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The Reversal Of Epigenetic Silencing Print E-mail
SciMed - Genetics & Genome
TS-Si News Service   
Thursday, 04 December 2008 22:00
Field of corn.Los Angeles, CA, USA. Scientists have demonstrated for the first time the reversal of what is called epigenetic silencing, a major breakthrough in the developmental process.
 
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.
Epigenetics & Epigenomics

Epigenetics & Epigenomics. Traditional genetics attributes human characteristics to a simple arithmetical combination of inheritable traits from unchanging genes. As a result, genetic mutations and recombinations have driven most descriptions of how traits are handed down from one generation to another.

The discovery and understanding of DNA, and the role of non-coding (junk) DNA, reveals a more complex — and subtle — situation. Today, scientists know that heritable changes in gene function can occur without a change in the DNA sequence. Called epigenetics, this insight has further changed the way researchers think about heredity. Epigenetics bridges the gap between nature and nurture.

Both epigenetics and epigenomics — the genomewide distribution of epigenetic changes — are related to many other topics requiring a thorough understanding of all aspects of genetics. The latter includes aging, agriculture, cloning, evolution, sexual differentiation, species conservation, stem cells, and synthetic biology.




There are more than 200 different cell types in the human body; each cell contains the same genetic information and can, in theory, synthesize the same proteins. However, each cell type is unique and synthesizes a specific set of proteins. Nerve cells synthesize proteins that are necessary for generating nerve cells, muscle cells synthesize those necessary for building muscle fibers, etc.

This specialization takes place during early embryonic development and continues throughout a person's life. Cells exercise control over their own development using a mechanism called epigenetic regulation, which “opens” or "closes" the DNA structure. Differences in protein synthesis result from the activation and inactivation of genes.

This is fundamental to all animals, humans, and plants (eukaryotic cells). It is involved in tissue regeneration and the preservation of stem cells and DNA.

Epigenetic processes are natural and essential to many organism functions, but disruptions can result in major adverse health and behavioral effects. Variations in epigenetic gene activity regulation are causally connected in human beings to disruptions in early embryonic development and serious diseases.

The cell has to condense two meters of DNA inside a 1/100 millimeter diameter body. During the condensation process, the cell mechanism determines which genes activate. A special group of proteins, called the histones, plays a central part during this process.

The DNA is wound around the histones — which also determine the DNA structure — during condensation. They attach a number of complex and relatively unknown combinations of small chemical modifications under the influence of different enzymes. This opens and closes parts of the DNA structure to regulate gene activation — specific for each of our distinct cell types.



Most epigenetic modifications are erased with each new generation, during gametogenesis and after fertilization. Recent reports suggest that some epigenetic changes may endure in at least four subsequent generations of organisms. If reproducible, the findings could suggest some interesting new approaches. Other studies have found that epigenetic effects occur not just in the womb, but over the full course of a human life span.


Imprinted genes don't rely on the traditional laws of Mendelian genetics, which describe the inheritance of traits as either dominant or recessive. In Mendelian genetics, both parental copies are equally likely to contribute to the outcome. The impact of an imprinted gene copy, however, depends only on which parent it was inherited from. For some imprinted genes, the cell only uses the copy from the mother to make proteins, and for others only that from the father.

In the mid 1980s, scientists studying mice discovered that normal development requires the inheritance of genetic material from both a male and a female. The resulting variances changed, depending on the material's origin.

One hypothesis has it that imprinting regulates embryonic growth. Maternally-expressed imprinted genes usually suppress growth, while those from the male parent usually enhance growth, ensuring continuation of the father's genes.

This is important for a species in which a single litter of offspring can result from the contributions of more than one male. However, the mother, interested in her own health maintenance (biologically speaking), "fights" the paternal genes and limits the size of the embryo or fetus.
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.
 
Dield of corn.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.
 
Dield of corn."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.
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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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