Etikettarkiv: epigenetics

Griffin & Nesseth ”The science of Orphan Black: the official companion”

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I didn’t know that science fiction series Orphan Black actually had a real Cosima: Cosima Herter, science consultant. After reading this interview and finishing season 5, I realised that there is also a new book I needed to read: The science of Orphan Black: The official companion by PhD candidate in development, stem cells and regenerative medicine Casey Griffin and science communicator Nina Nesseth with a foreword by Cosima Hertner.

(Warning: This post contains serious spoilers for Orphan Black, and a conceptual spoiler for GATTACA.)

One thing about science fiction struck me when I was watching the last episodes of Orphan Black: Sometimes it makes a lot more sense if we don’t believe everything the fictional scientists tell us. Like real scientists, they may be wrong, or they may be exaggerating. The genetically segregated future of GATTACA becomes no less chilling when you realise that the silly high predictive accuracies claimed are likely just propaganda from a oppressive society. And as you realise that the dying P.T. Westmorland is an imposter, you can break your suspension of disbelief about LIN28A as a fountain of youth gene … Of course, genetics is a little more complicated than that, and he is just another rich dude who wants science to make him live forever.

However, it wouldn’t be Orphan Black if there weren’t a basis in reality: there are several single gene mutations in model animals (e.g. Kenyon & al 1993) that can make them live a lot longer than normal, and LIN28A is involved in ageing (reviewed by Jun-Hao & al 2016). It’s not out of the question that an engineered single gene disruption that substantially increases longevity in humans could be possible. Not practical, and not necessarily without unpleasant side effects, but not out of the question.

Orphan Black was part slightly scary adventure, part festival of ideas about science and society, part character-driven web of relationships, and part, sadly, bricolage of clichés. I found when watching season five that I’d forgotten most of the plots of seasons two through four, and I will probably never make the effort to sit through them again. The first and last seasons make up for it, though.

The series seems to have been set on squeezing as many different biological concepts as possible in there, so the book has to try to do the same. It has not just clones and transgenes, but also gene therapy, stem cells, prion disease, telomeres, dopamine, ancient DNA, stem cells in cosmetics and so on. Two chapters try valiantly to make sense of the clone disease and the cure. It shows that the authors have encyclopedic knowledge of life science, with a special interest in development and stem cells.

But I think they slightly oversell how accurate the show is. Like when Cosima tells Scott to ”run a PCR on these samples, see if there are any genetic markers” and ”can you sequence for cytochrome c?”, and Scott replies ”the barcode gene? that’s the one we use for species differentiation” … That’s what screen science is like. The right words, but not always in the right order.

Cosima and Scott sciencing at university, before everything went pear-shaped. One of the good thing about Orphan Black was the scientist characters. There was a ton of them! The good ones, geniuses with sparse resources and self experimentation, the evil ones, well funded and deeply unethical, and Delphine. This scene is an exception in that it plays the cringe-inducing nerd angle. Cosima and Scott grew after than this.

There are some scientific oddities. They must be impossible to avoid. For example, the section on epigenetics treats it as a completely new field, sort of missing the history of the subfield. DNA methylation research was going on already in the 1970s (Gitschier 2009). Genomic imprinting, arguably the only solid example of transgenerational epigenetic effects in humans, and X inactivation were both being discovered during 70s and 80s (reviewed by Ferguson-Smith 2011). The book also makes a hash of genome sequencing, which is a shame but understandable. It would have taken a lot of effort to disentangle how sequencing worked when the fictional clone experiment started and how it got to how it works in season five, when Cosima runs Nanopore sequencing.

The idea of human cloning is evocative. Orphan Black flipped it on its head by making the main clone characters strikingly different. It also cleverly acknowledged that human cloning is a somewhat dated 20th century idea, and that the cutting edge of life science has moved on. But I wish the book had been harder on the premise of the clone experiment:

By cloning the human genome and fostering a set of experimental subjects from birth, the scientists behind the project would gain many insights into the inner workings of the human body, from the relay of genetic code into observable traits (called phenotypes), to the viability of manipulated DNA as a potential therapeutic tool, to the effects of environmental factors on genetics. It’s a scientifically beautiful setup to learn myriad things about ourselves as humans, and the doctors at Dyad were quick to jump at that opportunity. (Chapter 1)

This is the very problem. Of course, sometimes ethically atrocious fictional science would, in principle, generate useful knowledge. But when when fictional science is near useless, let’s not pretend that it would produce a lot of valuable knowledge. When it comes to genetics and complex traits like human health, small sample studies of this kind (even if it was using clones) would be utterly useless. Worse than useless, they would likely be biased and misleading.

Researchers still float the idea of a ”baseline”, though, but in the form of a cell line, where it makes more sense. See the the (Human) Genome Project-write (Boeke & al 2016), suggesting the construction of an ideal baseline cell line for understanding human genome function:

Additional pilot projects being considered include … developing a homozygous reference genome bearing the most common pan-human allele (or allele ancestral to a given human population) at each position to develop cells powered by ”baseline” human genomes. Comparison with this baseline will aid in dissecting complex phenotypes, such as disease susceptibility.

In the end, the most important part of science in science fiction isn’t to be a factually correct, nor to be a coherent prediction about the future. If Orphan Black has raised interest in science, and I’m sure it has, that is great. And if it has stimulated discussions about the relationship between biological science, culture and ethics, that is even better.

The timeline of when relevant scientific discoveries happened in the real world and in Orphan Black is great. The book has a partial bibliography. The ”Clone Club Q&A” boxes range from silly fun to great open questions.

Orphan Black was probably the best genetics TV show around, and this book is a wonderful companion piece.

Plaque at the Roslin Institute to the sheep that haunts Orphan Black. ”Baa.”

Literature

Boeke, JD et al (2016) The genome project-write. Science.

Ferguson-Smith, AC (2011) Genomic imprinting: the emergence of an epigenetic paradigm. Nature reviews Genetics.

Gitschier, J. (2009). On the track of DNA methylation: An interview with Adrian Bird. PLOS Genetics.

Jun-Hao, E. T., Gupta, R. R., & Shyh-Chang, N. (2016). Lin28 and let-7 in the Metabolic Physiology of Aging. Trends in Endocrinology & Metabolism.

Kenyon, C., Chang, J., Gensch, E., Rudner, A., & Tabtiang, R. (1993). A C. elegans mutant that lives twice as long as wild type. Nature, 366(6454), 461-464.

Interactions between genetic and epigenetic

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More speculation about epigenetics and ways that epigenetic mechanisms of gene regulation could contribute to differences between individuals. Many cases, both in plants and animals, have to do with transposable elements, which makes a lot of sense since DNA methylation is involved in silencing the expression of transposable elements. Think about genetical genomics studies such as Gibbs & al (2010), where gene expression and DNA methylation is mapped to genomic regions. First, when expression QTL and methylation QTL coincide, it might be a good idea to start looking for transposable element insertions. Finding them are not as easy as finding SNPs, but hopefully, there will be SNPs tagging the actual variant and DNA methylation will spread outside of the inserted element to CpGs that are being typed. The element itself could of course work as a promoter, but it could also spread methylation into regulatory sequences of the gene, suppressing expression, or increase expression by changing the effect of an insulator.

Second, apparently the DNA methylation of transposable elements can sometimes be variable. This is the case with axin fused, Cabp-IAP and the agouti epialleles (Druker & al 2004; Vasicek & al 1997; Morgan & al 1999); among mice that carry the insertion there is DNA methylation variation causing phenotypic differences. This means that in populations where the insertion segregates, there should be a DNA methylation by gene interaction in the effect on the phenotype. I think that is fun, and I’d like to see someone find that in a mapping study. It might make things more difficult, though. The methylation–gene expression association might be hard to detect because it only exists in one of the alleles.

Third, maybe that is actually how a DNA methylation variant might escape reprogramming. Since some transposable elements are among the sequences that are not demethylated after fertilisation, and if that effect also applies to the newly inserted copy of the transposable element, our hypothetical regulatory methylation difference might be preserved through meiosis that way.

Literature

Gibbs, J. R., van der Brug, M. P., Hernandez, D. G., Traynor, B. J., Nalls, M. A., Lai, S. L., … & Singleton, A. B. (2010). Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS genetics, 6(5), e1000952.

Morgan, H. D., Sutherland, H. G., Martin, D. I., & Whitelaw, E. (1999). Epigenetic inheritance at the agouti locus in the mouse. Nature genetics, 23(3), 314-318.

Vasicek, T. J., Zeng, L. I., Guan, X. J., Zhang, T., Costantini, F., & Tilghman, S. M. (1997). Two dominant mutations in the mouse fused gene are the result of transposon insertions. Genetics, 147(2), 777-786.

Druker, R., Bruxner, T. J., Lehrbach, N. J., & Whitelaw, E. (2004). Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic acids research, 32(19), 5800-5808.

Morning coffe: ”epigenetics” is also ambiguous

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IMG_20140228_175448

I believe there is an analogy between the dual meaning of the word ”gene” and two senses of epigenetics, that this distinction is easy to get wrong and that it contributes to the confusion about the meaning of epigenetics. Gene can mean a sequence that has a name and a function, or it can mean a genetic variant. I sometimes, half-jokingly, call this genetics(1) and genetics(2). The order is wrong from a historical perspective, since the study of heritable variation predates the discovery of molecular genes. The first deals with the function of sequences and their products. The second deals with differences between individuals carrying different variants.

The same can be said about epigenetics. On one hand there is epigenetics(1), aiming to understand the normal function of certain molecular features, i.e. gene regulatory states that can be passed on through cell division. On the other hand, epigenetics(2) aims to explain individual variation between individuals that differ not in their DNA sequence but in other types of heritable states. And the recurring reader knows that I think that, since a lot of genetics(2) makes no assumptions about the molecular nature of the variation it studies, it will mostly work even if some of these states turn out to be epigenetic. In that sense, epigenetics(2) is a part of genetics.

Paper: ”Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens”

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Since I love author blog posts about papers, I thought I’d write a little about papers I’ve contributed too. So far, they’re not that many, but maybe it can be a habit.

”Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens” was published in BMC Genomics in 2012. The title says it very well: the paper looks at differential expression and DNA methylation of a subset of genes in the hypothalamus of Red Junglefowl and domestic White Leghorn chickens. My contribution was during my MSc project in the group. Previously (Lindqvist & al 2007; Nätt & al 2009) Daniel Nätt, Pelle Jensen and others found a transgenerational effect of unpredictable light stress on domestic chickens. After that, and being interested in chicken domestication, a DNA methylation comparison of wild and domestic seems like a natural thing to do. And it turns out Red Junglefowl and White Leghorns differ in expression of a bunch of genes and in methylation of certain promoters (where promoter is operationally defined as a region around the start of the gene model). And when looking at two generations, the contrasts are correlated between parent and offspring. There is some heritable basis of the differences in gene expression and  DNA methylation.

In Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation.

What I did was methylation sensitive high resolution melting. HRM is a typing method based on real time PCR. After PCR you often make a melting curve by ramping up the temperature, denaturing the PCR product. The melting characteristics depend on the sequence, so you can use melting to check that you get the expected PCR product, and it turns out that the difference can be big enough to type SNPs. And if you can type SNPs, you can analyse DNA methylation. So we treat the DNA with bisulfite, which deaminates cytosines to uracil unless they are protected by methylation, and get a converted sequence where an unmethylated C is like a C>T SNP. We set up standard curves with a mixture of whole-genome amplified and in vitro methylated DNA and measured the degree of methylation.

That is averaging over the population of DNA molecules in the sample; I’ve been wondering how HRM performs when the CpGs in the amplicon have heterogenous methylation differences. We’ve used HRM for genotyping as well, and it works, but we’ve switched to pyrosequencing, which gives cleaner results and where the assay design is much easier to get right the first time. I don’t know whether the same applies for methylation analysis with pyro.

heritability_methylation_fig4b

My favourite part of the paper is figure 4b (licence: cc:by 2.0) which shows methylation analysis in the advanced intercross of Red Junglefowl and White Leghorns, which immediately leads to, as mentioned in the paper, the thought of DNA methylation QTL mapping.

Literature

Nätt, D., Rubin, C. J., Wright, D., Johnsson, M., Beltéky, J., Andersson, L., & Jensen, P. (2012). Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. BMC genomics, 13(1), 59.

Lindqvist C, Janczak AM, Nätt D, Baranowska I, Lindqvist N, et al. (2007) Transmission of Stress-Induced Learning Impairment and Associated Brain Gene Expression from Parents to Offspring in Chickens. PLoS ONE 2(4): e364. doi:10.1371/journal.pone.0000364

Nätt D, Lindqvist N, Stranneheim H, Lundeberg J, Torjesen PA, et al. (2009) Inheritance of Acquired Behaviour Adaptations and Brain Gene Expression in Chickens. PLoS ONE 4(7): e6405. doi:10.1371/journal.pone.0006405

Also: the spectre of epigenetic inheritance

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What is is that is so scandalous about epigenetic inheritance? Not much, in my opinion. Some of the points on the spectrum clearly happen in the wild: stable and fluctuating epigenetic inheritance in plants, parental effects in animals and genomic imprinting in both. Widespread epigenetic inheritance in animals would change a lot of things, of course, but even if epigenetic inheritance turns out to be really important and common, genetics and evolution as we know them will not break. The tools to study and understand them are there.

Looking back at the post from yesterday, there are different flavours of epigenetic inheritance. At the most heritable end of the spectrum, epigenetic variants behave pretty much like genetic variants. Because quantitative genetics is agnostic to the molecular nature of the variants, as long as they behave like an inheritance system, most high-level genetic analysis will work the same. It’s just that on the molecular level, one would have to look to epigenetic marks, not to sequence changes, for the causal variant. Even if a substantial proportion of the genetic variance is caused by epigenetic variants rather than DNA sequence variants, this would not be a revolution that changes genetics or evolution into something incommensurable with previous thought.

The most revolutionary potential lies somewhere in the middle of the scale, in parental effects with really high fidelity of transmission that are potentially responsive to the environment, but in principle these things can still be dealt with by the same theoretical tools. Most people just didn’t think they were that important. How about soft inheritance? It seems dramatic, but all examples deal with specific programmed mechanisms: soft inheritance of the sensitivity to a particular odour or of the DNA methylation and expression state of a particular locus. No-one has yet suggested a generalised Lamarckian mechanism; that is still out of the question. DNA mutations are still unable to pass from somatic cells to gametes. Whatever tricks transgenerational mechanisms use to skip over the soma–germline distinction, they must be pretty exceptional. Discoveries of widespread soft inheritance in nature would be surprising, a cause for rethinking certain things and great fun. But conceptually, it is parental effects writ large. We can understand that. We have the technology.

Morning coffee: the spectrum of epigenetic inheritance

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IMG_20140228_175433

Let us think aloud about the different possible meanings of epigenetic inheritance. I don’t want to contribute to unnecessary proliferation of terminology — people have already coined molar/molecular epigenetics (Crews 2009), intergenerational/transgenerational effects (Heard & Martienssen 2014), and probably several more dichotomies. But I thought it could be instructive to try to think about epigenetic inheritance in terms of the contribution it could make to variance components of a quantitative genetic model. After all, quantitative genetics is mostly agnostic about the molecular nature of the heritable variation.

At one end of the spectrum we find molecular epigenetic marks such as DNA methylation, as they feature in the normal development of the organism. Regardless of how faithfully they are transmitted through mitosis, or even if they pass through meiosis, they only contribute to individual variation if they are perturbed in different ways between individuals. If they do vary between individuals, though, in a fashion that is not passed on to the offspring, they will end up in the environmental variance component.

What about transmissible variation? There are multiple non-genetic ways for information to be passed a single generation: maternal or paternal effects need not be epigenetic in the molecular sense. They could be, like genomic imprinting, but they could also be caused by some biomolecule in the sperm, something that passes the blood–placenta barrier or something deposited by the mother into the egg. Transgenerational effects of this kind make related individuals more similar, they will affect the genetic variance component unless they are controlled. And in the best possible world of experimental design, parental effects can be controlled and modelled, and we can in principle separate out the maternal, paternal and genetic component. Think of effects like in Weaver & al (2004) that are perpetuated by maternal behaviour. If the behavioural transmission is strong enough they might form a pretty stable heritable effect that would appear in the genetic variance component if it’s not broken up by cross-fostering.

However, if the variation behaves like germ-line variation it will be irreversible by cross-fostering, inseparable from the genetic variance component, and it will have the potential to form a genuine parallel inheritance system. The question is: how stable will it be? Animals seem to be very good at resetting the epigenetic germline each generation. The most provocative suggestion is probably some type of variation that is both faithfully transmitted and sometimes responsive to the environment. Responsiveness means less fidelity of transmission, though, and it seems (Slatkin 2009) like epigenetic variants need to be stable for many generations to make any lasting impact on heritability. Then, at the heritable end of the spectrum, we find epigenetic variants that arise from some type of random mutation event and are transmitted faithfully through the germline. If they exist, they will behave just like any genetic variants and even have a genomic locus.

Epigenetics: what happened with this?

Publicerat i molekylärgenetik av

In 2012, Yan Li & Chris O’Neill published a paper about DNA methylation in the early mouse embryo, claiming that the first wave of demethylation following fertilisation in the mouse embryo doesn’t happen.

This picture, figure 1 from Seisenberger & al (2013; license: cc:by 3.0), shows what it is about. The curves represent DNA methylation level, and first time the curves drop represents the demethylation in question:

dna_demethylation_fig1

Li & O’Neill used a variation of immunostaining for methylated cytosine. Figures 8 and 3 summarise the results: eight shows embryos stained for methylated cytosine with two different preparation methods. The main claim of the paper is that the added trypsin treatment in the preparation helps unmask DNA methylation. So maybe the cytosine methylations are not removed, but temporarily hidden by something else. Figure 3 shows a Western blot for methyl-binding domain protein 1. The claim here is that if MBD1 is expressed, DNA methylation is also there. The obvious alternative hypothesis is that their variation on the protocol creates some kind of artefact and that MBD1 expression doesn’t matter.

journal.pone.0030687.g008

Figure 8, Li & O’Neill (cc:by 3.0).

The paper has been cited mostly by review papers, and I haven’t seen any further news on the subject. Does anyone know if anything more has happened?

Literature

Li Y, O’Neill C (2012) Persistence of Cytosine Methylation of DNA following Fertilisation in the Mouse. PLoS ONE 7(1) e30687. doi:10.1371/journal.pone.0030687

Seisenberger, S., Peat, J. R., Hore, T. A., Santos, F., Dean, W., & Reik, W. (2013). Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philosophical Transactions of the Royal Society B: Biological Sciences 368(1609), 20110330.

Morning coffee: epigenetic inheritance of odour sensitivity

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kaffe_tryffel

A while ago I wrote a bit about the recent paper on epigenetic inheritance of acetophenone sensitivity and odorant receptor expression. I spent most of the post talking about potential problems, but actually I’m not that negative. There is quite a literature building up about these transgenerational effects, that is quite inspiring if a little overhyped. I for one do not think epigenetic inheritance is particularly outrageous or disrupting to genetics and evolution as we know it. Take this paper: even if it means inheritance of an acquired trait, it is probably not very stable over the generations, and it is nothing like a general Lamarckian transmission mechanism that can work for any trait. It is probably very specific for odourant receptors. It might allow for genetic assimilation of fear of odours though, which would be cool, but probably not at all easy to demonstrate. But no-one knows how it works, if it does — there are even multiple unknown steps. How does fear conditioning translate to DNA methylation differences sperm that translates to olfactory receptor expression in the brain of the offspring?

A while after the transgenerational effects paper I saw this one in PNAS: Rare event of histone demethylation can initiate singular gene expression of olfactory receptors (Tan, Song & Xie 2013). I had no idea olfactory receptor expression was that fascinating! (As is often the case when you scratch the surface of another problem in biology, there turns out to be interesting stuff there …) Mice have lots and lots of odorant receptor genes, but each olfactory neuron only expresses one of them. Apparently the expression is regulated by histone 3 lycine 9 methylation. The genes start out methylated and suppressed, but once one of them is expressed it will keep all other down by downregulating a histone demethylase. This is a modeling paper that shows that if random demethylation happens slowly enough and the feedback to shut down further demethylation is fast enough, these steps are sufficient to explain the specificity of expression. There are some connections between histone methylation and DNA methylation: it seems that DNA methylation binds proteins that bring histone methylases to the gene (review Cedar & Bergman 2009). Dias & Ressler saw hypomethylation near the olfactory receptor gene in question, Olfr151. Maybe that difference, if it survives through to the developing brain of the offspring, can make demethylation of the locus more likely and give Olfr151 a head start in the race to become the first expressed receptor gene.

Literature

Brian G Dias & Kerry J Ressler (2013) Parental olfactory experience influences behavior and neural structure in subsequent generations Nature neuroscience doi:10.1038/nn.3594

Longzhi Tan, Chenghang Zong, X. Sunney Xie (2013) Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. PNAS 10.1073/pnas.1321511111

Howard Cedar, Yehudit Bergman (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nature reviews genetics doi:10.1038/nrg2540

Journal club of one: ”Parental olfactory experience influences behavior and neural structure in subsequent generations”

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Okay, neither chickens nor genetics, really, but a little epigenetic inheritance. Dias & Ressler in Nature neuroscience:

When an odor (acetophenone) that activates a known odorant receptor (Olfr151) was used to condition F0 mice, the behavioral sensitivity of the F1 and F2 generations to acetophenone was complemented by an enhanced neuroanatomical representation of the Olfr151 pathway.

Meaning that the offspring of conditioned mice score higher in an odour potentiated startle test (more about that below), avoid the odour at a lower concentration in an aversion test and have more neurons expressing that odorant receptor in their olfactory epithelium and bulb, counted by betagalactosidase staining in transgenic mice expressing M71, the product of Olfr151, coupled to LacZ.

Furthermore,

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.

That is, they detect a difference in methylation in one CpG dinucleotide in the 3′ region of the gene.

Comments:

First, I love how the journal does exactly the thing I like to see with figures: below each figure is a link that leads to a data file with the underlying data!

Olfactory behaviour is not my thing, so the tests are new to me, but I’m a bit puzzled by the way they calculate the results from the odour potentiated startle tests. The point is to test whether the presence of the odour make the mice react stronger to a noise. After buzzing the sound 15 times without odour, they perform ten trials with odour plus sound and ten trials with sound only. But in calculating the score, they use only the difference between the first trial with odour and the last trial with sound only divided by how much the mouse reacted to the last of the first 15 sounds. Maybe this is standard, but why throw away the trials in between?

It is not only the olfactory potentiated startle and the sensitivity test, but the staining results. Again, this is not my area, but the results all seem to point to increased sensitivity in the offspring of the treated animals. They react stronger in the startle test, react at lower concentration in the avoidance test and they (in this case, the transgenic mice) have more neurons expressing M71. The cross fostering and the fact that the males were treated but not the females points to genuine inheritance. So, how does the treatment get into the germline? It has to cross that boundary and enter the sperm somehow. Unless there is some mysterious way for information from the central nervous system to travel to the testis, acetophenone must affect the spermatogenesis as well as the olfactory neurons.

All this is very hypothetical, so a little skepticism is not surprising. Gonzalo Otazu wrote in a comment on the Nature news webpage:

The statistical tests in the paper, both for the behavioral measurements as well as for the size of the M71 glomeruli , use as n, number of samples, the number of F1 and F2 individuals. This would be fine if the individuals were actually independent samples. However, they arise from a presumably small number of FO males. The numbers of FO males are not given in the paper. This is a major concern given that there is a lot of variability in the levels of expression of olfactory receptors in these mice that might be inheritable …

I think this is a good point but it will not be solved, as the comment later suggests, by adjusting the degrees of freedom of the test. From the F1 generation and on, genetic differences between the treatment groups, if they do exist, will amplify into a bias issue. That is, it is a systematic difference that might be bigger or smaller than the treatment effect and go in the same or opposite direction — we don’t know. However, the bias should not be there all the time, and not in the same direction, so it strengthens the authors’ case that they’ve done the treatment at least twice (with C57B/6J and with M17-LacZ mice, if not more times).

Maybe my preference for genetics is showing, but I feel the big unadressed alternative hypothesis in most transgenerational effects experiments is cryptic heritability. If you divide individuals into two groups, treat one of them and look for treatment effects in the offspring, you need to be sure that there are not genetc differences between the founders of the two groups. In the subsequent generations, genetic and non-genetic inheritance will be counfounded by design.

Again, randomisation and replication will help, but to be really sure, maybe one can use founders of known relatedness to create a mixed population — say take founders from full-sibships and split them equally between treatment groups, allowing segregation to randomise the genotypes of the next generation. It doesn’t say in the methods — the authors might even have done something like this. One could even use a genetic mixed model that includes relatedness as to estimate treatment effects over in the prescence of a genetic effect. I have a suspicion this experiment would require a much larger sample size, which means more time, work and animals — but I also believe that many would find confounding genetic variation more plausible than transgenerational epigenetic effects of unknown mechanism.

Literature

Brian G Dias & Kerry J Ressler (2013) Parental olfactory experience influences behavior and neural structure in subsequent generations Nature neuroscience doi:10.1038/nn.3594