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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 expression state is heritable.(A) Ten Tloα12-GFP daughter cells were dissected away from their respective single mother cell. Both mother and daughter cells were grown independently for 18 hours and assayed for Tloα12-GFP expression by fluorescence microscopy of the resulting population. (B) Tloα12-GFP fluorescence of 50 cells for each population was collected by microscopy and the mean and standard deviation were plotted. Mother-daughter pairs were plotted together and generally show similar levels of mean expression between each pair, although more difference is evident in colonies 2 and 10 (C). The mean(ln) difference between cell expression data of mother-daughter pairs (red arrow) was tested against simulated datasets constructed from randomized mother-daughter affiliations(grey bars), and the association between mother-daughter pairs was highly significant.
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pgen-1004436-g003: TLO expression state is heritable.(A) Ten Tloα12-GFP daughter cells were dissected away from their respective single mother cell. Both mother and daughter cells were grown independently for 18 hours and assayed for Tloα12-GFP expression by fluorescence microscopy of the resulting population. (B) Tloα12-GFP fluorescence of 50 cells for each population was collected by microscopy and the mean and standard deviation were plotted. Mother-daughter pairs were plotted together and generally show similar levels of mean expression between each pair, although more difference is evident in colonies 2 and 10 (C). The mean(ln) difference between cell expression data of mother-daughter pairs (red arrow) was tested against simulated datasets constructed from randomized mother-daughter affiliations(grey bars), and the association between mother-daughter pairs was highly significant.

Mentions: To address the degree of heritability of Tloα12-GFP expression levels and expression noise, we analyzed the expression level of mother-daughter cell pairs by pedigree analysis. We isolated 10 mother-daughter pairs, dissected buds from mothers, and allowed them to grow separately on a plate for 18 hours (Fig. 3A). We compared populations of 50 cells from individual mothers to 50 cells from their own daughters to ask if these related populations were more similar to one another than expected by chance (Fig. 3B). The mean difference in absolute ln(expression) was 0.58 for the mother-daughter pairs and was 1.24 for randomized daughter pairs, with the 5% quantile at 0.96. Thus, the mother-daughter pairs were significantly similar to one another (p≤0.0001) than expected by chance (Figure 3C). Interestingly, two daughter populations (Colonies 2 and 10, Figure 3C) did not exhibit perfect overlap with their respective mother populations, indicating that expression similarity, although heritable, can diverge over a small number of generations.


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 expression state is heritable.(A) Ten Tloα12-GFP daughter cells were dissected away from their respective single mother cell. Both mother and daughter cells were grown independently for 18 hours and assayed for Tloα12-GFP expression by fluorescence microscopy of the resulting population. (B) Tloα12-GFP fluorescence of 50 cells for each population was collected by microscopy and the mean and standard deviation were plotted. Mother-daughter pairs were plotted together and generally show similar levels of mean expression between each pair, although more difference is evident in colonies 2 and 10 (C). The mean(ln) difference between cell expression data of mother-daughter pairs (red arrow) was tested against simulated datasets constructed from randomized mother-daughter affiliations(grey bars), and the association between mother-daughter pairs was highly significant.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004436-g003: TLO expression state is heritable.(A) Ten Tloα12-GFP daughter cells were dissected away from their respective single mother cell. Both mother and daughter cells were grown independently for 18 hours and assayed for Tloα12-GFP expression by fluorescence microscopy of the resulting population. (B) Tloα12-GFP fluorescence of 50 cells for each population was collected by microscopy and the mean and standard deviation were plotted. Mother-daughter pairs were plotted together and generally show similar levels of mean expression between each pair, although more difference is evident in colonies 2 and 10 (C). The mean(ln) difference between cell expression data of mother-daughter pairs (red arrow) was tested against simulated datasets constructed from randomized mother-daughter affiliations(grey bars), and the association between mother-daughter pairs was highly significant.
Mentions: To address the degree of heritability of Tloα12-GFP expression levels and expression noise, we analyzed the expression level of mother-daughter cell pairs by pedigree analysis. We isolated 10 mother-daughter pairs, dissected buds from mothers, and allowed them to grow separately on a plate for 18 hours (Fig. 3A). We compared populations of 50 cells from individual mothers to 50 cells from their own daughters to ask if these related populations were more similar to one another than expected by chance (Fig. 3B). The mean difference in absolute ln(expression) was 0.58 for the mother-daughter pairs and was 1.24 for randomized daughter pairs, with the 5% quantile at 0.96. Thus, the mother-daughter pairs were significantly similar to one another (p≤0.0001) than expected by chance (Figure 3C). Interestingly, two daughter populations (Colonies 2 and 10, Figure 3C) did not exhibit perfect overlap with their respective mother populations, indicating that expression similarity, although heritable, can diverge over a small number of generations.

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