Briefly, cells were inoculated into liquid YPAD cultures and grown overnight to stationary phase at 30C with constant shaking. the expression data identified significantly reduced noise for Tlo10 and Tlo12 associated with deletion of SIR2 but not for Nup49.(TIF) pgen.1004436.s008.tif (850K) GUID:?40A723B2-99AC-44E1-A7C1-D99BDB515855 Figure S9: Expression plasticity of individual and or expression. qRT-PCR measured transcript abundance of and when was either unselected, selected on media lacking uracil, or selected on media containing 5-FOA. Selection of expression did not significantly alter expression of either the adjacent or unlinked gene.(TIF) pgen.1004436.s011.tif (392K) GUID:?4024CB18-A9B7-4D1D-862F-71501EDAB15A Table S1: strains used in this study.(TIF) pgen.1004436.s012.tif (1.3M) GUID:?745BF976-F0AA-4BC2-8E44-135F40F3047C Table S2: Primers used for GSK1059865 strain construction.(TIF) pgen.1004436.s013.tif (2.0M) GUID:?C1A96EDF-9DB1-4413-BEFF-E13E8DA149D5 Table S3: Primers used for quantitative PCR.(TIF) pgen.1004436.s014.tif (781K) GUID:?7510C643-C77C-4255-B733-A31C6035840B Table S4: Gene expression coefficient of variation (CV) from qRT-PCR.(TIF) pgen.1004436.s015.tif (510K) GUID:?C9F6DE3B-3280-430F-AA3A-5EE21A5E9E2C Table S5: Correlation of GFP and mCherry fluorescence in tagged strains.(TIF) pgen.1004436.s016.tif (1.3M) GUID:?F28F12E1-CEEB-4496-AF72-5560B14FAF0E Abstract Cell-to-cell gene expression noise is thought to be an important mechanism for generating phenotypic diversity. Furthermore, telomeric regions are major sites for gene amplification, which is thought to drive genetic diversity. Here we found that individual subtelomeric genes exhibit increased variation in transcript and protein levels at both the cell-to-cell level as well as at the population-level. The cell-to-cell variation, termed Telomere-Adjacent Gene Expression Noise (TAGEN) was largely intrinsic noise and was dependent upon GSK1059865 genome position: noise was reduced when a gene was expressed at an ectopic internal locus and noise was elevated when a non-telomeric gene was expressed at a telomere-adjacent locus. This position-dependent TAGEN also was dependent on Sir2p, an NAD+-dependent histone deacetylase. Finally, we found that telomere silencing and TAGEN are tightly linked and regulated in gene resulted in reduced noise at the neighboring but not at other genes. This provides experimental support to computational predictions that the ability to shift between silent and active chromatin GSK1059865 states has a major effect on cell-to-cell noise. Furthermore, it demonstrates that these shifts affect the degree of expression variation at each telomere individually. Author Summary Genetic Colec11 diversity is often high at telomeres, the chromosome ends where genes are readily amplified and modified. Phenotypic diversity, e.g., growth properties under a given condition, is affected by stochastic variations in gene expression exhibited among cells in a homogenous environment. Our studies found that individual subtelomeric genes show high variability of gene expression both between cells within a single population and also between separate sub-populations. Cell-to-cell variation, termed Telomere-Adjacent Gene Expression Noise (TAGEN), affected single telomeric genes. We found that classical telomeric silencing and TAGEN are tightly linked, with both being dependent upon proximity to telomeres and the Sir2 chromatin modifying enzyme. In addition, both are coordinately regulated locallyat the DNA level: at a telomere with transcription that is continually silenced or activated, the level of expression variability is reduced. This work provides experimental support for computational work that predicted this relationship between stochastic chromatin silencing and expression plasticity at each telomere individually. Furthermore, it demonstrates that these shifts affect the degree of cell-to cell noise of telomere-adjacent loci. Introduction Responsiveness to minor changes in the environment requires exquisitely sensitive phenotypic plasticity. This can be executed via many different mechanisms, operating on different time scales, with different types of condition-specific responses, but usually includes changes in transcriptional and translational profiles. Variation between independent populations of cells that are presumed to be isogenic can be due to altered epigenetic properties, such as chromatin status of specific genes or chromosomal regions [1], [2], to cell-to-cell variations in gene expression [3], [4]. Such population and cellular variations are likely to operate continuously in natural environments. Microbes living within a mammalian host encounter a variety of host niches. For example, organisms that reside throughout the GI tract must be able to survive GSK1059865 conditions in the oral cavity (pH 6.5C6.9, 33C35C), the stomach (pH 2, 37C), the small intestine (pH 7.4, 37C40C), and anaerobic niches in the colon. Accordingly, the ability to acclimate rapidly to changing environments is thought to provide a selective advantage and is supported by studies in yeast and bacteria [5]C[9]. Gene expression noise, defined as cell-to-cell variation in levels of transcription and/or translation, provides phenotypic diversity within an isogenic population, enabling sister cells to respond differently to environmental challenges. Noise can be extrinsic, generally assumed to be due to differences in an environment or to natural variations in cell components such as transcription or translation factors that affect multiple alleles similarly.