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Don't wait! Try Yumpu. Start using Yumpu now! This provided direct evidence that principles of mass action were at work and that silencing at one locus could affect the epigenetic silencing at other locian idea originally put forth in studies on PEV in Drosophila, but not yet tested Locke et al. Another finding explained how DNA methylation could regulate gene expression through chromatin. Methylated DNA could serve as a point of recruiting deacetylases to a locus and thus facilitate silencing of nearby genes.
The 64th Symposium on "Signaling and Gene Expression in the Immune System" provided evidence about how monoallelic expression arose, and that it might be more widespread than previously thought. Monoallelic expression at the immunoglobulin loci had been obvious in lymphocytes for some time-it guaranteed the production of a single receptor type per lymphoid cell Mostoslavsky et al.
The allele to be expressed was chosen early in development, apparently at random: Both alleles began in a repressed state, but over time one became demethylated. It was unclear how a single allele was chosen, but the phenomenon appeared at other loci, too, where the necessity of monoallelism was not obvious. For instance, only one allele of genes encoding the cytokines IL- 2 and IL-4 was expressed Pannetier et al. The most significant epigenetics-related talk at the 65th Symposium concerned the discovery that the Sir2 protein was a histone deacetylase Imai et al.
This was the only Sir protein that had clear homologs in all other eukaryotes and that regulated PEY. It seemed to be the enzyme primarily responsible for removing acetyl moieties from histones in silent chromatin. Furthermore, because it was an NAD-dependent enzyme, it linked the regulation of silencing heterochromatin to cellular physiology. The 68th Symposium on "The Genome of Homo sapiens" was an important landmark in genetics, and although there is still much genetic work to be done, the complete sequencing of this and other genomes signified that it was time to move "above genetics"-a literal meaning of epigenetics.
This historical account highlights several themes shared with many other areas of research. First, it demonstrates the episodic nature of advances in epigenetics. Second, as molecular mechanisms underlying epigenetic phenomena began to be understood, it made it easier to connect epigenetics to biological regulation in general.
Third, it showed that people whom we now consider to be scientific luminaries had made these connections early on-it just took a while for most others to "see" the obvious. First, the differences between the two phenotypic states "OFF" and "ON" always have a corresponding difference in structure at a key regulatory point-form translates into function. Hence, identifying the two distinct structures, the components that compose them, and the compositional differences between them have been the primary tasks.
Second, the distinct structures must have the ability to be maintained and perpetuated in a milieu of competing factors and entropic forces. Thus, each structure requires selfreinforcement or positive feedback loops which ensure that it is maintained and propagated over many cellular divisions; in some cases, such as X-chromosome inactivation, this appears to be on the order of a lifetime.
Many of the mechanistic principles defined in the earlier symposia continued to be refined in the 69th Symposium, but there were also new developments. To put these new developments in context, it is important to note that two other discoveries had a major impact on epigenetics. The other was the discovery of mechanisms underlying the prion hypothesis.
Both of these fields have advanced rapidly in the past decade, with some of the studies contributing to knowledge about chromatin-based epigenetics and others providing new perspectives about heritable transmission of phenotypes. Many of the accomplishments reported at the Symposium are detailed in the chapters of this book, so I eschew discussing these topics here.
However, I will touch upon a few advances that caught my fancy and are not covered within these pages.
At the end, I will try to distill the most important concepts I took away from the meeting. Most of those I participated in, or overheard, were informal and rather lively. The proponents of the "code" cite examples such as tri-methylation of histone H3 at K9 and its greater affinity for the HP1 class of heterochromatin proteins Jenuwein and Allis Those on the other side cite biochemical and genetic evidence that the net charge on the amino-terminal tail of histone H4, irre- spective of which position the charge is at, has dramatic effects on DNA binding or phenotype Megee et al.
Grunstein presented data that included genome-wide analysis of histone acetylation modifications and chromatin-associated proteins using specific antibodies and ChIP-Chip in S. His focus was on the epigenetic switch associated with H4K16 acetylation for binding, or not binding, particular chromatin proteins-thus supporting the histone code hypothesis.
Although not discussed, some of his data appeared to support reports from others that for much of the genome, there is no correlation between specific histone modifications and gene expression i. Taking all the results together, I suspect that both specific modifications and general net charge effects will be used as mechanisms for regulating chromatin structure and gene expression.
Only when it was time for DNA replication would the impervious structure become relaxed. In thinking this way, I foolishly ignored principles of equilibrium dynamics I had learned in undergraduate chemistry.
The realization of its dynamic qualities forced a different view of no. It suggests that in some systems the epigenetic state can be reversed at any time, not just during DNA replication. Hence, we can infer that mechanisms of reinforcement and propagation for silenced chromatin must function constantly. Methylation of histones was widely held to be the modification that would indeed impart a "permanent" mark on the chromatin for review, see Kubicek and Jenuwein In contrast to all other histone modification e.
Furthermore, removing the methyl group under physiological conditions by simple hydrolysis was considered thermodynamically disfavored and thus unlikely to occur spontaneously.
Those thinking that methylation marks were permanent had their belief system shaken a bit by several reports. First, it was shown that a nuclear peptidylarginine deiminase PAD4 could eliminate monomethylation from histone H3 at arginine R residues Cuthbert et al. Although this methyl removal process results in the arginine residue being converted into citrulline, and hence is not a true reversal of the modification, it nevertheless provided a mechanism for eliminating a permanent methyl mark.
Robin Allshire provided a tantalizing genetic argument that the tis2 gene from S. Allshire, pers. He may have been on the right track, because a few months after the meeting, the unrelated LSD 1 enzyme from mammals was shown to specifically demethylate di- and monomethyl on histone H3 at K4 Shi et al.
Quite interestingly, LSD1 did not work on trimethylated H3K4-thus, methylation could be reversed during the marking process, but reversal was not possible once the mark was fully matured. However, Steve Henikoff presented a way by which a permanent trimethyllysine mark could be eliminated.
He showed that the variant histone H3. In essence, a histone that contained methyl marks for silencing could be removed and replaced with one that was more conducive to transcription. When total chromatin was isolated, histone H3.
Rath , there must be a more tenuous set of interactions that increase the probability that a silent state will be maintained, although they do not guarantee it. It was argued that this organization was necessary to keep the complexity of the genome and its regulation in a workable order. This idea was supported by studies in S.
Mutations that released the telomeres, or Sir4, from the nuclear periphery resulted in a loss of telomeric silencing Laroche et al. Furthermore, artificially tethering a partially silenced gene to the periphery caused it to become fully silenced Andrulis et al. In an insightful experiment, Gasser showed that if the teloineres and the silencing complex were both released from the periphery, and free to move throughout the nucleus, telomeric silencing was readily established Gasser et al.
Thus, there does not appear to be a special need for localizing loci to a compartment. This is more consistent with the findings that rapid movement of chromatin proteins on and off chromosomes can still mediate effective regulation such as silencing. Perhaps some of the localization is necessary to keep high local concentrations of relevant factors under special stressful? Alternatively, this may represent a combination of domains put together through evolution that worked long ago, but had no ultimate purpose.
In the simplest molecular sense, prions are proteins that can cause heritable phenotypic changes, by acting upon and altering their cognate gene product. No DNA sequence changes occur; rather, the prion typically confers a structural change in its substrate. The beststudied and understood class of prions causes soluble forms of a protein to change into amyloid fibers.
In many cases, the amyloid form reduces or abolishes normal activity of the protein, thus producing a change in phenotype. Wickner defined another class of prions that do not form amyloid filaments. These are enzymes that require activation by their own enzymatic activity. If a cell should have only inactive forms of the enzyme, then an external source of the active enzyme is required to start what would then become a self-propagating trait, as long as at least one active molecule was passed on to each cell.
Si presented preliminary evidence that a prion model may explain learned memory in Aplysia Si et al. Protein translation of a number of stored mRNAs in neuronal cells is important for the maintenance of shortterm memory in this snail. He found that a regulator of protein translation, CPEB, can exist in two forms, and that the activated form of CPEB acts dominantly to perpetuate itself. Testing of this idea is still in its early days, but it offers an exciting new way of considering the issue of how we remember.
One presentation in particular held my thoughts for weeks after the Symposium. Standard genetic analysis of mutant alleles of the HOTHEAD gene, which regulates organ fusion in Arabidopsis, revealed that normal rules of Mendelian genetics were not being followed Lolle et al.
This stunning level of wild-type reversion produced an exact duplicate, at the nucleotide level, of the wild-type gene seen in the earlier generations.
The gene product of HOTHEAD did not offer an obvious explanation as to how this could occur, but discussions certainly suggested that an archival copy of the wild-type gene was transmitted, perhaps via RNA, through successive generations. Although it could be argued that this phenomenon is outside the purview of "epigenetics"-due to the change in DNA sequence-the heritable transmission of the putative archived copy does not follow normal genetic rules.
Nevertheless, this phenomenon has enormous implications for genetics, especially in evolutionary thinking. For the most part, we are still collecting discovering the components.
Just as the full sequence of a genome has greatly facilitated progress in genetics, a clearer understanding for epigenetics will likely come when all the parts are known.
It is encouraging to see the great strides that have been made in the last decade. I confess that I cannot discern whether we are close to, or far away from, having an accurate mechanistic understanding about how epigenetic states are maintained and propagated.
The prion-based phenomenon may be the first to be understood, but those that are chromatin-based seem the farthest off. The polyvalent nature of interactions that seem to be required to establish a silenced state on a chromosome increases the complexity of the problem. This is further compounded by the dynamic nature of silent chromatin. The ability to know more about movement of components in and out of chromatin structures requires application of enhanced or new methods for an eventual understanding.
Whereas chromatin immunoprecipitation has been important in establishing which components reside in a structure, it has temporarily blinded us to the dynamics. I suspect that, given the complexity, simply measuring binding and equilibrium constants between all the components and trying to derive a set of differential equations to simulate epigenetic switches may not be an effective use of resources, nor will it necessarily result in better comprehension.
Rather, I speculate that a n'ew type of mathematical approach will need to be developed and combined with new experimental measuring methods, in order to eventually understand epigenetic events. Part of this may require development of in vitro systems, that faithfully recapitulate an epigenetic switch between states. The idea of competition between two states in most epigenetic phenomena likely reflects an "arms race" that is happening at many levels in the cell, followed by attempts to rectify "collateral damage.
However, because silencing proteins work through the ubiquitous nucleosomes, some critical genes become repressed. To overcome this, histone modifications e. Z evolved to prevent silencing proteins from binding to critical genes. Depending on subsequent events, these changes may be co-opted for other processes-e.
The silencing mechanisms may have been co-opted for other functions as well, such as promoting chromosome segregation. And so it goes For instance, S. Perhaps more than any other field of biological research, the study of epigenetics is founded on trying to understand unexpected observations, ranging from H. Muller's position-effect variegation, to polar overdominance in the callipyge phenotype Georges et al.
The hope of understanding something unusual serves as the bait to draw us in, but we soon become entranced by the cleverness of the mechanisms employed. This may explain why this field has drawn more than its share of light-hearted and clever minds.
I suspect it will continue to do so, as we develop a deeper understanding of the cleverness, and as new and unexpected epigenetic phenomena are discovered. Acknowledgments I thank my colleagues at the University of Chicago and the Fred Hutchinson Cancer Research Center for making my own studies on epigenetics so enjoyable, and I thank the National Institutes of Health for financial support.
References Abraham J. Sites required for position-effect regulation of mating-type information in yeast. Cold Spring Harbor Symp. AlIfrey v. Andrulis E. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature Escl, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Aparicio O. Overcoming telomeric silencing: A trans-activator competes to establish gene expression in a cell cycle-dependent way.
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Kubicek S. A crack in histone lysine methylation. La Volpe A. Coupled demethylation of sites in a conserved sequence of Xenopus ribosomal DNA. Laroche T. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curro BioI. Laurenson P.
Silencers, silencing, and heritable transcriptional states. Lewis E. Regulation of the genes of the bithorax complex in Drosophila. DNA methylation, genomic imprinting, and mammalian development. Locke J. Dosage-dependent modifiers of position effect variegation in Drosophila and a mass action model that explains their effect. Genetics Lolle S. Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. Losick R. Summary: Three decades after sigma.
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The generation and propagation of variegated chromosome structures. Wickner R. Prion genetics: New rules for a new kind of gene. Prions of yeast are genes made of protein: Amyloids and enzymes. Willard H. E, Brown CJ. Epigenetic and chromosomal control of gene expression: Molecular and genetic analysis of X chromosome inactivation.
Wood W. Aspects of dosage compensation and sex determination in Caenorhabditis elegans. Yarmolinsky M. Zheng C, and Hayes p. Structures and interactions of the core histone tail domains. Biopolymers Introduction, 16 5. The Role of Chromatin, 18 2. Clues from Genetics and Development, 16 6. All Mechanisms Are Interrelated, 19 3. But during the past 50 years, the meaning of the term "epigenetics" has itself undergone an evolution that parallels our dramatically increased understanding of the molecular mechanisms underlying regulation of gene expression in eukaryotes.
Until the s, however, the word epigenetics was used in an entirely different way to categorize all of the developmental events leading from the fertilized zygote to the mature organism-that is, all of the regulated processes that, beginning with the genetic material, shape the final product Waddington This concept had its origins in the much earlier studies in cell biology and embryology, beginning in the late 19th century, that laid the groundwork for our present understanding of the relationship between genes and development.
There was a long debate among embryologists about the nature and location of the components responsible for carrying out the developmental plan of the organism. In trying to make sense of a large number of ingenious but ultimately confusing experiments involving the manipulation of cells and embryos, embryologists divided into two schools: those who thought that each cell contained preformed elements that enlarged during development, and those who thought the process involved chemical reactions among soluble components that executed a complex developmental plan.
These views focused on the relative importance of the nucleus and cytoplasm in the developmental process. Following Flemming's discovery of the existence of chromosomes in , experiments by many. Thomas Hunt Morgan ultimately provided the most persuasive proof of this idea through his demonstration of the genetic linkage of several Drosophila genes to the X chromosome.
From that point onward, rapid progress was made in creating linear chromosome maps in which individual genes were assigned to specific sites on the Drosophila chromosomes Sturtevant Of course, the questions of classic "epigenesis" remained: What molecules within the chromosomes carried the genetic information, how did they direct the developmental program, and how was the information transmitted during cell division? It was understood that both nucleic acid and proteins were pres- ent in chromosomes, but their relative contributions were not obvious; certainly, no one believed that the nucleic acid alone could carryall of the developmental information.
Furthermore, earlier questions persisted about the possible contribution of the cytoplasm to developmental events.
Evidence from Drosophila genetics see below suggested that heritable changes in phenotype could occur without corresponding changes in the "genes. Ultimately, it became useful to redefine epigenetics so as to distinguish heritable changes that arise from sequence changes in DNA from those that do not. In , H. Muller Muller described a class of Drosophila mutations he called "eversporting displacements" "eversporting" denoting the high rate of phenotypic change.
These mutants involved chromosome translocations displacements , but "even when all parts of the chromatin appeared to be represented in the right dosage-though abnormally arranged-the phenotypic result was not always normal.
He thought that this was probably due to a "genetic diversity of the different eye-forming cells;' but further genetic analysis led him to connect the unusual properties with chromosomal rearrangement, and to conclude that "chromosome regions, affecting various characters at once, are somehow concerned, rather than individual genes or suppositious 'gene elements.
During that period, chromosomal rearrangements of all kinds were the object of a great deal of attention. It was apparent that genes were not completely independent entities; their function could be affected by their location within the genome-as amply demonstrated by the many Drosophila mutants that led to variegation, as well as by other mutants involving translocation to euchromatic regions, in which more general non-variegating position effects could be observed.
The role of transposable elements in plant genetics also became clear, largely through the work of McClintock A A second line of reasoning came from the study of developmental processes. It was evident that during development there was a divergence of phenotypes among differentiating cells and tissues, and it appeared that such distinguishing features, once established, could be clonally inherited by the dividing cells.
Although it was understood at this point that cell-specific programming existed, and that it could be transmitted to daughter cells, how this was done was less clear. A number of mechanisms could be imagined, and were considered. Particularly for those with a biochemical point of view, a cell was defined by the multiple interdependent biochemical reactions that maintained its identity.
For example, it was suggested in by Delbruck quoted in Jablonka and Lamb that a simple pair of biochemical pathways, each of which produced as an intermediate an inhibitor of the other pathway, could establish a system that could switch between one of two stable states. Actual examples of such systems were found somewhat later in the lac operon of Escherichia coli Novick and Weiner and in the phage switch between lysogenic and lytic states Ptashne Functionally equivalent models could be envisioned in eukaryotes.
The extent to which nucleus and cytoplasm each contributed to the transmission of a differentiated state in the developing embryo was of course a matter of intense interest and debate; a self-stabilizing biochemical pathway would presumably have to be maintained through cell division. A second kind of epigenetic transmission was clearly demonstrated in Paramecia and other ciliates, in which the ciliary patterns may vary among individuals and are inherited clonally Beisson and Sonneborn Altering the cortical pattern by microsurgery results in transmission of a new pattern to succeeding generations.
It has been argued that related mechanisms are at work in metazoans, in which the organization of cellular components is influenced by localized cytoplasmic determinants in a way that can be transmitted during cell division Grimes and Aufderheide Work by Briggs and King in Rana pipiens and by Laskey and Gurdon in Xenopus had demonstrated that introduction of a nucleus from early embryonic cells into enucleated oocytes could result in development of an embryo.
But as late as , Laskey and Gurdon could state that "It has yet to be proved that somatic cells of an adult animal possess genes other than those necessary for their own growth and differentiation. It was now clear that the program of development, and the specialization of the repertoire of expression seen in somatic cells, must involve signals that are not the result of some deletion or mutation in the germ-line DNA sequence when it is transmitted to somatic cells.
Of course, there are ways in which the DNA of somatic cells can come to differ from that of the germ line, with consequences for the cellular phenotype: For example, transposable elements can alter the pattern of expression in somatic cells, as demonstrated by the work of Barbara McClintock and other plant geneticists.
Similarly, the generation of antibody diversity involves DNA rearrangement in a somatic cell lineage. This rearrangement or more precisely its consequences can be considered a kind of epigenetic event, consistent with the early observations of position-effect variegation described by Muller.
In part to account for this kind of inactivation, Riggs and Holliday and Pugh proposed that DNA methylation could act as an epigenetic mark. The key elements in this model were the ideas that sites of methylation were palindromic, and that distinct enzymes were responsible for methylation of unmodified DNA and DNA already methylated on one strand. A methylation mark present on a parental strand would be copied on the daughter strand following replication, resulting in faithful transmission of the methylated state to the next generation.
Shortly thereafter, Bird took advantage of the fact that the principal target of methylation in animals is the sequence CpG Doskocil and Sorm to introduce the use of methylation-sensitive restriction enzymes as a way of detecting the methylation state.
Subsequent studies Bird ; Bird and Southern then showed that endogenous CpG sites were either completely unmethylated or completely methylated. The predictions of the model were thus confirmed, establishing a mechanism for epigenetic transmission of the methylation mark through semiconservative propagation of the methylation pattern. In the years following these discoveries, a great deal of attention has been focused on endogenous patterns of DNA methylation, on the possible transmission of these patterns through the germ line, on the role of DNA methylation in silencing gene expression, on possible mechanisms for initiation or inhibition of methylation at a fully unmethylated site, and on the identification of the enzymes responsible for de novo methylation and for maintenance of methylation on already methylated sites.
Although much of the DNA methylation seen in vertebrates is associated with repetitive and retroviral sequences and may serve to maintain these sequences in a permanently silent state, there can be no question that in many cases this modification provides the basis for epigenetic transmission of the state of gene activity. At the same time, it was clear that this could riot be the only mechanism for epigenetic transmission of information. For example, as noted above, position-effect variegation had been observed many years earlier in Drosophila, an organism that has extremely low levels of DNA methylation.
Furthermore, in subsequent years, Drosophila geneticists had identified the Polycomb and Trithorax groups of genes, which appeared to be involved in permanently "locking in" the state of activity, either off or on, respectively, of clusters of genes during development. The fact that these states were stably transmitted during cell division suggested an underlying epigenetic mechanism. Well before most of the work on DNA methylation began, Stedman and Stedman proposed that the histones could act as general repressors of gene expression.
They argued that since all somatic cells of an organism had the same number of chromosomes, they had the same genetic complement although this was not demonstrated until some years later, as noted above. Understanding the subtlety of histone modifications was far in the future, so the Stedmans operated on the assumption that different kinds of cells in an organism must have different kinds of histones in order to generate the observed differences in phenotype.
Histones can indeed reduce levels of transcript far below those commonly observed for inactive genes in prokaryotes. Subsequent work addressed the capacity of chromatin to serve as a template for transcription, and asked whether that capacity was restricted in a cell-type-specific manner.
In a paper, Bonner Bonner et al. The result was specific to this tissue. With the advent of hybridization methods, the transcript populations from such in vitro experiments could be examined Paul and Gilmour and shown to be specific for the particular tissue from which the chromatin was derived. Other results suggested that this specificity reflected a restriction in access to transcription initiation sites Cedar and Felsenfeld Nonetheless, there was a period in which it was commonly believed that the histones were suppressor proteins that passively silenced gene expression.
In this view, activating a gene simply meant stripping off the histones; once that was done, it was thought, transcription would proceed pretty much as it did in prokaryotes.
There was, however, some evidence that extended regions of open DNA did not exist in eukaryotic cells Clark and Felsenfeld Furthermore, even if the naked DNA model was correct, it was not clear how the decision would be made as to which histone-covered regions should be cleared. The resolution of this problem began as early as , when Allfrey Allfrey et al. In the ensuing decade, there was A great interest in examining the relationship between histone modifications and gene expression.
Modifications other than acetylation methylation and phosphorylation were identified, but their functional significance was unclear. It became much easier to address this problem after the discovery by Kornberg and Thomas of the structure of the nucleosome, the fundamental chromatin subunit. The determination of the crystal structure of the nucleosome, first at 7 A and then at 2.
Beginning in and extending over some years, Grunstein and his collaborators Wallis et al. The ultimate connection to detailed mechanisms began with the critical demonstration by Allis Brownell et al.
Since then, of course, there has been an explosion of discovery of histone modifications, as well as a reevaluation of the roles of those that were known previously. This still did not answer the question of how the sites for modification were chosen in vivo. It had been shown, for example Pazin et al. Activation was accompanied by repositioning of nucleosomes, and it was suggested that this was the critical event in making the promoter accessible.
It was not clear how information about the state of activity could, employing these mechanisms, be transmitted through cell division; their role in epigenetic transmission of information was thus unclear. It was found, for example, that methylation of histone H3 lysine 9 resulted in the recruitment of the heterochromatin protein HP1 Bannister et al.
Furthermore, HP1 could recruit the enzyme Suv39 h 1 that is responsible for that methylation. This led to a model for propagation of the silenced chromatin state along the region through a processive mechanism Fig. Equally important, it provided a reasonable explanation of how that state could be transmitted and survive through the replication cycle Fig.
Analogous mechanisms for propagation of an active state have been proposed that involve methylation of histone H3 lysine 4 and the recruitment of Trithorax group proteins Wysocka et al.
Different kinds of propagation mechanisms have been suggested that depend on variant histones rather than modified histones Ahmad and Henikoff ; McKittrick et al.
Histone H3 is incorporated into chromatin only during DNA replication. In contrast, the histone variant H3. It has been proposed that the presence of H3. The consequent transcription would result in replacement of H3 containing nucleosomes with H3. Whereas these mechanisms give us some ideas about how the heterochromatic state may be maintained, they do not explain how silencing chromatin structures are first established.
It has only recently become clear that this involves the production of RNA transcripts, particularly from repeated sequences, which are processed into small RNAs through the action of proteins such as Dicer, Argonaute, and RNA-dependent RNA polymerase. These RNAs are subsequently recruited to the homologous DNA sites as part of complexes that include components of the Polycomb group of proteins, thus initiating the formation of heterochromatin.
CpG on one strand has a corresponding CpG on the other. The maintenance DNA methyltransferase recognizes a hemimethylated site, and methylates the cytosine on the new strand, so that the pattern of methylation is undisturbed.
The modified histone tail m interacts with a protein binder pb that has a binding site specific for that modification. During replication, the newly deposited histones which are interspersed with parental histones can thus acquire the parental modification. A similar mechanism would allow propagation of histone modifications from a modified region into an unmodified one at any stage of the cell cycle.
In addition to imprinting at many loci, and the allele-specific and random X-chromosome inactivation described above, there are epigenetic phenomena involved in antibody expression, where the rearrangement of the immunoglobulin genes on one chromosome is selectively inhibited, and in the selection for expression of single odorant receptor genes in olfactory neurons Chess et al.
In Drosophila, the Polycomb group genes are responsible for establishing a silenced chromatin domain that is maintained through all subsequent cell divisions. Epigenetic changes are also responsible for paramutation in plants, in which one allele can cause a heritable change in expression of the homologous allele Stam et al. This is an example of an epigenetic state that is inherited meiotically as well as mitotically, a phenomenon documented in plants but only rarely in animals Jorgensen Much of the evidence for the mechanisms described above has come from work on the silencing of mating-type locus and centromeric sequences in Schizosaccharomyces pombe Hall et al.
In addition, the condensed chromatin structure characteristic of centromeres in organisms as diverse as flies and humans has been shown to be transmissible through centromereassociated proteins rather than DNA sequence.
In all of these cases, the DNA sequence remains intact, but its capacity for expression is suppressed. This is likely in all cases to be mediated by DNA methylation, histone mod- A ification, or both; in some cases, we already know that to be true. Finally, the epigenetic transmission of "patterns;' described above for Paramecia, now extends to the prion proteins, which maintain and propagate their alternatively folded state to daughter cells.
Although this has been presented as a sequential story, it should more properly be viewed as a series of parallel and overlapping attempts to define and explain epigenetic phenomena.
The definition of the term epigenetics has changed, but the questions about mechanisms of development raised by earlier generations of scientists have not. Contemporary epigenetics still addresses those central questions. Seventy years have passed since Muller described what is now called position-effect variegation. It is gratifying to trace the slow progress from observation of phenotypes, through elegant genetic studies, to the recent analysis and resolution at the molecular level.
With this knowledge has come the understanding that epigenetic mechanisms may in fact be responsible for a considerable part of the phenotype of complex organisms. As is often the case, an observation that at first seemed interesting but perhaps marginal to the main issues turns out to be central, although it may take a long time to come to that realization.
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