Genome-wide landscape of position effects on heterogeneous gene expression in Saccharomyces cerevisiae

Abstract

BackgroundIntegration of heterogeneous genes is widely applied in synthetic biology and metabolic engineering. However, knowledge about the effect of integrative position on gene expression remains limited.ResultsWe established a genome-wide landscape of position effect on gene expression in Saccharomyces cerevisiae. The expression cassette of red fluorescence protein (RFP) gene was constructed and inserted at 1044 loci, which were scattered uniformly in the yeast genome. Due to the different integrative loci on the genome, the maximum relative intensity of RFP is more than 13-fold over the minimum. Plots of the number of strains to RFP relative intensity showed normal distribution, indicating significant position effect on gene expression in yeast. Furthermore, changing the promoters or reporter genes, as well as carbon sources, revealed little consequences on reporter gene expression, indicating chromosomal location is the major determinant of reporter gene expression.ConclusionsWe have examined the position effects to integration genes expression in large number loci around whole genome in S. cerevisiae. The results could guide the design of integration loci for exogenous genes and pathways to maximize their expression in metabolic engineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0872-3) contains supplementary material, which is available to authorized users.

Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis

“…A global survey characterized the position effects observed when the red fluorescent protein (RFP) gene was integrated at 1044 different genomic positions. Based on location, there was a 13-fold difference in fluorescence seen between difference loci [61]. Additional analysis of KAN R expression across the yeast deletion library revealed significant differences in the level of KAN R expression from locus to locus, with upto 35% of expressional differences attributed to position effects (Table 1) [62].…”

“…Global analyses of position effects reveal that centromeric and telomeric regions, a distance defined as +/− 20 kB from the repeat sequence, result in reduced gene expression compared to integration sites positioned further away [61]. These regions, however, are not completely silent in all cases.…”

“…Genomic regions further away represent target sites that are more conducive for higher levels of gene expression, although position effects only result in high levels of expression in 25% of the genome. Hot spots that support high levels of expression include the YDR448W, YGR240C, YHR142W, YML059C, YPL014W, and YPR028W loci, and represent excellent starting points for researchers who want to synthesize highly expressed pathways [61]. One caveat is the effect of any non-native metabolite on the budding yeast.…”

Multidimensional single-cell benchmarking of inducible promoters for precise dynamic control in budding yeast

“…24 The yEVenus-PEST construct has been extensively used in the past, including as a transcriptional reporter in budding yeast. 25,26 Several factors such as the genomic integration site 27,28 , the distance between the promoter and the gene 29 , and the terminator sequence 30 are known to influence the expression level of the reporter gene in budding yeast. In addition, genetic constructs can be integrated with different copy numbers in the genome, resulting in different levels of expression and noise.…”

An Efficient Exogenous Gene Insertion Site in CHO Cells with High Transcription Level to Enhance AID‐Induced Mutation

“…The integration site of a transgene in the chromosome plays important roles in the expression level and stability of GOI, termed as position effects and has been reported in Escherichia coli K‐12, [ 13 ] Saccharomyces cerevisiae , [ 14 ] Yeast, [ 15 ] mammalian cells, [ 16,17 ] etc. Akhtar et al.…”