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Silencing is noisy: population and cell level noise in telomere-adjacent genes is dependent on telomere position and sir2.

Anderson MZ, Gerstein AC, Wigen L, Baller JA, Berman J - PLoS Genet. (2014)

Bottom Line: Finally, we found that telomere silencing and TAGEN are tightly linked and regulated in cis: selection for either silencing or activation of a TLO-adjacent URA3 gene resulted in reduced noise at the neighboring TLO but not at other TLO genes.This provides experimental support to computational predictions that the ability to shift between silent and active chromatin 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Cell Biology and Development, University of Minnesota - Twin Cities, Minneapolis, Minnesota, United States of America.

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 TLO 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 genome position: noise was reduced when a TLO 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 cis: selection for either silencing or activation of a TLO-adjacent URA3 gene resulted in reduced noise at the neighboring TLO but not at other TLO genes. This provides experimental support to computational predictions that the ability to shift between silent and active chromatin 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.

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Related in: MedlinePlus

TLO noise and expression plasticity is greater in colonies than in liquid culture.Six Tloα12-GFP colonies in either a WT (A) or sir2Δ/Δ background (B) were picked from plates (D0) and passaged in liquid culture each day for two days (D2). Cells from these time points were fixed and analyzed by flow cytometry. (C) Flow cytometry profiles for Tloα12-GFP in the WT and sir2Δ/Δ background were analyzed for mean expression and robust CV for both the D0 and D2 time points and variability in both measures. Black lines connect the same cell population from D0 to D2. Variability in both mean expression and robust CV were reduced at D2 compared to D0 for both WT and sir2Δ/Δ backgrounds. Yet, Tloα12-GFP was always more variable in the WT than the sir2Δ/Δ background. Simultaneously, two regions of single Tloα12-GFP colonies were picked and assayed for fluorescence by flow cytometry in either a WT (D) or sir2Δ/Δ background (E). Fluorescence profiles of the two regions differed in the WT background but were much more similar when SIR2 was deleted.
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pgen-1004436-g002: TLO noise and expression plasticity is greater in colonies than in liquid culture.Six Tloα12-GFP colonies in either a WT (A) or sir2Δ/Δ background (B) were picked from plates (D0) and passaged in liquid culture each day for two days (D2). Cells from these time points were fixed and analyzed by flow cytometry. (C) Flow cytometry profiles for Tloα12-GFP in the WT and sir2Δ/Δ background were analyzed for mean expression and robust CV for both the D0 and D2 time points and variability in both measures. Black lines connect the same cell population from D0 to D2. Variability in both mean expression and robust CV were reduced at D2 compared to D0 for both WT and sir2Δ/Δ backgrounds. Yet, Tloα12-GFP was always more variable in the WT than the sir2Δ/Δ background. Simultaneously, two regions of single Tloα12-GFP colonies were picked and assayed for fluorescence by flow cytometry in either a WT (D) or sir2Δ/Δ background (E). Fluorescence profiles of the two regions differed in the WT background but were much more similar when SIR2 was deleted.

Mentions: Expression variability between isolates could be the result of expression differences between whole populations or due to cell-to-cell variation within a population. We hypothesized that this high level of variability from population to population could be due to TLO gene expression differences originating from variability between colonies grown on solid agar plates. Based on the assumption that colony growth on solid media subjects cells to intense founder effects and/ot different local environments [52], [53], we asked if Tlo expression differences become less evident after cells from single colonies were propagated in liquid medium, assumed to be a more uniform environment that is also less sensitive to founder effects because cells are continuously mixed. To address this question, we compared Tloα12-GFP expression profiles from 6 individual colonies, originating from a single parent colony, that were grown on solid media plates and the same six populations after two days of passaging in a constantly agitated liquid medium (Fig. 2A). The irregular shapes of expression profiles for cells from individual colonies that were prepared for flow cytometry (by propagation in liquid medium for two hours), suggested that these cultures contained mixtures of different subpopulations. Furthermore, these profile shapes were different for the six colonies, suggesting different founder effects. Because cells lifted from a colony are closely related both genetically and epigenetically (more likely to be in the same silencing state), we think variability in silencing states and, potentially, the local environments within a colony produce these profile differences. In contrast, passaging the same colony isolates in liquid medium for two days resulted in expression profiles that were more regularly shaped and more similar to one another (Figure 2).


Silencing is noisy: population and cell level noise in telomere-adjacent genes is dependent on telomere position and sir2.

Anderson MZ, Gerstein AC, Wigen L, Baller JA, Berman J - PLoS Genet. (2014)

TLO noise and expression plasticity is greater in colonies than in liquid culture.Six Tloα12-GFP colonies in either a WT (A) or sir2Δ/Δ background (B) were picked from plates (D0) and passaged in liquid culture each day for two days (D2). Cells from these time points were fixed and analyzed by flow cytometry. (C) Flow cytometry profiles for Tloα12-GFP in the WT and sir2Δ/Δ background were analyzed for mean expression and robust CV for both the D0 and D2 time points and variability in both measures. Black lines connect the same cell population from D0 to D2. Variability in both mean expression and robust CV were reduced at D2 compared to D0 for both WT and sir2Δ/Δ backgrounds. Yet, Tloα12-GFP was always more variable in the WT than the sir2Δ/Δ background. Simultaneously, two regions of single Tloα12-GFP colonies were picked and assayed for fluorescence by flow cytometry in either a WT (D) or sir2Δ/Δ background (E). Fluorescence profiles of the two regions differed in the WT background but were much more similar when SIR2 was deleted.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109849&req=5

pgen-1004436-g002: TLO noise and expression plasticity is greater in colonies than in liquid culture.Six Tloα12-GFP colonies in either a WT (A) or sir2Δ/Δ background (B) were picked from plates (D0) and passaged in liquid culture each day for two days (D2). Cells from these time points were fixed and analyzed by flow cytometry. (C) Flow cytometry profiles for Tloα12-GFP in the WT and sir2Δ/Δ background were analyzed for mean expression and robust CV for both the D0 and D2 time points and variability in both measures. Black lines connect the same cell population from D0 to D2. Variability in both mean expression and robust CV were reduced at D2 compared to D0 for both WT and sir2Δ/Δ backgrounds. Yet, Tloα12-GFP was always more variable in the WT than the sir2Δ/Δ background. Simultaneously, two regions of single Tloα12-GFP colonies were picked and assayed for fluorescence by flow cytometry in either a WT (D) or sir2Δ/Δ background (E). Fluorescence profiles of the two regions differed in the WT background but were much more similar when SIR2 was deleted.
Mentions: Expression variability between isolates could be the result of expression differences between whole populations or due to cell-to-cell variation within a population. We hypothesized that this high level of variability from population to population could be due to TLO gene expression differences originating from variability between colonies grown on solid agar plates. Based on the assumption that colony growth on solid media subjects cells to intense founder effects and/ot different local environments [52], [53], we asked if Tlo expression differences become less evident after cells from single colonies were propagated in liquid medium, assumed to be a more uniform environment that is also less sensitive to founder effects because cells are continuously mixed. To address this question, we compared Tloα12-GFP expression profiles from 6 individual colonies, originating from a single parent colony, that were grown on solid media plates and the same six populations after two days of passaging in a constantly agitated liquid medium (Fig. 2A). The irregular shapes of expression profiles for cells from individual colonies that were prepared for flow cytometry (by propagation in liquid medium for two hours), suggested that these cultures contained mixtures of different subpopulations. Furthermore, these profile shapes were different for the six colonies, suggesting different founder effects. Because cells lifted from a colony are closely related both genetically and epigenetically (more likely to be in the same silencing state), we think variability in silencing states and, potentially, the local environments within a colony produce these profile differences. In contrast, passaging the same colony isolates in liquid medium for two days resulted in expression profiles that were more regularly shaped and more similar to one another (Figure 2).

Bottom Line: Finally, we found that telomere silencing and TAGEN are tightly linked and regulated in cis: selection for either silencing or activation of a TLO-adjacent URA3 gene resulted in reduced noise at the neighboring TLO but not at other TLO genes.This provides experimental support to computational predictions that the ability to shift between silent and active chromatin 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Cell Biology and Development, University of Minnesota - Twin Cities, Minneapolis, Minnesota, United States of America.

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 TLO 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 genome position: noise was reduced when a TLO 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 cis: selection for either silencing or activation of a TLO-adjacent URA3 gene resulted in reduced noise at the neighboring TLO but not at other TLO genes. This provides experimental support to computational predictions that the ability to shift between silent and active chromatin 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.

Show MeSH
Related in: MedlinePlus