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Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation.

Jeffery DC, Wyse BA, Rehman MA, Brown GW, You Z, Oshidari R, Masai H, Yankulov KY - Nucleic Acids Res. (2013)

Bottom Line: Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state.These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively.We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada and Department of Genome Medicine, Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

ABSTRACT
Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state. Consequently, the active state then persists with occasional conversions to the repressed state. These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively. In this study, we have addressed an important but often neglected aspect of PEV: the frequency of conversions at such loci. We have developed a model and have projected various PEV scenarios based on various rates of conversions. We have also enhanced two existing assays for gene silencing in Saccharomyces cerevisiae to measure the rate of switches from repressed to active state and vice versa. We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing. The assays have revealed that the histone chaperone Chromatin Assembly Factor I is involved in the control of epigenetic conversions. Together, our model and assays provide a comprehensive methodology for further investigation of epigenetic stability and position effects.

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A general model for PEV. (A) A diagram showing the proportion of cells with the active and the silent gene at a PEV locus is shown. The conversion rates between silent and active state are depicted by gray bend arrows. The ‘conservative’ transmission of the two states is shown in black arrows. The formula for the calculation of the proportion of cells with active gene (YA) in any given n generation is shown on the right. (B) A diagram of possible replication-coupled and replication-independent transmissions and conversions of a gene at a PEV locus is shown. Our model does not distinguish between these scenarios.
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gkt623-F1: A general model for PEV. (A) A diagram showing the proportion of cells with the active and the silent gene at a PEV locus is shown. The conversion rates between silent and active state are depicted by gray bend arrows. The ‘conservative’ transmission of the two states is shown in black arrows. The formula for the calculation of the proportion of cells with active gene (YA) in any given n generation is shown on the right. (B) A diagram of possible replication-coupled and replication-independent transmissions and conversions of a gene at a PEV locus is shown. Our model does not distinguish between these scenarios.

Mentions: Positional variegation is defined by infrequent A→S and S→A conversions of a gene. We recaptured this process through modeling and simulation. A diagram depicting the parameters we used is shown in Figure 1. A distribution algorithm was applied to calculate the proportion of cells with silenced (YS) and active (YA) gene in a given generation (n − 1, n, n + 1 …) based on the proportion of cells with silenced and active gene in the preceding generation and two coefficients of conversions (CS→A and CA→S) (Figure 1A). The equations and related calculations are presented in Appendix 1 (Supplementary Materials). We used the formula Y(A)n = Y(A)n-1−Y(A)n-1C(A→S) + (1 −Y(A)n−1)C(S→A) to simulate the frequency of conversions at any PEV locus. Y(A)n is the proportion of cells with an active gene in any generation (n − 1, n, n + 1 …), C(A→S) is the coefficient of conversions from active to silent state and C(S→A) is the coefficient of conversions from silent to active state. The analysis of this recurrence relation (Appendix 1) shows that the rates of conversion (CS→A and CA→S) must be between 0 and 100%, and that they are independent of the proportions of cells with silent (YS) and active (YA) gene. More importantly, they are independent of each other. This formula allows for the projection of experimental outcomes based on the CS→A and CA→S conversion rates and fixed initial values of Y(A)0. It also provides means for the calculation of the CS→A and CA→S rates based on experimental data. The calculated CS→A and CA→S values represent a direct measure of the ‘A→S’ and ‘S→A’ rates.Figure 1.


Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation.

Jeffery DC, Wyse BA, Rehman MA, Brown GW, You Z, Oshidari R, Masai H, Yankulov KY - Nucleic Acids Res. (2013)

A general model for PEV. (A) A diagram showing the proportion of cells with the active and the silent gene at a PEV locus is shown. The conversion rates between silent and active state are depicted by gray bend arrows. The ‘conservative’ transmission of the two states is shown in black arrows. The formula for the calculation of the proportion of cells with active gene (YA) in any given n generation is shown on the right. (B) A diagram of possible replication-coupled and replication-independent transmissions and conversions of a gene at a PEV locus is shown. Our model does not distinguish between these scenarios.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3794585&req=5

gkt623-F1: A general model for PEV. (A) A diagram showing the proportion of cells with the active and the silent gene at a PEV locus is shown. The conversion rates between silent and active state are depicted by gray bend arrows. The ‘conservative’ transmission of the two states is shown in black arrows. The formula for the calculation of the proportion of cells with active gene (YA) in any given n generation is shown on the right. (B) A diagram of possible replication-coupled and replication-independent transmissions and conversions of a gene at a PEV locus is shown. Our model does not distinguish between these scenarios.
Mentions: Positional variegation is defined by infrequent A→S and S→A conversions of a gene. We recaptured this process through modeling and simulation. A diagram depicting the parameters we used is shown in Figure 1. A distribution algorithm was applied to calculate the proportion of cells with silenced (YS) and active (YA) gene in a given generation (n − 1, n, n + 1 …) based on the proportion of cells with silenced and active gene in the preceding generation and two coefficients of conversions (CS→A and CA→S) (Figure 1A). The equations and related calculations are presented in Appendix 1 (Supplementary Materials). We used the formula Y(A)n = Y(A)n-1−Y(A)n-1C(A→S) + (1 −Y(A)n−1)C(S→A) to simulate the frequency of conversions at any PEV locus. Y(A)n is the proportion of cells with an active gene in any generation (n − 1, n, n + 1 …), C(A→S) is the coefficient of conversions from active to silent state and C(S→A) is the coefficient of conversions from silent to active state. The analysis of this recurrence relation (Appendix 1) shows that the rates of conversion (CS→A and CA→S) must be between 0 and 100%, and that they are independent of the proportions of cells with silent (YS) and active (YA) gene. More importantly, they are independent of each other. This formula allows for the projection of experimental outcomes based on the CS→A and CA→S conversion rates and fixed initial values of Y(A)0. It also provides means for the calculation of the CS→A and CA→S rates based on experimental data. The calculated CS→A and CA→S values represent a direct measure of the ‘A→S’ and ‘S→A’ rates.Figure 1.

Bottom Line: Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state.These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively.We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada and Department of Genome Medicine, Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

ABSTRACT
Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state. Consequently, the active state then persists with occasional conversions to the repressed state. These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively. In this study, we have addressed an important but often neglected aspect of PEV: the frequency of conversions at such loci. We have developed a model and have projected various PEV scenarios based on various rates of conversions. We have also enhanced two existing assays for gene silencing in Saccharomyces cerevisiae to measure the rate of switches from repressed to active state and vice versa. We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing. The assays have revealed that the histone chaperone Chromatin Assembly Factor I is involved in the control of epigenetic conversions. Together, our model and assays provide a comprehensive methodology for further investigation of epigenetic stability and position effects.

Show MeSH
Related in: MedlinePlus