Abstract
The bottleneck in elucidating gene function through high-throughput gain-of-function genome screening is the limited availability of comprehensive libraries for gene overexpression. Lentiviral vectors are the most versatile and widely used vehicles for gene expression in mammalian cells. Lentiviral supernatant libraries for genome screening are commonly generated in the HEK293T cell line, yet very little is known about the effect of introduced sequences on the produced viral titer, which we have shown to be gene dependent. We have generated an arrayed lentiviral vector library for the expression of 17,030 human proteins by using the GATEWAY® cloning system to transfer ORFs from the Mammalian Gene Collection into an EF1alpha promoter-dependent lentiviral expression vector. This promoter was chosen instead of the more potent and widely used CMV promoter, because it is less prone to silencing and provides more stable long term expression. The arrayed lentiviral clones were used to generate viral supernatant by packaging in the HEK293T cell line. The efficiency of transfection and virus production was estimated by measuring the fluorescence of IRES driven GFP, co-expressed with the ORFs. More than 90% of cloned ORFs produced sufficient virus for downstream screening applications. We identified genes which consistently produced very high or very low viral titer. Supernatants from select clones that were either high or low virus producers were tested on a range of cell lines. Some of the low virus producers, including two previously uncharacterized proteins were cytotoxic to HEK293T cells. The library we have constructed presents a powerful resource for high-throughput gain-of-function screening of the human genome and drug-target discovery. Identification of human genes that affect lentivirus production may lead to improved technology for gene expression using lentiviral vectors.
Highlights
To fully understand functions of the,23,000 protein-coding genes in the human genome, the ability to manipulate their expression under different biological conditions and in a variety of cellular backgrounds is essential
cytomegalovirus immediate-early (CMV) and elongation factor 1a (EF1a) Promoter Comparison in Stable Cell Lines Prior to generating a genome-wide overexpression library, we confirmed that the EF1a promoter provides more stable long-term expression compared to the CMV promoter
The open reading frame (ORF) were tagged with IRES-GFP so that transduced cells could be tracked by fluorescence
Summary
To fully understand functions of the ,23,000 protein-coding genes in the human genome, the ability to manipulate their expression under different biological conditions and in a variety of cellular backgrounds is essential This task can be efficiently tackled using arrayed libraries, in which thousands of agents for gene overexpression or knockdown are confined to relatively small volume in microwell plates. Available siRNA and shRNA libraries for gene knockdown and reported loss-of- function genome screens greatly outnumber gain-of- function screens and tools available for high-throughput mammalian gene overexpression [1] This is in part a reflection of increased difficulty of generating full length constructs for gene overexpression and introducing them into cells, compared to synthesis and introduction of small siRNA molecules into target cells. The range of available promoters, reporter genes, selection cassettes, and viral packaging systems is continually increasing
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