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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 noise has a large intrinsic component.(A) Schematic of the dual reporter system to identify intrinsic noise from expression of the two alleles for a single gene. Cells with the same amount of each tagged protein appear yellow, but cells expressing more of one fluorescent protein than the other appear green or red. (B) Relative GFP and mCherry abundance of tagged Nup49 and Tloβ2 is shown separately and as a merge. Cells are outlined to indicate similar or different levels of either fluorophore. Abundance of the GFP and mCherry-tagged alleles was similar for Nup49, indicating extrinsic noise. Tagged alleles of Tloβ2 exhibited a range of relative abundance and indicates significant intrinsic noise. (C) The intrinsic and extrinsic components to for Nup49, Tloα12, and Tloβ2 gene noise were calculated based on Elowitz et al, 2003. Both forms of noise contributed equally to Nup49 noise. However, intrinsic noise contributed to the majority of Tlo noise.
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pgen-1004436-g005: TLO noise has a large intrinsic component.(A) Schematic of the dual reporter system to identify intrinsic noise from expression of the two alleles for a single gene. Cells with the same amount of each tagged protein appear yellow, but cells expressing more of one fluorescent protein than the other appear green or red. (B) Relative GFP and mCherry abundance of tagged Nup49 and Tloβ2 is shown separately and as a merge. Cells are outlined to indicate similar or different levels of either fluorophore. Abundance of the GFP and mCherry-tagged alleles was similar for Nup49, indicating extrinsic noise. Tagged alleles of Tloβ2 exhibited a range of relative abundance and indicates significant intrinsic noise. (C) The intrinsic and extrinsic components to for Nup49, Tloα12, and Tloβ2 gene noise were calculated based on Elowitz et al, 2003. Both forms of noise contributed equally to Nup49 noise. However, intrinsic noise contributed to the majority of Tlo noise.

Mentions: Two general sources of cell-to-cell variation have been explored extensively in many different species [1], [3], [12], [13], [40]. Extrinsic noise is due to conditions that differ between cells, such as a general level of ribosome or a local exposure to different growth conditions (Fig. 2). In contrast, intrinsic noise operates independently on different alleles of the same gene or promoter. The classic method to distinguish between extrinsic and intrinsic noise is to tag two different alleles of the same gene/promoter with two different fluorescent proteins and to observe the relative levels of each on a cell-by-cell basis. Accordingly, we tagged both alleles of TLOα12 or TLOβ2, using GFP for one allele and mCherry for the other, and determined the degree to which each of the alleles was expressed in individual cells by fluorescence microscopy (Fig. 5A). Extrinsic noise manifests as variable yet correlated expression of the two alleles, while intrinsic noise results in independent, allele-specific expression levels.


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 has a large intrinsic component.(A) Schematic of the dual reporter system to identify intrinsic noise from expression of the two alleles for a single gene. Cells with the same amount of each tagged protein appear yellow, but cells expressing more of one fluorescent protein than the other appear green or red. (B) Relative GFP and mCherry abundance of tagged Nup49 and Tloβ2 is shown separately and as a merge. Cells are outlined to indicate similar or different levels of either fluorophore. Abundance of the GFP and mCherry-tagged alleles was similar for Nup49, indicating extrinsic noise. Tagged alleles of Tloβ2 exhibited a range of relative abundance and indicates significant intrinsic noise. (C) The intrinsic and extrinsic components to for Nup49, Tloα12, and Tloβ2 gene noise were calculated based on Elowitz et al, 2003. Both forms of noise contributed equally to Nup49 noise. However, intrinsic noise contributed to the majority of Tlo noise.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004436-g005: TLO noise has a large intrinsic component.(A) Schematic of the dual reporter system to identify intrinsic noise from expression of the two alleles for a single gene. Cells with the same amount of each tagged protein appear yellow, but cells expressing more of one fluorescent protein than the other appear green or red. (B) Relative GFP and mCherry abundance of tagged Nup49 and Tloβ2 is shown separately and as a merge. Cells are outlined to indicate similar or different levels of either fluorophore. Abundance of the GFP and mCherry-tagged alleles was similar for Nup49, indicating extrinsic noise. Tagged alleles of Tloβ2 exhibited a range of relative abundance and indicates significant intrinsic noise. (C) The intrinsic and extrinsic components to for Nup49, Tloα12, and Tloβ2 gene noise were calculated based on Elowitz et al, 2003. Both forms of noise contributed equally to Nup49 noise. However, intrinsic noise contributed to the majority of Tlo noise.
Mentions: Two general sources of cell-to-cell variation have been explored extensively in many different species [1], [3], [12], [13], [40]. Extrinsic noise is due to conditions that differ between cells, such as a general level of ribosome or a local exposure to different growth conditions (Fig. 2). In contrast, intrinsic noise operates independently on different alleles of the same gene or promoter. The classic method to distinguish between extrinsic and intrinsic noise is to tag two different alleles of the same gene/promoter with two different fluorescent proteins and to observe the relative levels of each on a cell-by-cell basis. Accordingly, we tagged both alleles of TLOα12 or TLOβ2, using GFP for one allele and mCherry for the other, and determined the degree to which each of the alleles was expressed in individual cells by fluorescence microscopy (Fig. 5A). Extrinsic noise manifests as variable yet correlated expression of the two alleles, while intrinsic noise results in independent, allele-specific expression levels.

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