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| The Reversal Of Epigenetic Silencing |
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| SciMed - Genetics & Genome | |||
| TS-Si News Service | |||
| Thursday, 04 December 2008 22:00 | |||
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Although nearly every cell in our body is genetically identical, each
cell type expresses a distinct set of genes. Changes to the proteins around which DNA is wound are called epigenetic modifications, because they alter patterns of this gene expression without changing the actual DNA sequence. However, like changes in DNA sequence, epigenetic modifications can be passed on from parent cell to daughter cell, ensuring each cell line has the proper characteristics consistently over many generations.The findings reported in PLoS Genetics are important to develop a better understanding of gene regulation. The discovery may lead to new insights into how epigenetic processes work in the human body, which could assist in developing new ways of modifying our genetic makeup to help us avoid a variety of birth conditions and such intractable diseases as cancer.
A Position Effect on the Heritability of Epigenetic Silencing. Jaswinder Singh, Michael R. Freeling, Damon Lisch. PLoS
Genetics 4(10): e1000216. doi: 10.1371 / journal.pgen.1000216.
One kind of gene is quite distinct from all of the others, because it is nearly always epigenetically inactivated. These are the genes carried by transposons, or "jumping genes." Transposons are mutagens, genes that can modify their host cell in different ways, and lead to a predisposition to cancer, for example. The researchers' experiments with corn (technically, maize) suggest the propensity to maintain epigenetic states can vary depending on the position of the transposons within the genome.
This process must be repeated each generation, and there is good evidence in animals that, during early development, there is a wave of epigenetic reprogramming that effectively "resets" this system. Some genes, it seems, must be more actively reset than others. And genes that do the same thing in every cell, regardless of tissue type, may not have to be reset at all.
Many organisms, from worms to humans to plants, have learned to tame transposons by epigentically "silencing" them: if they can't express their genes they can't jump. If they can't jump for long enough, their DNA sequence slowly accumulates errors, and they become molecular fossils. Most transposons in most organisms are silenced in this way, but some remain quite active.
Previous studies from the laboratory of two of the article's authors, Damon Lisch and Michael Freeling at the University of California (UC), Berkeley, demonstrated epigenetic silencing in maize. Once triggered, the maize plant "remembers," and keeps the transposon "silenced" for generation after generation, even after the trigger is lost. "However, we have found that at some positions in the genome, this is not the case. At these positions, although the trigger works fine, and the transposon is silenced, once the trigger is lost, the transposon reawakens," said Jaswinder Singh, a professor in the Plant Sciences Department at from McGill University, and lead author of the new article. This "molecular amnesia" has never been associated with a particular position in the genome of any species before, nor has it been documented in plants. These data suggest the epigenetic landscape more subtle and interesting than previously thought, with the ability to remember epigenetic silencing varying depending on position. This initial study of plant genomes may be just be the start of more extensive research.
"This may relate to the degree to which a given gene or group of genes must be reprogrammed each generation," Singh said. "We can now use transposons to probe for variations in the epigenetic landscape of the maize genome. It may turn out that forgetting can be as important as remembering. Our findings suggest that erasure of heritable information may be an important component of epigenetic machinery."
More immediately, the findings from plant science can assist in the continuing quest to breed enhanced crops that produce higher yields — especially those that are more resistant to disease and can better tolerate environmental stress.
FundingThis work was funded by a grant to Damon Lisch [A3] and Michael Freeling [A2] from the US National Science Foundation (NSF).
Authors[A1] Jaswinder Singh, Plant Science Department, McGill University.
[A2] Michael Freeling, Department of Plant and Microbial Biology, University of California (UC), Berkeley. [A3] Damon Lisch, Department of Plant and Microbial Biology, University of California (UC), Berkeley. CitationA Position Effect on the Heritability of Epigenetic Silencing. Jaswinder Singh, Michael R. Freeling, Damon Lisch. PLoS Genetics 4(10): e1000216. doi: 10.1371 / journal.pgen.1000216.
Download PDF 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.Author Summary Epigenetics involves the heritable alteration of gene activity without changes in DNA sequence. Although clearly a repository for heritable information, what makes epigenetic states distinct is that they are far more labile than those associated with DNA sequence. The epigenetic landscape of eukaryotic genomes is far from uniform. Vast stretches of them are effectively epigenetically silenced, while other regions are largely active. The experiments described here suggest that the propensity to maintain heritable epigenetic states can vary depending on position within the genome. Because transposable elements, or transposons, move from place to place within the genome, they make an ideal probe for differences in epigenetic states at various positions. Our model system uses a single transposon, MuDR in maize, and a variant of MuDR, Mu killer (Muk). When MuDR and Muk are combined genetically, MuDR elements become epigenetically silenced, and they generally remain so even after Muk is lost in subsequent generations. However, we have identified a particular position at which the MuDR element reactivates after Muk is lost. These data show that there are some parts of the maize genome that are either competent to erase epigenetic silencing or are incapable of maintaining it. These results suggest that erasure of heritable information may be an important component of epigenetic regulation.
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Previous studies from the laboratory of two of the article's authors, Damon Lisch and Michael Freeling at the
"However, we have found that at some positions in the genome, this is not the case. At these positions, although the trigger works fine, and the transposon is silenced, once the trigger is lost, the transposon reawakens," said Jaswinder Singh, a professor in the Plant Sciences Department at from
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