Epigenetics and adaptive evolution: which wins?

(this is a slightly revised version of this post: see last paragraph)

Yesterday we discussed some aspects of epigenetics, that is, the modification of DNA that does not alter its nucleotide sequence but does induce or repress expression of genes in the modified area of the chromosome.  There were a lot of comments and replies on that post that you might want to browse.  

However, one reader tweeted a very interesting question that we'd like to address here where others could see his and our thinking. He wrote: Could epigenetic inheritance make genetic assimilation more potent since environmentally induced phenotype is multigenerational?

We thought this was worth addressing here, as it raises important issues about how evolution works.  

For readers who may not know the term, 'genetic assimilation' refers to a situation in which some environmental factor induces one of a particular set of possible states (sometimes called polyphenism).  This has long been studied in many different species, though much of the work was done in the early 20th century's pre-gene era--that is, when actual known genes were few and far between.  Earlier studies had to rely on traits for which there was reasonably specific evidence, even if indirect, that their variation was due to genetic variation.

Clearly we now know that many traits, including behavioral traits of various kinds, are affected by epigenetic changes as well as DNA sequence variation.  In itself, traits due to epigenetic changes have not seemed to be inherited:  Although since gene expression is directly the result of environmental changes a cell detects, epigenetic changes are a major mechanism of local adaptation.  However, the idea has been that state of an organism's trait would not be inherited.  Each organism starts life afresh in terms of its gene usage.

Yet there are by now many studies in various species, direct and indirect, observational and experimental, that show not just that changes in cell behavior involve epigenetic mechanisms, but that epigenetic changes may sometimes be inherited--perhaps even for multiple generations.  This has been seen as a threat to Darwinian theory, to the extent that such assertions have been sneered at as almost ante-diluvian Lamarckian nonsense.  Still, there is the evidence, and it's from legitimate investigators, not crack-pots, and from legitimate journals (well, some of them are like Nature and Science, that go for sensationalistic stories, sometimes not looking all that closely at the evidence).  So those who react against anything that smacks of environmentalism should stop and take a breath. 

There is nothing at all surprising about organisms reacting to their environment and since we are made of cells that express genes, about that reaction involving gene-usage changes.  Epigenetic changes are not mystic, mechanisms are clearly known, and they at most would change the criteria to which the term 'inheritance' is applied.  This in the same way that, because of increased understanding of DNA, the term 'gene' has rapidly lost its standard 20th century meaning--with no threat to basic genetic or evolutionary theory.

Genetic assimilation
This is a term coined by CH Waddington in the mid-20th century, but that applies to phenomena studied in the late 19th century under names like the Baldwin effect (for more on this history, you could see my 2004 Evolutionary Anthropology article, "Doin' what comes naturally").  Classic experiments were done to show that genetic assimilation can happen.  [Waddington was a quirky character who made lots of enemies and was dismissed by many, often for political reasons but that's irrelevant here]

CH Waddington

Traits, including behavior, were thought occasionally to be such that they might lead to higher reproductive success, and if in the same environment this success was consistently achieved by having the trait, it could be beneficial for mutations that arose, which generated the trait, to increase in frequency.  That is, if such mutations arose, selection could favor them so that eventually traits that had once been environmentally induced became genetically hard-wired.

How often this actually happens in nature is debatable and controversial because it has seemed by some to verge on non-Darwinian evolution.  But if or when it happens,, genetic assimilation would, in a sense, guarantee that the individual had the advantageous trait. This is what led our correspondent to ask whether epigenetic changes that could be passed down over some generations might give normal genetic evolutionary mechanisms a chance to occur, by presenting the favored trait to the environment more stably and consistently than if it depended on chance epigenetic mechanisms each generation.

The obvious answer is that this is certainly plausible. But it would have to persist for far longer than has been observed, to our knowledge, to match the slowness and random-mutational aspect of normal evolution.  As important, to us, is that if one thinks carefully about evolution, it is not so clear what would actually happen.

But good or bad?  Is epigenetic or genetic causation more 'fit'?
If the trait were hard-wired because of mutations, environmental induction wouldn't be necessary.  If the environment is present, the organism doesn't have to rely on any chance aspects of epigenetics to make it fit, relative to natural selection, compared to a less likely competitor who had to rely on that chance.  Of course, the mutations shouldn't reduce the chance of a response, say by erasing the DNA signal for epigenetic marking. But if they guaranteed the trait, the organism starts out life in an adapted state.

Yet one can ask when it is a good for a species to be hard-wired.  One could argue that it is not such a good thing, because the organism may be far less able to adapt to different or changing circumstances.  Depending on the species, its population size and habits and reproductive biology, it might be far better for each individual or local set of kin to adapt in an epigenetic way, when or if the environmental circumstance arises.  An epigenetic response would be reversible when environments change.  Let the environment do the talking, so long as the organism can respond to it.

However, an obvious analogue to natural selection applies to epigenetic traits: if they are really passed down from one generation to the next, that is itself like a form of hard-wiring that's only somewhat 'softer' than incorporating the trait into a deterministic DNA sequence.  It might be better not to transmit the trait even epigenetically.

If the environmental factor is utterly inevitable, hard-setting by DNA sequence might be as good as or even surer than epigenetic transmission.  But otherwise, maybe the risk of having to experience the environment and then adjust to it epigenetically, is worth the ability not to make that epigenetic change until it's necessary.  In other words, both genetic and epigenetic pre-determination may both be risky.  In a less certain environment, it may be better for each individual to learn by experience how to respond to what it faces; in that case, epigenetic marking is a good way to go, but not necessarily epigenetic transmission across generations.

Here we have some testable, sensible scientific issues with no obvious answer.  Of course, one first has to accept the reality of epigenetic effects and their transmission under at least some conditions, before one can even ask the question.  But whether conceptual assimilation by scientists is as real as genetic assimilation is not so clear.

Added after posting:  Today the current June 2014 issue of Trends in Genetics arrived in my box.  It has a nice review of epigenetic mechanisms, including discussion of the evidence (D'Urso and Brickner, vol. 30(6): 230-236).  It notes trans-generational effects, in the context of fitness and evolution.  It probably is not circumspect in this respect, in terms of how long such effects last (as discussed above), but is a good review for readers who would like to know more about the actual phenomenon and the evidence.

Epigenetics: the burden of proof vs the folly of dismissal

We haven't written much about epigenetics for a while, in part because it's so trendy that it's impossible to know what much of it means or how it's all going to shake out, and in part because there are so many different interpretations of the word that it's hard to know whether everyone's talking about the same thing.  Tools to detect epigenetic changes in the genome, that is, specific locations that have been chemically modified in ways that affect nearby gene transcription, are now available.  Still, it is clearly a fad in the sense that once tools are there the scientific community seizes them in a bandwagon effect, showing up in study designs and grant applications and so on, in ways that can exceed the reality.  Everybody now simply 'has' to do an epigenetic analysis on their favorite project.  And partly for this reason, not everyone else accepts that epigenetics will prove in the long run to be a significant actor in development and disease.

Epigentics: what is it?
We've posted about epigenetics in the past (e.g., here and here).  Relevant to today's post, the idea of epigenetic changes is that DNA can be chemically modified not by changing its nucleotide sequence itself, but by altering the packaging of the chromosome near genes that are to be expressed (or repressed).  Since different cells in the body are different because of their differential use of genes (cells in your brain and your skull have the same DNA, but turn on different sets of genes to become what they are, as well as to do what they do throughout life), this is simply a statement of one of the mechanisms by which it's achieved.  That's not the controversy.

The controversy goes a bit deeper and reaction to claims of epigenetic changes are emotional and often vehement.  There are two reasons for this.  First, what causes epigenetic marking of specific chromosome regions is the state of the cell at a given time, and that can change in response to the conditions it senses--its environment.  The evidence is, further, that until active mechanisms alter the epigenetic marking of chromosomes, the gene-expression pattern of the cell is inherited when it divides.  Since the inducing mechanism is part of the environmental situation of the cell, this gets uncomfortably close to Lamarckian inheritance.  The cartoon example of Lamarck's pre-Darwinian idea is the giraffe stretching to reach high leaves and, if successful, passing on long-neck genes to its offspring.  This is the antithesis of modern Darwinian theory (though Darwin himself toyed with it in his own theory of inheritance).  That Darwinian theory has randomly arising mutation being screened by natural selection to pick the successful genes: the lucky giraffe that happened to have inherited a long-neck genetic variant ate better and had more girafflets than its shorter-necked peers.  Here, the facts speak for themselves, and nothing known suggests that striving for something can in itself engineer heritable genetic change, specific DNA mutations, to make that something happen.

Masai giraffe; Wikipedia

But the second reason that epigenetics touches raw ideological nerves, especially in regard to humans, is that one school of thought wants to see everything human as written deterministically in our genomes: you (including your behavior) are what your DNA sequences prescribes.  Anyone offering any other suggestion is by this group widely denigrated without inhibition as a soft-headed denier of the importance of heredity.  That's because if environments really do affect your achieved nature, then genetic determinism and all that goes with it are no longer biological universals set in stone.

But what if, beyond environmental effects on gene expression in an individual during its lifetime, those effects were heritable into the next and future generations?  That would suggest that we are not just dealing with a fad made possible by a fancy bit of gear that can help you get a grant, but that there are things about our achieved natures and our evolution that we don't yet really understand.  And a couple of papers, one from last year, and one more recent, struck us as worth writing about, for different reasons.

Epigenetic---and then some?
A lot of attention was paid to a December 2013 paper in Nature Neuroscience ("Parental olfactory experience influences behavior and neural structure in subsequent generations", Dias and Ressler). Their point was first to show that your experiences involving odor detection are specific and can leave a long-lasting chemical and behavioral 'memory'.  Dias and Ressler exposed mice to a particular well-studied single-molecule odor, and coupled that exposure with a shock to the mouse's foot, to condition the animals to fear the odor (a logic resembling Pavlov's famous dog experiments).  This triggered the activation of cells that express a particular odor-detection (olfactory receptor, or OR) gene, out of the repertoire of about 1000 such genes, as well as the conditioned fear response upon smelling the odor, even absent the shock. But the authors reported something much more remarkable, and challenging to understand.

What they found was that the behavioral response to that same odor is activated in at least two future generations that had not been exposed to the fear-conditioning.

We subjected FO mice to odor fear conditioning before conception and found that subsequently conceived F1 and F2 generations had an increased behavioral sensitivity to the FO-conditioned odor, but not to other odors... Bisulfite sequencing of sperm DNA from conditioned F0 males and F1 naive offspring revealed CpG hypomethylation in the Olfr151 gene.  In addition, in vitro fertilization, F2 inheritance and cross-fostering revealed that these transgenerational effects are inherited via parental gametes.  Our findings provide a framework for addressing how environmental information may be inherited transgenerationally at behavioral, neuroanatomical and epigenetic levels.

A very important part of this is that the transmission was by males who had been conditioned, via their sperm, to females who had no such experience....and then to their sons' offspring (that is, the marking was present on the sons' sperm cells, directing hyper-expression of the OR gene in the grandchild-mice).

Reaction to this paper seemed to fall along party lines, with determinists doubting that the results could be real, and others intrigued.  Indeed, this is curious because the experience affects not just the startled males' odor-detecting mechanism in its nose cells where odors are detected, and fear response, but seems to imprint the specific effect on sperm cells.  There is no means known (to us, at least) by which this could occur, unless all cells' OR genes are affected during the F0 males' conditioning, nor are we qualified or patient enough to judge whether the study, or its set-up in some way has led to a misleading result.  To be fair, while the authors didn't demur to send their paper to a Nature journal, nor (in expected fashion) did the Nature journal demur from publishing without requiring such a mechanism to be shown, the authors themselves in fact did not venture a mechanism and recognized the issue in the Discussion.

If this sort of specific epigenetic mechanism does in fact persist across generations, without further conditioning, many questions are raised.  Not only is the targeting mechanism important to know, but since every generation has different experiences, what sort of expression mishmash would new pups have after millions of years of evolution in all sorts of environments?  Nonetheless, mice (and we, and trees, and even bacteria) are differentiating organisms that respond to environmental conditions in ways that certainly include altered gene expression.  So being skeptical may be fully justified, and this is not in any sense an "Aha!" moment for Lamarckians.  But its strangeness to what is currently known is also no reason to dismiss it because it doesn't fit your, say, genomic determinist or selectionist predilections. This is especially so because there is in fact a lot of evidence for environmentally induced changes in gene usage, and hence in the traits, of organisms including humans.  And that brings us to the other, more recent paper.

Do big bodies mean big epigenetic news?
The other paper is a recent report in The Lancet ("DNA methylation and body-mass index: a genome-wide analysis," Dick et al., 2014), which describes the results of a genome-wide analysis of methylation at CpG sites and its association with obesity, measured by BMI.  CpG refers to a C nucleotide being next to a G nucleotide along a DNA strand.  Methylation is a way of chemically attaching a small tag to that CpG in gene regulating areas of a chromosome, that makes it hard for the proteins that are needed to express a nearby gene to bind to the DNA to do their job.  That is, the expression of methylated genes is repressed.

A commentary in the June 7 Lancet applauds the work of Dick et al., and heralds the beginning of the "EWAS [epigenome-wide association study] era."  Of course, one's first reaction might be a sigh of 'here we go again!' in regard to hype far out-performing hope, a new fad for rescuing hopeless non-replicable findings, and journals having to sell copy and holding no standards of circumspection. But how should one react?

The possible significance of epigenetics to disease has not been lost on epidemiologists, and a new field called epigenetic epidemiology is abornin', counting on the importance of non-sequence modifications of DNA, in particular methylation and acetylation patterns, to (finally!) explain patterns of disease.  In that sense EWAS may be important, or may to a cynic just be an E-for-G swap to keep the GWAS funding flowing.

The Dick et al. paper is from this burgeoning field.  Epidemiology had many successes in the last century identifying environmental causes of disease, but when complex chronic diseases overtook infectious diseases as leading causes of death, the field had a much rougher time finding the causes of major diseases, and predicting who would get them.  So, epidemiology turned to genetics, but ran into the same problem genetics itself was up against -- complexity.  But if specific epigenetic changes can now be attributed in a useful way to environmental factors, on say the McFood-O-Meter scale, the claim will be that reductionist science has found the mechanism that shows that new epidemiological studies will have to be funded to focus on the risk factor that causes the epigenetic change.

It's not an entirely new idea.  For some years, George Davey Smith, an epidemiologist at the University of Bristol, has been advocating the use of 'Mendelian randomisation ', a strategy to see whether a variant in a gene whose function relates to processing some environmental factor has the same effect in people not exposed to that factor as those who are.  Maybe someone will cook up other prevention or treatment strategies if epigenetic mechanisms prove important.  

Dick et al. identified five methylation sites in the genome that in their sample were associated with being overweight by the Body Mass Index (BMI) criterion: three were in intron 1 of the HIF3A gene. HIF3A is a gene that regulates response to reduced oxygen levels.  The authors note that "Although the main focus on HIF has been its role in cellular and vascular response to changes in oxygen tension during normal development or pathological processes (eg, cardiovascular disease and cancer), compelling and increasing experimental data suggest that the HIF system also plays a key part in metabolism, energy expenditure, and obesity."

Have Dick et al. found the cause of obesity?  Well, no.  As the Lancet commentary points out, there are numerous difficulties in epigenetic research, a primary one being that a gene won't be modified in every tissue, nor all the time, nor even necessarily in every cell of the appropriate type in a given tissue.  That means that the choice of tissues in which to search for methylation and when to look are crucially important considerations.  Dick et al. did test various tissues, and found that methylation varied.

Another important issue in epigenetic studies is determining the order of events -- which came first, the disorder or the DNA modification?  That is, does the disorder lead to methylation of genes involved, or does methylation of related genes cause the disorder?

Dick and colleagues attempt to address the issue of causality by applying a mendelian randomisation approach to interrogate the causal relation between HIF3A methylation and BMI. This approach uses a genetic proxy for DNA methylation (namely, methylation quantitative trait loci) to identify a causal relation between an exposure or trait and epigenetic variation, assuming that genetic associations are largely immune to residual confounding and reverse causation. Dick and colleagues identified two upstream single nucleotide polymorphisms that were independently associated with DNA methylation at a HIF3A locus in both the discovery and replication cohorts. However, these single nucleotide polymorphisms were not associated with BMI in the study cohorts or the high-powered GIANT consortium dataset, suggesting that hypermethylation at the HIF3A locus is likely to be a result of increased BMI rather than a causal association between increased methylation and BMI.

So, apparently the obesity came first, methylation later, and has nothing necessarily to do with the cause of obesity. Interestingly, The Lancet still describes this as an important study. "Dick and colleagues’ study represents an important advance for both obesity-related research and the specialty of epigenetic epidemiology." Why? "The widespread uptake of instruments such as the Illumina 450K HumanMethylation array means that large collaborative EWAS meta-analyses can be done, building on the success of similar approaches in genetics."

Have instrument, will use it.

The burden of proof vs the folly of dismissal
It's early days yet in the understanding of the role of epigenetics in disease and behavior, and there's a lot left to be learned.  There is now a wealth of experimental literature on cells as well as a variety of laboratory species, demonstrating some of the mechanisms of gene regulation that involve epigenetic changes of DNA.  There are carefully done experimental studies that show multi-generational transmission of such changes. There have also been epidemiological and even experimental studies of intra-uterine or maternal experience affecting things like body weight in offspring.  Thus, even without specific epigenetic data at the genome level we have every reason to expect that life experience at any age could affect even complex traits.  And what would be more likely than some sort of epigenetic mechanism to be responsible?

One should also keep in mind that trans-generational correlation can look very much like regular genetic transmission and make a trait look 'genetic' in the classical sense, rather than in the epigenetic sense.

It clearly befalls those advocating, and those dismissing, epigenetic inheritance to keep their powder dry until we can see more clearly into the whites of the genome's eyes.  In fact, since we are obviously differentiated organisms descended from a single cell, who respond in all sorts of physical and behavioral ways to our internal and external environments, it seems obvious that some such mechanisms are fundamental to genome function, as experience clearly suggests.  But how well complex traits like body shape or odor detection would be transmitted not just across cell divisions in specific types of responding cells, but also across generations, is far from clear.

Keeping our powder dry should be automatic for scientists, as this is a very important question well worthy of careful investigation.  But whether we can keep obfuscation by ideology and equipment salesmen at bay is just as serious a question.

Epigenetics isn't everything but it is something

'Epigenetics' is the new 'gene for.'  A good way to tell if a field in biology is hot is if it's become an -ome, with a Wiki page, and epigenetics has.  The 'epigenome' will now explain everything from why identical twins aren't, to why we get the diseases we'll get and why we behave as we do, and science studies and gender studies and social critics are using epigenetics to reconfigure their approach to understanding how biology and society are intertwined.

Epigenetics

There are a couple of issues here.  One is that some people use 'epigenetic' to refer to things like, say, obesity due to overeating because diet interacts with one's genetically based metabolism.  However, the current 'hot' meaning is that environmental factors directly affect gene expression, rather than just the result of normal gene expression.  So, a dietary component might lead to a gene being inactivated.

Now the fashionable aspect of this is, of course, that those in the area seem to want everything to be 'epigenetic' -- after all, one can get funded to do the epigenomics!  We mean not to disparage the field wholesale -- there is certainly something to it, but, like the human genome project, the epigenome can't possibly fill all the promises being made in its name.  It is, in this sense, a political ploy for funding and attention, as well as an enthusiasm for what seems new and possibly profound.

Still, epigenetic effects mean that DNA sequences alone do not determine what genes do, and the epigenetic modifications can have substantial effects, and be inherited.

The state of the art
A paper in the latest Trends in Genetics ("Bridging the transgenerational gap with epigenetic memory," Lim and Brunet) does an admirable job describing what's actually currently known about epigenetics, or 'non-Mendelian', non-genetic inheritance.  They point out that patterns of non-genetic inheritance have been described for almost 100 years, including Waddington's description of the inheritance of wing patterns influenced by heat shock in fruit flies in the 1940s -- it was Waddington who coined the term 'epigenetic', though his meaning was more general than ours today.

Parental imprinting, discovered during the 1980's, is another example of non-genetic inheritance.  This is when alleles from only one parent are inherited, the other set being silenced by DNA methylation and/or histone modification.  At the same time, Lim and Brunet point out, the discovery of transgenerational epigenetic inheritance (TEI) in mice was reported, in that case affecting coat color.  And many more instances have been reported since then, in many different organisms.  It became apparent as well that epigenetic modifications could last for at least several generations.

Lim and Brunet describe a recent experiment in which

mice with an insertion of LacZ into the Kit gene gave rise to genetically wild type offspring that still exhibited the tail and paw color phenotype characteristic of Kit mutants for at least two generations.  Genetically wild type descendants of ancestors that had the Kit mutant phenotype showed an altered pattern of Kit RNA expression, with RNA molecules of shorter size in brain and testis.  Microinjection of RNA from heterozygous mutant animals into one-cell embryos was sufficient to recapitulate the mutant phenotype in the following generation.

Our objections to the use of 'wild-type' and 'mutant' notwithstanding, the persistence of the traits from the altered mice into the next generations is of interest. The authors suggest that the transgene (the LacZ inserted into the Kit gene) disrupts a specific locus in the parental genome, which causes the production of abnormal RNA in sperm, which is then transmitted to at least the next two generations.  How this 'epigenetic memory' works is not yet clear but the apparent role of RNA in this process has been replicated in experiments with other traits.  One example is the injection of fertilized eggs with micro RNAs targeting specific enzymes that regulate cardiac growth, which had the capacity to slow the growth of the heart for several generations, though it seems that not all RNA has a similar capacity. 

Work has recently been done on transgenerational epigenetic inheritance in the model worm, C. elegans, as well, specifically on longevity and fertility.  The inheritance of sterility and longevity influenced by histone modifications -- demethylation -- has been documented, and observed to last for at least 5 generations. 

TEI and environmental stimuli
Another mode of TEI, which is perhaps more relevant to life as it's lived outside the lab, is that that might be induced by metabolic changes.  Over- or undernutrition of parents is the example we've heard most about, with respect, e.g., to the multi-generational consequences of widespread famine. 

Exposure to a chronic high-fat diet in rat fathers results in impaired insulin metabolism and pancreatic cell gene expression in female F1 offspring.  Female offspring from fathers fed a high fat diet mated with mothers fed a control diet exhibited an increase in blood glucose ... and a decrease in insulin secrettion compared with offspring with both parents fed a control diet.

Analysis of gene expression in islet cells showed differential levels of expression of various types, including signaling factors.  Other experiments have shown altered phenotypes and gene expression two generations after male mice were overfed, suggesting again that this is due to a TEI rather than genetic changes.  Some hypothesize that the epigenetic changes are to the contents of sperm and seminal fluid (which includes chromatin, RNA and metabolites).

The effects of undernutrition can also be inherited, including "increased expression of genes involved in fat and cholesterol biosynthesis" and genes involved in DNA replication.  Alterations in lipid metabolism and cell proliferation have been demonstrated in offspring of mice who've been deprived of food.  At least one study demonstrated epigenetic changes in the sperm of parental mice on restricted diets.

The effects of famine during World War II on a large family cohort in the Netherlands have been examined, and metabolic consequences shown to last for at least two generations.  A family cohort from 19th century Sweden shows much the same, as well as that food intake during adolescence of grandparents correlated with survival of grandchildren, suggesting that there may be a critical period for production of healthy gametes.

Further examples include the effects of heat shock in Drosophila, TEI of small RNAs from viruses in C. elegans with gene silencing consequences, TEI of behavior patterns such as depression, via exposure to psychological stress in utero, and olfactory imprinting behavior in C. elegans.

Transgenerational epigenetic inheritance can be via DNA methylation, histone modifications, noncoding RNAs, short RNAs and other aspects of RNA function.  Lim and Brunet point out that the mechanism or mechanisms behind these modes of inheritance are not yet well understood.  They list questions that remain to be answered, including how the signals are eventually erased, how the changes are maintained, and whether the strength of the environmental stimulus affects the number of generations the effect is maintained.

TEI and evolution
Finally, they suggest that because transgenerational epigenetic inheritance is known to occur in many organisms, it must have been selected.  They postulate that perhaps it was advantageous to pass on information about the environment -- but environments change so quickly that it seems more likely to us that the ability to adapt would have been what was selected for, rather than the ability to stay the same, and TEI is certainly one adaptive ability.

Or, they suggest, TEI might increase the evolvability or rate of evolution of an organism.  Perhaps it affects the accessibility of chromatin to DNA repair enzymes, thus making certain loci more and less mutable.

An active mechanism that can obscure
There are active genetically encoded mechanisms for applying and removing epigenetic changes such as methylation.  These can be very specific and differ between males and females.  Much of the genome is 'set' differently in the generation of sperm or egg cells.  But once modified, unless it is re-set each generation, the effect can appear to be DNA-encoded in epidemiological studies but non 'Mendelian': family members share the trait, but not because of specific DNA variants, since some may have inherited modified, and others unmodified copies of the same variant. This is one major reason why epigenetic factors can obscure studies, like genomewide scans, to find genes that contribute to important traits like disease.

Not non-Mendelian!
Note that the phrase 'non-Mendelian inheritance' is thoroughly wrong, but probably ineradicable from the current jargon.  Genes are inherited in a Mendelian way.  Each of us carries two instances of human genomes, and we more or less randomly transmit a copy of one of them to each sperm or egg cell.  This random transmission is what is Mendelian:  Mendel didn't know about genes, but used traits to signal the inheritance of these 'elements' or 'factors'.

But the traits are not--that is not--inherited!  Only the genes are inherited.  It is only if traits are tightly tied to specific genetic variants that the appeance of the trait is highly correlated with the genetic variant that was inherited that the trait seems to be 'Mendelian'.  Therefore epigenetic patterns of occurrence in families that are not 'Mendelian' refer to alleles that were inherited but that, because of epigenetic modification, their effect is not manifest.  The inheritance itself is in these instances not affected.

It is very sloppy to speak of Mendelian inheritance in regard to any phenotype, and we can lead ourselves into trouble if we aren't careful.  There is, in fact, a phenomenon of non-Mendelian inheritance (called segregation distortion) in which the two alleles a person carries are not transmitted with equal probability.

We also noted more verbal sloppiness in the literature, by terms such as 'non-genetic inheritance' and 'wild type'.  So, we quoted this earlier: "an insertion of LacZ into the Kit gene gave rise to genetically wild type offspring."  If the mouse is genetically altered, how can it have the wild type genotype?  What was meant, we think, was that the genetically modified animal had the phenotype of the unmodified animals.  But it inherited the modified not the wild type genome.

But we've probably said enough already about how self- as well as other-misleading such loaded terminology can be.

Epigenetics -- what else don't we know?

Epigenetics -- a hot topic
Epigenetics* is a buzzword these days, in genetics, yes, but it is appealing enough that it is trending in general usage as well. For better or worse.  While the idea that factors other than changes in DNA can affect development was hypothesized almost a century ago, and called epigenesis by CH Waddington, epigenetics is now more often considered to be changes in the genome that don't involve changes in DNA sequence. Generally this involves chemical modification of nucleotides that causes a gene to be silenced, and many instances have been documented, pathological and not.

Epigenetic mechanisms. Source: Wikimedia Commons

But, much as, say, political scientists invoke genetics to explain why we vote the way we do, or economists to explain our economic behavior, people are invoking epigenetics to explain things like the 'culture of poverty' (due to epigenetic changes because of maternal malnutrition during pregnancy), or psychiatric diseases that seem to be genetic but for which genes have not been identified, or even homosexuality (due to epigenetic signaling that is usually beneficial to the parent, but can be transferred to a fetus of the opposite sex, affecting subsequent sexual behavior). 

Epigenetics is appealing because it's not strict genetic reductionism, and finding genes 'for' traits, particularly behaviors, has proven to be frustratingly difficult (well, at least when done properly), and yet epigenetics explains traits in terms of tractable biological markers, such as methylation of mRNA or histone modification. Whether epigenetics is always correctly applied is another matter.

Epigenetics documented
But the actual, documentable science of epigenetics marches on.  A paper in the Dec 14 issue of Science ("Epigenetic Regulation by Long Noncoding RNAs," Lee) adds a new twist to the epigenetic story, addressing long noncoding RNAs and asks about their function.  Thousands of lncRNAs have been found in the last five years, and their function is just beginning to be documented.

The ENCODE project has shown that 70-90% of the mammalian genome is transcribed, yielding a very large 'transcriptome' of long (defined as greater than 100 nucleotides) noncoding RNA (lncRNA), and that this 'pervasive transcription' actually happens seems to be emerging as the consensus view (though, see this post on differences of opinion on this).

ENCODE, again, has shown that there are about 10 "isoforms overlapping any previously annotated genes, thereby challenging the traditional definition of a gene."  That is, whereas the classic view of messenger RNA is that it is transcribed from coding regions within protein-coding genes -- which comprise only about 1% of the genome -- now it seems that most of the non-coding genome is also transcribed, and that the transcripts start and stop in unexpected places, given accepted wisdom.  These transcripts are "often poorly conserved, unstable, and/or present in few copies" and whether they always have a function is unknown, though Lee suggests that much of this RNA is involved in epigenetic regulation of gene expression. 

lncRNAs were first seen to play a role in genomic imprinting and inactivation of the X-chromosome, with the X-inactive-specific transcript (XIST/Xist) being among the first lncRNAs to be identified in mammals.  Males have 1 X chromosome and females have 2, which means that genes on the X chromosome could be expressed twice as much in females than in males.  This doesn't happen, however, and lncRNA is part of the reason for this.

Nowhere is the abundance of lncRNA more evident than the X-inactivation center (Xic). To balance X-chromosome gene expression between males and females, the Xic on the mammalian X chromosome controls the initiation steps of XCI through a series of RNA-based switches. Today, the Xic serves as a model for understanding epigenetic regulation by lncRNA.

Xist codes for a long piece of RNA that is never translated; the RNA coats the inactive X-chromosome, which results in the silencing of its genes, though it is complicated -- Xist itself is regulated by two other lncRNAs, with downstream effects.  

Lee writes that

"[A]lthough lncRNAs now dominate the Xic, this region was once coding.  Evolution of random XCI 150 million years ago in eutherian mammals coincided with a shift from coding to noncoding space, suggesting that lncRNAs offer distinct advantages over proteins for some forms of epigenetic regulation." 

Why lncRNAs rather than the usual, ubiquitous regulatory elements that turn genes on?  LncRNAs are so large that they seem to address only a unique location in the genome.  Transcription factors, on the other hand, are short and bind with short DNA sequences that often are found in thousands of places in the genome.

Lee presents several classes of lncRNA, those involved in genomic imprinting, which is when only one of the two inherited copies of a gene is expressed; lncRNAs that are involved in non-allelically regulated loci; lncRNAs can activate gene expression as well as repress it; lncRNAs may be found as parts of pseudogenes, from whence they silence or activate the still functional form of the gene.  Lee concludes that much is yet to be discovered about these molecules.  "Indeed, the Wild West is a rich landscape waiting to unfold."

And it is unfolding at a fast rate.  E.g., two papers in the last week's issue of Science document epigenetic involvement in embryonic stem cell pluripotency (here), and epigenetic influences on gene expression as a response to metabolic state (here).  Epigenetics is being over- and too often improperly applied, by people who'd like a simple yet rigorous, scientific explanation for a complex trait, but, like genetics itself, the field is developing to the point where it is possible to begin to sort fact from fiction.

What we don't know
But, just as single genes aren't the explanation for every trait or illness, epigenetics isn't going to be the explanation either.  Naturally enough, we always try to make complete stories from incomplete data -- before we knew about short RNAs or DNA methylation, we thought we understood gene expression.  But, every age has its 'normal science,' as Thomas Kuhn called it in "The Structure of Scientific Revolutions."  It's only when enough challenges arise to that normal science that understanding can broaden and build those challenges into a new and different picture.  The picture may change to encompass new data, but the sense that we actually understand does not; we always think we do.  We never know how much we don't know. 

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*Nice introductions to epigenetics:
Neuroscientist Kevin Mitchell nicely sums up the history of epigenetics, and its current trendiness -- and misapplication -- in a two-part blog series starting here.

Here's a quick YouTube discussion.

Sperm, Meth, Rock'n'Roll

If you're interested in epigenetics at all--which  you should be if you're interested in how evolution works and if you're following any of this Lamarckian Renaissance--then you'll be interested in at least trying to read this paper: Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates by Molaro et al.

This is the "graphical abstract" and as you can see, all their findings are as crystal clear as their importance.

(That was sarcasm. Although, if you stare at this long enough it does start to make sense through the alien acronyms and jargon.)

The authors report, based on sperm studies, that methylation has evolved separately in chimps and humans and has diverged (as we'd expect) and they also explain how methylation changes can drive changes to the DNA sequence.

If you're interested in reading more into this topic, Eva Jablonka is just one scientist I know of who ascribes such evolutionary importance to methylation and maybe there are others (that I am unaware of because this is outside my area).  And she had a nice review in QRB about inheriting epigenetic changes.

Methylation as a force of evolution? Rock'n'roll!