller JL (2017) Puromycin Selection Confounds the RNA-Seq Profiles of Primary Human Erythroblasts. Transcriptomics 5:140. doi: 10.4172/2329-8936.1000140
Copyright: © 2017 Guo RL, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Lentiviral transduction followed by puromycin selection is a well-recognized procedure for gene transfer and expression experiments using a variety of cell types including human hematopoietic stem and progenitor cells. Despite its widespread application, research regarding the potential effects of bacterial puromycin N-acetyltransferase (pac) gene expression in mammalian cell cultures is incomplete. Here the potential for puromycin selection to affect transcriptome profiles was examined using a well-studied model for human erythropoiesis. Experiments were performed using primary CD34(+) cells from six adult healthy human donors transduced with two commercially available pac-encoding lentiviral vectors and compared to non-transduced control cells. RNA-Seq gene expression profiles were generated at the proerythroblast stage of differentiation, then differential gene expression was analyzed with DEseq2 in R-Studio software. Inter-donor variation in the gene expression profiles and variations between puromycin selected populations after transduction of the separate lentiviral vectors was manifested by significant differences in the RNA detection levels of less than 0.1%. However, puromycin selection after pac gene transduction caused significant changes in over 5% of the mRNA when compared to non-transduced controls. The results suggest that consideration should be given for the potential of puromycin selection to confound the interpretation of RNA-Seq transcriptome profiles.