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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

Gene noise and expression plasticity is elevated at the subtelomere in C. albicans.(A) A schematic identifies the ectopic location of subtelomeric Nup49-GFP and internal Tloα9-GFP in the gene position swap. (B) Fluorescence microscopy was performed for Nup49-GFP and Tloα-GFP at either the NUP49 or TLOα9 locus. GFP expression was stronger and more uniform for either gene at the NUP49 locus compared to the subtelomeric TLOα9 locus. (C) GFP expression from (B) was quantified for 100 cells from 2 biological replicates. Expression of either gene at the NUP49 locus was higher than at the TLOα9 locus. (D) Flow cytometry of Nup49-GFP and Tloα9-GFP also indicated reduced expression, increased expression plasticity, and increased noise at the subtelomeric TLOα9 locus compared to the internal NUP49 locus. * denotes p<0.05. ** denotes p<0.01.
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pgen-1004436-g006: Gene noise and expression plasticity is elevated at the subtelomere in C. albicans.(A) A schematic identifies the ectopic location of subtelomeric Nup49-GFP and internal Tloα9-GFP in the gene position swap. (B) Fluorescence microscopy was performed for Nup49-GFP and Tloα-GFP at either the NUP49 or TLOα9 locus. GFP expression was stronger and more uniform for either gene at the NUP49 locus compared to the subtelomeric TLOα9 locus. (C) GFP expression from (B) was quantified for 100 cells from 2 biological replicates. Expression of either gene at the NUP49 locus was higher than at the TLOα9 locus. (D) Flow cytometry of Nup49-GFP and Tloα9-GFP also indicated reduced expression, increased expression plasticity, and increased noise at the subtelomeric TLOα9 locus compared to the internal NUP49 locus. * denotes p<0.05. ** denotes p<0.01.

Mentions: Many studies of S. cerevisiae found that differences in promoter structure correlate with differences in the amplitude of gene noise [54], [55]. To determine the extent to which telomere position and promoter structure affect the variability of TLO gene expression, we constructed two TLO-NUP49 swap strains (Fig. 6A): NUP49-GFP@TLO, in which the control gene NUP49-GFP, together with its native promoter, was moved to the sub-telomeric TLOα9 locus on the left end of Chromosome 4 (YJB12963); and TLOα9-GFP@NUP49, in which TLOα9-GFP, together with its native promoter, was moved to the internal NUP49 locus on the right arm of Chromosome 1 (YJB12966). Importantly, when either Nup49-GFP or Tloα9-GFP were expressed at the NUP49 locus, noise (as measured by fluorescence microscopy) was significantly lower than when either of these proteins was expressed from the TLOα9 locus (Fig. 6A–C, Fig. S6; p<0.05). Expression of Nup49-GFP and Tloα9-GFP was also significantly lower at the TLOα9 locus compared to the NUP49 locus (Fig. 6A–C; NUP49: t85.42 = 16.43, p<0.00001; TLOα9: t85.44 = 4.71, p<0.00001). Flow cytometric analysis of the four strains (two with tagged genes at their native loci and two with swapped loci) also indicated that genes at the subtelomeric TLOα9 locus exhibit a significant decrease in the mean fluorescence signal (position: F1 = 5.04, p = 0.038, gene: F1 = 0.93, p = 0.35) and an increase in the level of gene noise (Robust CV; position: F1 = 10.12, p = 0.005, gene: F1 = 2.10, p = 0.17) relative to the internal NUP49 locus (Fig. 6D). This suggests that the subtelomeric TLOα9 locus is sufficient to cause increased noise because it is telomere-adjacent and affected by Telomere-Adjacent Gene Expression Noise (TAGEN), which influences both population-to-population (expression plasticity) and cell-to-cell (noise) variability. Furthermore, TAGEN appears to be independent of the promoters tested.


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)

Gene noise and expression plasticity is elevated at the subtelomere in C. albicans.(A) A schematic identifies the ectopic location of subtelomeric Nup49-GFP and internal Tloα9-GFP in the gene position swap. (B) Fluorescence microscopy was performed for Nup49-GFP and Tloα-GFP at either the NUP49 or TLOα9 locus. GFP expression was stronger and more uniform for either gene at the NUP49 locus compared to the subtelomeric TLOα9 locus. (C) GFP expression from (B) was quantified for 100 cells from 2 biological replicates. Expression of either gene at the NUP49 locus was higher than at the TLOα9 locus. (D) Flow cytometry of Nup49-GFP and Tloα9-GFP also indicated reduced expression, increased expression plasticity, and increased noise at the subtelomeric TLOα9 locus compared to the internal NUP49 locus. * denotes p<0.05. ** denotes p<0.01.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004436-g006: Gene noise and expression plasticity is elevated at the subtelomere in C. albicans.(A) A schematic identifies the ectopic location of subtelomeric Nup49-GFP and internal Tloα9-GFP in the gene position swap. (B) Fluorescence microscopy was performed for Nup49-GFP and Tloα-GFP at either the NUP49 or TLOα9 locus. GFP expression was stronger and more uniform for either gene at the NUP49 locus compared to the subtelomeric TLOα9 locus. (C) GFP expression from (B) was quantified for 100 cells from 2 biological replicates. Expression of either gene at the NUP49 locus was higher than at the TLOα9 locus. (D) Flow cytometry of Nup49-GFP and Tloα9-GFP also indicated reduced expression, increased expression plasticity, and increased noise at the subtelomeric TLOα9 locus compared to the internal NUP49 locus. * denotes p<0.05. ** denotes p<0.01.
Mentions: Many studies of S. cerevisiae found that differences in promoter structure correlate with differences in the amplitude of gene noise [54], [55]. To determine the extent to which telomere position and promoter structure affect the variability of TLO gene expression, we constructed two TLO-NUP49 swap strains (Fig. 6A): NUP49-GFP@TLO, in which the control gene NUP49-GFP, together with its native promoter, was moved to the sub-telomeric TLOα9 locus on the left end of Chromosome 4 (YJB12963); and TLOα9-GFP@NUP49, in which TLOα9-GFP, together with its native promoter, was moved to the internal NUP49 locus on the right arm of Chromosome 1 (YJB12966). Importantly, when either Nup49-GFP or Tloα9-GFP were expressed at the NUP49 locus, noise (as measured by fluorescence microscopy) was significantly lower than when either of these proteins was expressed from the TLOα9 locus (Fig. 6A–C, Fig. S6; p<0.05). Expression of Nup49-GFP and Tloα9-GFP was also significantly lower at the TLOα9 locus compared to the NUP49 locus (Fig. 6A–C; NUP49: t85.42 = 16.43, p<0.00001; TLOα9: t85.44 = 4.71, p<0.00001). Flow cytometric analysis of the four strains (two with tagged genes at their native loci and two with swapped loci) also indicated that genes at the subtelomeric TLOα9 locus exhibit a significant decrease in the mean fluorescence signal (position: F1 = 5.04, p = 0.038, gene: F1 = 0.93, p = 0.35) and an increase in the level of gene noise (Robust CV; position: F1 = 10.12, p = 0.005, gene: F1 = 2.10, p = 0.17) relative to the internal NUP49 locus (Fig. 6D). This suggests that the subtelomeric TLOα9 locus is sufficient to cause increased noise because it is telomere-adjacent and affected by Telomere-Adjacent Gene Expression Noise (TAGEN), which influences both population-to-population (expression plasticity) and cell-to-cell (noise) variability. Furthermore, TAGEN appears to be independent of the promoters tested.

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