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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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TLO expression is highly plastic at the transcript and protein level.qRT-PCR measured transcript abundance for ten TLOs representing all three clades in SC5314 and two control genes, SOD2 and HGT20, that are expressed at similar levels. TLO abundance was measured for cells in logarithmic growth at (A) 30°C, (B) 39°C, and (C) under standard growth conditions supplemented with 10% serum. Transcript abundance was generally more variable for TLOs compared to control genes for all condition tested (variability indicated by the length of each box, which demarcates the first and third quartiles). (D) Protein abundance of Tlos and histone H4 was measured by Western blotting assay using Cdc28 as a loading control when cells were grown at either (E) 30°C or (F) 39°C. Tlo abundance was more variable compared to H4 in either condition regardless of clade. A Tloγ clade member, Tloγ5, was also similar variable but is expressed at much lower levels not on a similar scale to these proteins.
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pgen-1004436-g001: TLO expression is highly plastic at the transcript and protein level.qRT-PCR measured transcript abundance for ten TLOs representing all three clades in SC5314 and two control genes, SOD2 and HGT20, that are expressed at similar levels. TLO abundance was measured for cells in logarithmic growth at (A) 30°C, (B) 39°C, and (C) under standard growth conditions supplemented with 10% serum. Transcript abundance was generally more variable for TLOs compared to control genes for all condition tested (variability indicated by the length of each box, which demarcates the first and third quartiles). (D) Protein abundance of Tlos and histone H4 was measured by Western blotting assay using Cdc28 as a loading control when cells were grown at either (E) 30°C or (F) 39°C. Tlo abundance was more variable compared to H4 in either condition regardless of clade. A Tloγ clade member, Tloγ5, was also similar variable but is expressed at much lower levels not on a similar scale to these proteins.

Mentions: In the course of measuring TLO gene expression under a range of growth conditions, we found that expression levels for many individual TLO genes was strikingly variable (up to several orders of magnitude) between isogenic biological populations grown from single colonies under identical conditions (Fig. 1A–C). Furthermore, the level of TLO gene expression variation, measured as the coefficient of variation (CV; standard deviation divided by the mean; at least five replicates per gene-condition) [49], was far greater than that seen for two control genes, SOD2 and HGT20, that were expressed at similar average levels, irrespective of the growth conditions (Table S4). Transcript abundance measurements were reproducible for individual populations (average standard deviation among technical replicates = 0.63 cycles vs. 4.43 cycles between biological replicates), further supporting the idea that the population-level expression of individual TLO genes varied considerably.


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 is highly plastic at the transcript and protein level.qRT-PCR measured transcript abundance for ten TLOs representing all three clades in SC5314 and two control genes, SOD2 and HGT20, that are expressed at similar levels. TLO abundance was measured for cells in logarithmic growth at (A) 30°C, (B) 39°C, and (C) under standard growth conditions supplemented with 10% serum. Transcript abundance was generally more variable for TLOs compared to control genes for all condition tested (variability indicated by the length of each box, which demarcates the first and third quartiles). (D) Protein abundance of Tlos and histone H4 was measured by Western blotting assay using Cdc28 as a loading control when cells were grown at either (E) 30°C or (F) 39°C. Tlo abundance was more variable compared to H4 in either condition regardless of clade. A Tloγ clade member, Tloγ5, was also similar variable but is expressed at much lower levels not on a similar scale to these proteins.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004436-g001: TLO expression is highly plastic at the transcript and protein level.qRT-PCR measured transcript abundance for ten TLOs representing all three clades in SC5314 and two control genes, SOD2 and HGT20, that are expressed at similar levels. TLO abundance was measured for cells in logarithmic growth at (A) 30°C, (B) 39°C, and (C) under standard growth conditions supplemented with 10% serum. Transcript abundance was generally more variable for TLOs compared to control genes for all condition tested (variability indicated by the length of each box, which demarcates the first and third quartiles). (D) Protein abundance of Tlos and histone H4 was measured by Western blotting assay using Cdc28 as a loading control when cells were grown at either (E) 30°C or (F) 39°C. Tlo abundance was more variable compared to H4 in either condition regardless of clade. A Tloγ clade member, Tloγ5, was also similar variable but is expressed at much lower levels not on a similar scale to these proteins.
Mentions: In the course of measuring TLO gene expression under a range of growth conditions, we found that expression levels for many individual TLO genes was strikingly variable (up to several orders of magnitude) between isogenic biological populations grown from single colonies under identical conditions (Fig. 1A–C). Furthermore, the level of TLO gene expression variation, measured as the coefficient of variation (CV; standard deviation divided by the mean; at least five replicates per gene-condition) [49], was far greater than that seen for two control genes, SOD2 and HGT20, that were expressed at similar average levels, irrespective of the growth conditions (Table S4). Transcript abundance measurements were reproducible for individual populations (average standard deviation among technical replicates = 0.63 cycles vs. 4.43 cycles between biological replicates), further supporting the idea that the population-level expression of individual TLO genes varied considerably.

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