Epigenetics has the potential to help us understand key differences in how divergent species control gene expression. Recent work published by Brown et al. in GENETICS delves into the epigenetic mechanisms of Pristionchus pacificus, providing significant insights into the evolutionary dynamics of epigenetic regulation.

Many developmental traits are sensitive to environmental factors, and the differences in how close evolutionary relatives respond to their environments can help demystify development. The nematode Pristionchus pacificus has been established as a comparative system to the well-studied Caenorhabditis elegans, but a thorough exploration of the conservation of epigenetic pathways between the two species has not been conducted—until now.

P. pacificus is known for its remarkable morphological plasticity, especially in its feeding structures. It appears to be a perfect model to study the epigenetic regulation of these adaptive changes; however, its relative newness as a model system means its epigenetic “toolkit” isn’t well-defined. To manipulate the proteins and modifications involved in the epigenetics of plasticity, they first must be identified.

To address this gap, Brown et al. began with an in-silico approach to identify potential epigenetic genes, followed by biochemical analysis to identify histone posttranslational modifications. By orthology, they then predicted which proteins might be responsible for adding or removing these marks. Their work provides a comprehensive “epigenetic toolkit” for P. pacificus and reveals significant differences in epigenetic machinery between P. pacificus and C. elegans, highlighting the evolutionary flexibility of epigenetic regulation and underscoring the importance of understanding species-specific epigenetic landscapes.

One of the authors’ most striking findings is that P. pacificus lacks the repressive PRC2 complex, which is usually crucial for histone methylation. Surprisingly, the enzymatic product H3K27me3 is still present, suggesting an unknown methyltransferase is responsible for this modification. The revelation that P. pacificus can maintain a critical histone modification while missing its canonical enzyme opens the door to myriad new paths of investigation.

This work serves as a foundational resource for future studies on developmental plasticity and epigenetic regulation in P. pacificus. It also provides a comparative framework for studying similar mechanisms in other species, offering new avenues for research in evolutionary biology and epigenetics.

New Faculty Profiles allow GSA members who are establishing their first labs to introduce themselves to our wider community. If you’d like to submit your profile, please complete this form.

David Garcia

Assistant Professor
Institute of Molecular Biology
University of Oregon
Lab website

Briefly describe the ongoing and expected research projects as your lab gets up and running.

We study prion proteins as a model for understanding epigenetic mechanisms that are important for RNA regulation. I studied the molecular basis for microRNA function during my PhD, and for my postdoc I wanted to study protein-based mechanisms that regulate RNA biology. I found a perfect example in prions because they are protein-based units of inheritance that change protein conformation and function. By focusing on enzymes that chemically modify RNA and also have prion behavior, we are working toward the goal of understanding how these chemical modifications can be regulated to promote adaptation to stress and new environments. Working in yeast empowers our discovery and profiling of these epigenetic states, and the RNA biology that we study is extremely well-conserved. In the future, we will search for conserved examples of these phenomena in metazoans, where it would be exciting to see if such regulation impacts development and disease.

If your position involves teaching, which subjects or courses are you expecting to teach?

I just began my position in December 2018 and have a break from teaching duties for the first year or so, but teaching will be an important part of my position in the near future. I think I would love to teach genetics and molecular biology. I am also interested in developing a course on inheritance, from postulated mechanisms from over a century ago up to CRISPR babies. I’ve really enjoyed reading Carl Zimmer’s She Has Her Mother’s Laugh, and I would like to use some of this material as a basis for lessons. Our understanding of inheritance has evolved over hundreds of years and still is evolving. I think it could be an excellent learning experience to review that history. Sadly, this subject is also rife with examples of tragic failures in human rationalization, which I think is also worth educating students about—how the misuse of scientific concepts or misinterpretation of data can lead to terrible, long-lasting social problems.

How has being a member of GSA helped you advance in your career? Why do you think societies like GSA are important? 

I greatly benefitted from attending the GSA Yeast meeting last year. I met many generous scientists who offered helpful advice for getting my lab started. During the coffee break after a session in which I presented a short talk, Fred Winston, who was in attendance to give the Lee Hartwell Lecture, told me about a paper from his lab from 10 years prior that had some interesting data on a protein that I also study and had discussed in my talk. I think he might have even pulled out his iPad and showed me some figures. The GSA yeast community is warm, supportive, and innovative in their science. The Genes to Genomes blog is also a great resource for me and my lab to get updates on conferences, funding opportunities, and other relevant news.

Are you looking to recruit students and/or postdocs? If so, please describe and be sure to also post the opportunity to GeneticsCareers.org. 

Yes, we are! Graduate student candidates can matriculate through either the Biology or Chemistry departments at the University of Oregon. Postdoc candidates can check out my lab website for more details about what information to send me.

What is your favorite thing about science or about your work? 

I love mentoring. It’s so satisfying to see my trainees succeed, and I like the challenge of teaming up with them on a weekly basis to refine our questions and thinking and troubleshoot whatever impedes progress.

What do you like to do when you’re not at work? 

Spending time with my family is a joy and a wonderful balance for my work. We love the outdoors, seeking out/cooking delicious food, and finding art and music. I also love playing music—I am a jazz drummer—and cycling (both road and MTB). Eugene is a famous running town, and I’ve enjoyed my regular runs on “Pre’s Trail” (designed by famous Oregon product Steve Prefontaine), which begins only a 10-minute walk from the lab. I confess, though, that I’m not fast!

Previous training experiences:

• BS, University of California, Santa Cruz
• PhD, MIT (with Prof. David Bartel)
• Postdoctorate, Stanford University School of Medicine (with Prof. Daniel Jarosz)

Parent-of-origin effects help determine how lab rats respond to stress.

Although your father and mother each contribute a copy of your genes, these copies don’t always play equal roles. Instead, one parent’s gene can have a disproportionate effect on the offspring’s phenotype, resulting in complex patterns of inheritance. In G3: Genes|Genomes|Genetics, Mont et al. examined such effects in the behavior of lab rats.

One example of parent-of-origin effects (PoE) is genomic imprinting, a phenomenon in which only either the maternal or paternal allele of a gene is expressed. Imprinting is associated with a range of developmental and behavioral phenotypes in mammals, and disruption of certain imprinted genes can cause human diseases like Prader-Willi, Angelman, and Beckwith-Wiedemann syndromes.

Although a great deal of work has been done on PoE in mice, much less is understood in rats, which show more complex behaviors. Thus, the authors began their study with a broad assessment of 199 phenotypes in a large cross of rats for which parental information was available. To look for potential examples of PoE, they developed a way to separate out the portion of trait variance that was dependent on inheritance in the usual sense—where there is no difference between maternally and paternally inherited alleles—from that which contrasts the mother versus the father. The latter component can arise from several causes, including true PoE, maternal effects (i.e. gene expression in the mother that influenced offspring taits), paternal effects (the equivalent for the father), and environmental effects from sharing a cage with the mother and some of the siblings. If there were no PoE, then values for each parent would be equivalent; however, the authors found that they were different for 86% of the phenotypes assessed.

If imprinted loci are known to be rare, why are these PoE-related effects seemingly so pervasive? The rat results are consistent with experiments done in mice, which also found widespread PoE-like phenomena and suggested that these effects may be due in part to the indirect effects of imprinted loci—that is, the effects of imprinting can ripple through the genome to trigger many additional phenotypic consequences.

Of particular note, the authors found that coping behaviors—how the animals reacted to stress—showed some of the most significant differences between maternal and paternal contributions, which is suggestive of PoE. However, confounding variables, such as dominance, can also generate PoE, so further experimentation was required to confirm this finding.

To test for PoE related to coping behaviors, the authors crossed two rat strains: RHA and RLA. Stressed RHA rats tend to display active behaviors, such as fleeing, whereas RLA rats tend to be passive when stressed, either freezing or self-grooming. These behaviors were assessed in the offspring of reciprocal crosses using the elevated zero maze, in which rats are placed in a ring-shaped elevated platform with alternating open and walled sections. The rats are then observed for anxiety-like behaviors around the open sections, since rats prefer closed spaces when they are exploring a new environment. The behavior of offspring in the maze tended to fit the behavior profile of the maternal strain: rats with RHA mothers and RLA fathers exhibited more active behavior (matching their RHA mothers), and vice versa.

The authors suggest that these differences might be due to known differences in epigenetic modifications on neurotransmitter receptor genes in the two rat strains, although further research is needed to define the exact mechanism for this phenomenon.

CITATION:

Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

Carme Mont, Polinka Hernandez Pilego, Toni Cañete, Ignasi Oliveras, Cristóbal Río-Álamos, Gloria Blázquez, Regina López-Aumatell, Esther Martínez-Membrives, Adolf Tobeña, Jonathan Flint, Alberto Fernández-Teruel, Richard Mott

G3: Genes|Genomes|Genetics October 2018 8: 3283-3291;

http://www.g3journal.org/content/8/10/3283

https://doi.org/10.1534/g3.118.200489

Tissue culture causes heritable methylation changes in plants.

Tissue culture is a useful tool for plant scientists and horticulturalists in large part because it allows them to produce clones. Inconveniently, however, these clones are not always identical to the original, as one might expect them to be. In a report in GENETICS, Han et al. examined how propagation by tissue culture induces heritable epigenomic changes in maize.

When a portion of a plant is grown in tissue culture, it de-differentiates into an amorphous callus. This deprogrammed tissue can be induced to form roots or shoots or even to regenerate an entire plant—but this complex process can leave its marks on the genome and epigenome of the progeny. To get a picture of how tissue culture affects the epigenome, the authors compared methylation patterns in parental plants, plants that had been cultured, and the progeny of those cultured plants.

They found that most methylation was highly stable; it was consistent among all plants and unaffected by culturing. However, a subset of the methylome was variable between cultured and uncultured plants.  Many of these DNA methylation differences were passed on to the progeny of the cultured plants. Importantly, some of the changes the authors identified were shared among independently regenerated progeny, suggesting that tissue culture can prompt consistent, heritable epigenetic effects in maize.

In theory, these epigenetic changes might be due to general stress; for example, the culture process might cause the methylation machinery to become dysregulated. However, since most methylation in the genome was largely unaffected, and many changes were consistent among cultured plants, it’s more likely that these changes are targeted, with certain alleles being more sensitive than others to heritable epigenetic changes during culture. The mechanisms that lead to methylation modifications and the genetic and phenotypic consequences of those changes will be interesting avenues for further study; however, since most plant genome editing requires a culture step, researchers should be cautious about unintended epigenetic consequences.

CITATION:

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

Zhaoxue Han, Peter A. Crisp, Scott Stelpflug, Shawn M. Kaeppler, Qing Li, Nathan M. Springer

GENETICS August 2018 209: 983-995; https://doi.org/10.1534/genetics.118.300987

http://www.genetics.org/content/209/4/983

Imprinted genes can have oppositional effects on adult behavior in mice.

Mammalian genomes show the marks of a genetic tug-of-war between mothers and fathers. These imprinted genes are marked by epigenetic modifications, which means the expression of an imprinted allele depends on whether it was inherited from the mother or the father. A new report in GENETICS expands our understanding of this phenomenon by describing a pair of imprinted genes with opposing effects on adult mouse behavior.

Seeking the evolutionary underpinnings of imprinting has fueled a number of theories and debates. One explanation is based on the conflicting evolutionary pressures on alleles with different parental origins. This theory of intragenomic conflict suggests that the function of imprinting is to control the expression of genes that have opposite effects on maternal and paternal fitness. For example, a paternally inherited allele might favor the growth of offspring as large as possible, but a gene inherited from the mother might instead favor conserving maternal resources for future offspring. Supporting this idea, a number of examples have been found where pairs of genes with antagonistic effects on embryonic growth and early development have inverse patterns of imprinting (i.e. one is expressed only from the paternal allele and the other only from the maternal allele).

In the mouse central nervous system, only the maternal copy of Nesp55 is expressed, while only the paternal copy of Grb10 is expressed. The authors of the GENETICS study previously found that mice lacking maternal Nesp55 make more impulsive choices, but the role of Grb10 was unknown. Given that the two genes have similar expression patterns, the authors hypothesized that they might play related roles.

To address this question, the authors used the same experimental setup they had used for their previous study of Nesp55. They tested mice lacking paternal Grb10 and their wild-type littermates with two different measures of impulsivity. First, they tested impulsive choice by using a delayed reinforcement test, in which mice have to choose between a small reward immediately or a larger reward after a wait. Then, they measured impulsive action by using a stop-signal reaction time test, where mice had to learn to stop a prepotent action in order to get a reward. Although “impulsive choice” and “impulsive action” are deceptively similar terms, they refer to discrete behaviors.

In their previous study, the authors found that mice lacking maternal Nesp55 make more impulsive choices, i.e. they show a preference for a small but quick reward. In this study, mice lacking paternal Grb10 showed the exact opposite phenotype; they made significantly fewer impulsive choices. The behavioral effect was quite specific; all the mice studied showed no change in impulsive action. This suggests that these two genes have opposing effects on this particular aspect of mouse behavior—and this behavior could be subject to conflicting selection pressures, in line with the theory of intragenomic conflict.

This is the first report of imprinted genes acting in opposition in adult behavior, and it suggests that the genomic tug-of-war between parental alleles could have effects that extend into adulthood—far beyond those observed in utero and in early development. The authors suggest that such imprinted genes may even play roles in human disorders that involve impulsivity, like addiction.

CITATION:

Impulsive Choice in Mice Lacking Paternal Expression of Grb10 Suggests Intragenomic Conflict in Behavior

Claire L. Dent, Trevor Humby, Katie Lewis, Andrew Ward, Reiner Fischer-Colbrie, Lawrence S. Wilkinson, Jon F. Wilkins, Anthony R. Isles

GENETICS May 1, 2018 vol. 209 no. 1 233-239; DOI: 10.1534/genetics.118.300898

http://www.genetics.org/content/209/1/233 

[wysija_form id=”1″]

Although epigenetic modifications contribute to trait variability, their effect pales in comparison to standing genetic variation.

The raw material of evolution is genetic variation, but proponents of the “extended evolutionary synthesis” add a new layer to this model: heritable variation in epigenetics. The packaging and tagging of DNA can alter traits without changing the DNA sequence, and in some cases, these changes can be inherited across generations. Can this epigenetic variation play a role in adaptation? Though this question is still under debate, a report published in G3: Genes|Genomes|Genetics suggests that the influence of epigenetic variation on trait variability may be comparatively feeble.

Aller et al. set out to directly compare the influence of genetic and epigenetic variation on an adaptive trait in the flowering plant Arabidopsis thaliana. To do this, they used epigenetic Recombinant Inbred Lines (epiRILs), which are bred from closely related plants with and without a specific mutation in a gene important for maintenance of DNA methylation, such that almost all of the heritable variation in their progeny is attributable to differences in which parts of the genome are methylated— i.e. epigenetic variation. The lines are essentially genetically identical, but each has a different stably-inherited pattern of DNA methylation.

For each epiRIL, the authors measured adaptive traits such as flowering time and accumulation of glucosinolates, which are compounds the plants produce for defence against herbivores and pathogens. The team then compared the variation in this epigenetic system to other studies that investigated the genetic variation underlying those same traits.

Although the authors found significant variation within their epigenetically-driven model, it was much lower than variation in genetically-driven equivalents. This suggests that epigenetic changes are much weaker drivers of variability than the major engine of adaptation: alterations of the genetic code.

CITATION:

Comparison of the Relative Potential for Epigenetic and Genetic Variation To Contribute to Trait Stability

Emma S.T. Aller, Lea M. Jagd, Daniel J. Kliebenstein, Meike Burow

G3: Genes|Genomes|Genetics 2018 8: 1733-1746. DOI: 10.1534/g3.118.200127

http://www.g3journal.org/content/8/5/1733 

Monomethylated H3K27 is more than just an intermediate.

We often talk about biological traits as if they’re written in our DNA, but some of them aren’t in our DNA at all—instead, they’re on it in the form of chemical tags on the histone proteins our genomic DNA is wrapped around. During development, each cell’s genome is indexed with these tags, which help determine whether a stretch of DNA should be actively transcribed or silent. In a new study published in GENETICS, Wang et al. investigated how the marks left by one of the most important players in this system are interpreted.

PRC2 is a complex of proteins that turns off genes by flagging histones around the genes with methyl groups. One at a time, PRC2 adds these groups to a specific lysine residue (K27) of histone H3 through a process called methylation. Specifically, trimethylation of H3K27 is required for silencing; if there are any fewer than three methyl groups, the gene won’t be turned off.

DNA silenced in this way is relatively rare, with trimethylated H3K27 only being found at around 100 sites in the genome. In contrast, genomic regions littered with mono- and dimethylated H3K27 are more common. Wang et al. wondered whether these mono- and dimethylated H3K27 were simply intermediates left behind by PRC2 or had their own purposes.

To test for function of H3K27 monomethylation, the group engineered a version of PRC2 that was adept at adding one methyl group but very inefficient at adding more. They found that, in a fruit fly cell line, this version of PRC2 led to increased expression of genes that PRC2 normally targets for silencing. However, this wasn’t enough to show that monomethylation has a specific function, since silencing is known to require trimethylation of H3K27.

The real insight came from comparing this result to what happened when they ran the same experiment using a version of PRC2 that’s inefficient at adding any number of methyl groups. Cells with this defective PRC2 had lower expression of PRC2-target genes than cells with the monomethylating PRC2 did, indicating that having a single methyl group on H3K27 may specifically increase gene expression above baseline.

This study adds to a growing collection of work on the importance of the number of methyl groups added to histones. Monomethylation on a different lysine residue (K9) of the histone H3 is associated with active genes, whereas di- or trimethylation usually indicates gene repression. If different numbers of methyl groups lead to multiple, distinct states, this could be exploited in drug design. Many cancers are associated with faulty gene regulation, so a targeted drug that precisely tuned the number of methyl groups on histones could help restore order by rewriting the genome’s index.

CITATION:

A Role for Monomethylation of Histone H3-K27 in Gene Activity in Drosophila
Liangjun Wang, Preeti Joshi, Ellen L. Miller, LeeAnn Higgins, Matthew Slattery and Jeffrey A. Simon
Genetics 2018 208: 1023–1036; https://doi.org/10.1534/genetics.117.300585
http://www.genetics.org/content/208/3/1023

The Genetics Society of America (GSA) is pleased to announce that Barbara Meyer is the recipient of the 2018 Thomas Hunt Morgan Medal, which is awarded for lifetime achievement in genetics. This honor is given in recognition of her groundbreaking work on chromosome behaviors that govern gene expression, development, and heredity.

Barbara Meyer

Meyer’s studies of how chromosomes determine sex began during her postdoctoral period in the laboratory of Sydney Brenner, who later won a Nobel Prize for establishing the nematode worm Caenorhabditis elegans as an important model organism for research on development. Meyer’s early work focused on how C. elegans “counts” the number of X chromosomes and sets of autosomes to determine its sex, as well as how it adjusts to the imbalance in the number of X chromosomes between the two sexes.

In C. elegans, individuals with two X chromosomes are self-fertilizing hermaphrodites; those with only one X chromosome are males. A popular hypothesis when Meyer began her postdoctoral work was that the worms compensate for the difference in the number of copies of genes on the X chromosome between the two sexes. But it wasn’t clear whether the worms accomplished this by upregulating genes on the X chromosome in males or by downregulating genes on the X chromosome in hermaphrodites—in fact, no one had conclusively shown dosage compensation occurs at all.

As a postdoctoral researcher and after establishing her own lab, Meyer confirmed at the molecular level that the worm engages in a dosage compensation process. She then identified genes involved in the process and showed that dosage compensation works by reducing expression of X-linked genes in hermaphrodites.  

Further analysis of the mechanism underlying dosage compensation produced many key insights into gene regulation. Because the sex of C. elegans individuals is determined by the ratio of X chromosomes to sets of autosomes, she knew there must be a molecular mechanism for sensing this ratio. Her lab identified a gene they named xol-1 as the master switch for sex determination: when the gene is turned off, the animals are hermaphrodites, and when it’s turned on, the animals are male. xol-1 controls both sex determination and dosage compensation in response to the ratio of X chromosomes to sets of autosomes, the sex-determination signal.

Meyer’s group found that transcription factors encoded by both the X chromosome and the autosomes battle to control whether xol-1 is transcriptionally active or inactive. After a victor emerges in this molecular tug-of-war, proper maintenance of xol-1’s state is ensured by a splicing factor—also studied in Meyer’s lab—that acts on xol-1 mRNA. Active xol-1 directs male development by inducing repression of sdc-2, a second master sex-switch gene. Without xol-1-mediated repression, sdc-2 would direct hermaphrodite development by repressing yet another gene—one that heads a sex-determination cascade that causes male development. Additionally, active sdc-2 would trigger assembly of a dosage compensation complex on both X chromosomes in the hermaphrodites.

These key findings formed the foundation of many fruitful research projects across the field, including extensive analysis in Meyer’s own lab. By characterizing the dosage compensation complex in C. elegans, the group discovered that the same protein complexes that tightly condense chromosomes and repress transcription during mitosis (condensins) can be repurposed to turn down transcription during interphase. These condensin complexes act as structural elements to remodel the higher-order structure of X chromosomes and regulate entire regions of the chromosomes.

“Her elegant genetic analysis, followed by beautiful molecular and cellular studies, have continued to yield a deep and fascinating picture of these processes,” says Cynthia Kenyon, Vice President of Aging Research at Calico Labs.

In addition to leading excellent research projects through a career spanning more than 30 years, Meyer has mentored many graduate students and postdoctoral researchers, fostering their career success. She is currently an investigator of the Howard Hughes Medical Institute and a professor at the University of California, Berkeley, where she previously served as chair of the Genetics Division in the Department of Molecular and Cell Biology and as director of the department’s graduate program.

The Thomas Hunt Morgan Medal is awarded to scientists with a rich history of achievement in genetics, encompassing their full bodies of work. The Medal honors the memory of Thomas Hunt Morgan (1866–1945), one of the most recognized figures in the history of genetics. Among his many discoveries, Morgan is known for being the first to show that chromosomes are the carriers of genetic information.

In the 1940s, C. H. Waddington discovered a peculiar phenomenon in fruit flies: traits could appear in response to environmental stress in an individual’s lifetime and then be passed down to future generations. Waddington proposed that this wasn’t the inheritance of acquired traits, but actually due to pre-existing genetic variation that had no effect until the flies were stressed. In the August issue of GENETICS, Fanti and Piacentini et al. revisit Waddington’s famous experiments with modern sequencing technology to show that this phenomenon can also be driven by newly arising DNA mutations.  

The authors followed Waddington’s fairly simple experimental framework: take flies from natural populations and expose them to high temperatures for a short time during pupation. Observe the adult phenotypes, and then do it all again the next generation. Repeat this process until strange phenotypes emerge following the heat shock treatment.

The authors focused on four phenotypes caused by well-studied mutations in fruit flies, including sepia eye color and forked bristle mutations. These phenotypes began to appear after heat shock treatment between four and twelve generations after the experiment began. The scientists then selected for a phenotype by crossing the flies displaying it. They repeated this procedure until the phenotypes appeared not only after heat stress but were stably maintained in regular conditions.

They confirmed the presence of genetic mutations in the heat shocked mutant stocks using DNA sequencing. In the fixed mutant stocks, they found clear genetic causes of the mutant phenotypes. In two cases, a deletion mutation disrupted the protein coding sequence, and the other two genes carried transposable element insertions. None of the mutations were present in the genomes of the parental flies; these mutations were new, arising during the course of the experiment. Clearly, they were what allowed the phenotypes to be maintained stably without heat stress.

These results show that Waddington was wrong: inheritance of the abnormal post-heat shock phenotypes was not due to cryptic variation present in the parent lines. A different mechanism must be responsible. Heat shock stress may cause double-stranded DNA breaks, which can lead to deletions like the ones observed here. It may also activate transposable elements since the authors found higher levels of transposable element transcripts in flies that had been heat shocked.

But how could these new mutations appear in the same genes that were initially disabled by heat shock? How can a stress-dependent phenotype become genetically encoded? The authors suggest epigenetic changes may be involved. Heat stress could result in epigenetic alteration of particular loci to change their expression, leading to the observed heat-dependent phenotypes. This same epigenetic activity may make this stretch of DNA more susceptible to mutation, which could be very likely in the face of heat shock-induced double-stranded breaks or activated transposable elements.

If this model holds true, it could have serious evolutionary implications. In the wild, plastic traits like these post-heat shock phenotypes are often adaptive and help organisms survive in difficult, changing environments. It has been proposed that under natural selection such environmentally-induced traits can eventually become genetically encoded. Called the Baldwin Effect, this process illustrates how heritable behaviors like the human capacity for language might evolve. The results of this study provide a viable mechanism for this powerful evolutionary phenomenon.

CITATION

Canalization by Selection of de Novo Induced Mutations

Inheriting a trait from a grandparent doesn’t always involve their DNA sequences. In many organisms, some traits can be passed down for multiple generations via non-sequence based mechanisms, a phenomenon called transgenerational epigenetic inheritance. The most familiar example is that human disease risk might be influenced by the lifestyle of a person’s grandparents. But by far, the most unambiguous and robustly-studied cases occur in tiny laboratory workhorses like yeast and the nematode worm C. elegans. In the July issue of GENETICS, Spracklin et al. identify the genetic components required for RNA interference (RNAi) inheritance—a type of transgenerational epigenetic inheritance that occurs in C. elegans. They also show that this machinery is required for maintenance of the germline, suggesting an important natural role for this intriguing mode of inheritance.  

Normally, small double-stranded RNAs (dsRNAs) are produced by the organism to regulate mRNA expression and transposable element activity. This regulatory machinery intercepts particular transcripts, marks them for degradation, and sometimes triggers epigenetic changes that suppress further expression. RNAi is a powerful genetic tool that allows researchers to easily manipulate gene expression levels by taking advantage of the worm’s natural regulatory systems.

In the lab, treatment with specially designed dsRNAs co-opts this regulation to dampen expression of a target gene. But the RNAi-mediated epigenetic alterations affect not only the worm initially treated with dsRNA, they persist in up to five generations of its offspring. That is, RNAi knockdown is heritable in worms. Some of the genetic components required for RNAi inheritance have been identified already, but much about this process is still unknown.

In this study, Spracklin et al. used a straightforward genetic screen to identify the RNAi inheritance machinery. They took worms expressing green fluorescent protein (GFP) in their germline cells and exposed them to mutagens to randomly break genes across the genome. Then they inhibited the expression of GFP with RNAi and let the worms reproduce. They chose offspring that didn’t inherit the RNAi and still expressed GFP for further study. After screening an astounding 6 million haploid germline genomes, they found six unique, newly identified genes needed for RNAi inheritance.

Not only do these mutant alleles disrupt RNAi inheritance, they doom their carrier’s descendants to extinction. In all eukaryotes, germline cells retain the ability to divide forever—they are immortal. Previous work found mutations that interfered with RNAi inheritance also resulted in germline mortality: in three to five generations the individual’s offspring become sterile. The new mutations identified by Spracklin et al. also cause germline mortality.

Critically, they also showed that germline mortality is likely caused by deregulation of an epigenetic process and not DNA changes from transposable elements gone awry, as previously hypothesized. Indeed, one of the genes they identified as part of the RNAi machinery is a histone tail methyltransferase responsible for making epigenetic marks. This work shows that epigenetic changes that persist across generations are a fundamental factor necessary for one of the most important processes in a living organism—preserving germ cells critical for reproduction.    

CITATION

The RNAi Inheritance Machinery of Caenorhabditis elegans

George Spracklin, Brandon Fields, Gang Wan, Diveena Becker, Ashley Wallig, Aditi Shukla and Scott Kennedy

GENETICS July 1, 2017 vol. 206 no. 3 1403-1416

https://doi.org/10.1534/genetics.116.198812

http://www.genetics.org/content/206/3/1403