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A position effect on the heritability of epigenetic silencing.

Singh J, Freeling M, Lisch D - PLoS Genet. (2008)

Bottom Line: In animals and yeast, position effects have been well documented.In contrast, there are few examples of position effects in plants, and there are no documented examples in either plants or animals for positions that are associated with the reversal of previously established silenced states.To our knowledge, this is the first documented example of a position effect that is associated with the reversal of epigenetic silencing.

View Article: PubMed Central - PubMed

Affiliation: Plant Science Department, McGill University, Macdonald Campus, Ste Anne de Bellevue, Quebec, Canada.

ABSTRACT
In animals and yeast, position effects have been well documented. In animals, the best example of this process is Position Effect Variegation (PEV) in Drosophila melanogaster. In PEV, when genes are moved into close proximity to constitutive heterochromatin, their expression can become unstable, resulting in variegated patches of gene expression. This process is regulated by a variety of proteins implicated in both chromatin remodeling and RNAi-based silencing. A similar phenomenon is observed when transgenes are inserted into heterochromatic regions in fission yeast. In contrast, there are few examples of position effects in plants, and there are no documented examples in either plants or animals for positions that are associated with the reversal of previously established silenced states. MuDR transposons in maize can be heritably silenced by a naturally occurring rearranged version of MuDR. This element, Muk, produces a long hairpin RNA molecule that can trigger DNA methylation and heritable silencing of one or many MuDR elements. In most cases, MuDR elements remain inactive even after Muk segregates away. Thus, Muk-induced silencing involves a directed and heritable change in gene activity in the absence of changes in DNA sequence. Using classical genetic analysis, we have identified an exceptional position at which MuDR element silencing is unstable. Muk effectively silences the MuDR element at this position. However, after Muk is segregated away, element activity is restored. This restoration is accompanied by a reversal of DNA methylation. To our knowledge, this is the first documented example of a position effect that is associated with the reversal of epigenetic silencing. This observation suggests that there are cis-acting sequences that alter the propensity of an epigenetically silenced gene to remain inactive. This raises the interesting possibility that an important feature of local chromatin environments may be the capacity to erase previously established epigenetic marks.

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Genetic and Southern blot analysis of a family derived from a plant that carried MuDR(p5) and MuDR(p4) in which reactivation was delayed and both elements were still methylated in the first generation following the loss of Muk.A) XhoI digests of a family segregating for MuDR(p5) and MuDR(p4), in which the female parent carried methylated MuDR(p5) and MuDR(p4). Kernels were separated into classes based on somatic excision frequency, planted, and the resulting progeny plants were subjected to Southern blot analysis. B) Summarized frequency of spotted kernels in progeny of test crosses of plants depicted in panel A.
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pgen-1000216-g007: Genetic and Southern blot analysis of a family derived from a plant that carried MuDR(p5) and MuDR(p4) in which reactivation was delayed and both elements were still methylated in the first generation following the loss of Muk.A) XhoI digests of a family segregating for MuDR(p5) and MuDR(p4), in which the female parent carried methylated MuDR(p5) and MuDR(p4). Kernels were separated into classes based on somatic excision frequency, planted, and the resulting progeny plants were subjected to Southern blot analysis. B) Summarized frequency of spotted kernels in progeny of test crosses of plants depicted in panel A.

Mentions: For comparison, we examined the heritable activity of MuDR(p4) in plants in which there had been a delay in MuDR(p5) reactivation. As described above, these plants carried methylated MuDR and Mu1 TIRs in the generation immediately after the loss of Muk (Figures 3 and 4). However, when these plants were test crossed, they gave rise to an average of 50% heavily spotted progeny kernels (Table 1). One plant and its progeny were examined in detail. In this plant, both MuDR(p5) and MuDR(p4) had remained at least partially inactive in the first generation after the loss of Muk (Figure 4B, lanes 9 and 10, and 4D). Despite having two potentially active elements, this and all similar families segregated only 50% spotted progeny kernels, as if only one of these two MuDR elements had become reactivated in this generation (Table 1). Southern blot analysis of progeny of this plant revealed that MuDR(p5), but not MuDR(p4), co-segregated with activity (Figure 7A). All the plants grown from spotted kernels in this family carried MuDR(p5), but the presence or absence of MuDR(p4) had no effect on activity; three of ten plants grown from spotted kernels carried MuDR(p4), as did seven of nine plants grown from pale kernels. This experiment demonstrated that MuDR(p4) was not active in this family. It also showed that in this generation, an active MuDR(p5) element had no influence on the heritable activity of MuDR(p4). Plants that carried both MuDR(p5) and MuDR(p4), when test crossed, gave rise to only 50% spotted progeny (Table 4 and Figure 7B). Together, these results suggest that MuDR(p4) could be responsive to a reactivated MuDR(p5), but only in the generation immediately following the loss of Muk.


A position effect on the heritability of epigenetic silencing.

Singh J, Freeling M, Lisch D - PLoS Genet. (2008)

Genetic and Southern blot analysis of a family derived from a plant that carried MuDR(p5) and MuDR(p4) in which reactivation was delayed and both elements were still methylated in the first generation following the loss of Muk.A) XhoI digests of a family segregating for MuDR(p5) and MuDR(p4), in which the female parent carried methylated MuDR(p5) and MuDR(p4). Kernels were separated into classes based on somatic excision frequency, planted, and the resulting progeny plants were subjected to Southern blot analysis. B) Summarized frequency of spotted kernels in progeny of test crosses of plants depicted in panel A.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2563033&req=5

pgen-1000216-g007: Genetic and Southern blot analysis of a family derived from a plant that carried MuDR(p5) and MuDR(p4) in which reactivation was delayed and both elements were still methylated in the first generation following the loss of Muk.A) XhoI digests of a family segregating for MuDR(p5) and MuDR(p4), in which the female parent carried methylated MuDR(p5) and MuDR(p4). Kernels were separated into classes based on somatic excision frequency, planted, and the resulting progeny plants were subjected to Southern blot analysis. B) Summarized frequency of spotted kernels in progeny of test crosses of plants depicted in panel A.
Mentions: For comparison, we examined the heritable activity of MuDR(p4) in plants in which there had been a delay in MuDR(p5) reactivation. As described above, these plants carried methylated MuDR and Mu1 TIRs in the generation immediately after the loss of Muk (Figures 3 and 4). However, when these plants were test crossed, they gave rise to an average of 50% heavily spotted progeny kernels (Table 1). One plant and its progeny were examined in detail. In this plant, both MuDR(p5) and MuDR(p4) had remained at least partially inactive in the first generation after the loss of Muk (Figure 4B, lanes 9 and 10, and 4D). Despite having two potentially active elements, this and all similar families segregated only 50% spotted progeny kernels, as if only one of these two MuDR elements had become reactivated in this generation (Table 1). Southern blot analysis of progeny of this plant revealed that MuDR(p5), but not MuDR(p4), co-segregated with activity (Figure 7A). All the plants grown from spotted kernels in this family carried MuDR(p5), but the presence or absence of MuDR(p4) had no effect on activity; three of ten plants grown from spotted kernels carried MuDR(p4), as did seven of nine plants grown from pale kernels. This experiment demonstrated that MuDR(p4) was not active in this family. It also showed that in this generation, an active MuDR(p5) element had no influence on the heritable activity of MuDR(p4). Plants that carried both MuDR(p5) and MuDR(p4), when test crossed, gave rise to only 50% spotted progeny (Table 4 and Figure 7B). Together, these results suggest that MuDR(p4) could be responsive to a reactivated MuDR(p5), but only in the generation immediately following the loss of Muk.

Bottom Line: In animals and yeast, position effects have been well documented.In contrast, there are few examples of position effects in plants, and there are no documented examples in either plants or animals for positions that are associated with the reversal of previously established silenced states.To our knowledge, this is the first documented example of a position effect that is associated with the reversal of epigenetic silencing.

View Article: PubMed Central - PubMed

Affiliation: Plant Science Department, McGill University, Macdonald Campus, Ste Anne de Bellevue, Quebec, Canada.

ABSTRACT
In animals and yeast, position effects have been well documented. In animals, the best example of this process is Position Effect Variegation (PEV) in Drosophila melanogaster. In PEV, when genes are moved into close proximity to constitutive heterochromatin, their expression can become unstable, resulting in variegated patches of gene expression. This process is regulated by a variety of proteins implicated in both chromatin remodeling and RNAi-based silencing. A similar phenomenon is observed when transgenes are inserted into heterochromatic regions in fission yeast. In contrast, there are few examples of position effects in plants, and there are no documented examples in either plants or animals for positions that are associated with the reversal of previously established silenced states. MuDR transposons in maize can be heritably silenced by a naturally occurring rearranged version of MuDR. This element, Muk, produces a long hairpin RNA molecule that can trigger DNA methylation and heritable silencing of one or many MuDR elements. In most cases, MuDR elements remain inactive even after Muk segregates away. Thus, Muk-induced silencing involves a directed and heritable change in gene activity in the absence of changes in DNA sequence. Using classical genetic analysis, we have identified an exceptional position at which MuDR element silencing is unstable. Muk effectively silences the MuDR element at this position. However, after Muk is segregated away, element activity is restored. This restoration is accompanied by a reversal of DNA methylation. To our knowledge, this is the first documented example of a position effect that is associated with the reversal of epigenetic silencing. This observation suggests that there are cis-acting sequences that alter the propensity of an epigenetically silenced gene to remain inactive. This raises the interesting possibility that an important feature of local chromatin environments may be the capacity to erase previously established epigenetic marks.

Show MeSH
Related in: MedlinePlus