Published online: November 8, 2014
Science & Society
Lifestyle in the sperm There is growing evidence that epigenetic marks can be inherited. But what is the nature of the information they store and over how many generations do they prevail? Katrin Weigmann
M
ore than 200 years ago, JeanBaptiste Lamarck (1744–1829) proposed a theory for the major question in biology: How do organisms change over time to adapt to their environment and create new species? Lamarck reasoned that if an organism changes to better adapt to its environment, these changes would be passed on to its offspring, and this would explain changes over generations. He was eventually refuted, however, by Charles Darwin’s theory of evolution by natural selection, and Gregor Mendel’s genetics, which explained how random mutations, not adaptive changes, generate diversity. The discovery of the structure of DNA, which mechanistically explained inheritance and mutations, finally moved Lamarck’s theory to the huge pile of disproven scientific hypotheses. Recent research has re-opened a debate about Lamarck, however, as so-called epigenetic inheritance—based on reports that stress, nutrition, toxins, and infections not only affect an individual’s behavior, body weight, and health and defense system, but also that of its offspring—goes some way to rehabilitating his theory. “A Revolution in Evolution: A Return to Lamarck?” wrote Gregg Henriques, Professor of Psychology at James Madison University, in December last year on the blog of Psychology Today (http://www.psychologytoday.com/), while Science magazine asked whether the discovery that epigenetic changes can be inherited is “evolutionary heresy” [1]. In reality, epigenetics does not really challenge our basic model of evolutionary inheritance, founded on the work of Darwin and Mendel, but it does add some important features to the
model, and research into epigenetics and whether such epigenetic marks are heritable is expanding rapidly.
G
enerally, epigenetics is the study of heritable changes in gene regulation that are not a result of changes to the underlying DNA sequence. Mechanisms that produce such changes include chemical modifications to the DNA, such as DNA methylation, or to proteins associated with the DNA (such as histone modification), but also other factors, most notably non-coding RNAs. Epigenetic processes play a central role in cell development and explain how the same genome can give rise to many different cell types; how these cells maintain their identity throughout life; and how this information is passed on to daughter cells. Two recent developments have contributed to the growing interest in epigenetic inheritance. First, it has become clear that environmental factors—such as toxins, nutrition, or stressful experiences—can leave their marks on the epigenome, permanently altering gene expression and impacting on health, disease, and behavior many years later. Second, and even more fascinating, epigenetic changes can be inherited across generations, despite the fact that nearly all epigenetic marks are thought to be erased during gametogenesis and in early embryonic development in a process called “epigenetic reprogramming”. But to prove Lamarck right, epigenetic inheritance would have to meet a number of additional criteria. Do epigenetic changes induced by the environment reflect beneficial adaptations to the environment? And if so, are these changes inherited over many generations in an
epigenetic fashion or are they eventually fixed into the genome itself to play a role in evolution? The best evidence for the inheritance of environmentally induced traits in humans comes from epidemiological studies of the so-called Dutch hunger winter and the ¨ verkalix cohort. During the winter of O 1944–1945, the German-occupied part of the Netherlands suffered a devastating famine. Women who were pregnant during that winter gave birth to children who developed a number of clinical disorders, and their grandchildren also suffered from ¨ verkalix is a remote commupoor health. O nity in northern Sweden for which detailed accounts of harvests, births, and deaths are available. Tracing back family trees, researchers have found correlations between food availability during the prepuberty years of grandparents and the mortality risk of subsequent grandchildren. These studies suggest that starvation during critical periods of development—fetal development and early adolescence— induces epigenetic changes in the germline that persist to the children and possibly grandchildren.
O
f course, these studies are merely observational and retrospective and carry the risk of possible bias and confounding factors. However, several recent rodent studies further support the idea that acquired traits can be transmitted across generations. Most of these studies have focused on the inheritance from fathers rather than mothers to rule out maternal effects that are not germline specific, such as in utero embryonic development or maternal care after birth. For
Freelance journalist in Oldenburg, Germany. E-mail: [email protected] DOI 10.15252/embr.201439759 | Published online 8 November 2014
ª 2014 The Author
EMBO reports Vol 15 | No 12 | 2014
1233
Published online: November 8, 2014
EMBO reports
example, a high-fat diet in male rats induced adiposity, impaired glucose tolerance, and insulin sensitivity in their female offspring, along with an altered expression of pancreatic islet genes. The sperm of pre-diabetic male mice had altered methylation patterns, and their offspring showed increased glucose intolerance. In addition, the progeny of male
1234
EMBO reports Vol 15 | No 12 | 2014
Lifestyle in the sperm
mice that had been fed a low-protein diet exhibited altered expression of genes involved in lipid and cholesterol metabolism [2]. Oliver Rando, a molecular biologist at the University of Massachusetts Medical School in Worcester, USA, and lead author of the low-protein study, is looking for the mechanisms behind this effect. Together with his
Katrin Weigmann
colleagues, he has initiated an epigenomewide mapping of histone modification, cytosine methylation, and small RNAs. Although the researchers see at least some changes in all three types of marks, some seem to be more promising than others. “As a guess, I am most optimistic about the small RNAs. But the cytosine methylation changes we find are also appealing to us
ª 2014 The Author
Published online: November 8, 2014
Katrin Weigmann
because they occur at regions that escape demethylation at fertilization”, Rando said. In addition to nutrition, scientists are also investigating other examples of epigenetic inheritance. Isabelle Mansuy, a neuroscientist at the University Zu¨rich and the Swiss Federal Institute of Technology in Zu¨rich, Switzerland, has demonstrated that early postnatal trauma in mice can affect behavior across generations. In her experiments, she separates newborn mice from their mothers at unpredictable times every day for 2 weeks. “The effect is quite dramatic”, Mansuy said, “it severely alters the animals’ behavior”. When the pups become adult, they suffer from depression, loss of behavioral control, impaired cognitive functions, and social skills. These symptoms, along with the altered expression of several genes, including stressrelated genes, are transmitted to the progeny for several generations.
......................................................
“The extent to which useful adaptations can be inherited epigenetically may depend on what Rando calls the “bandwidth” of epigenetic information in sperm” ...................................................... In a recent article, Mansuy and her colleagues identified small non-coding RNAs as potential mediators of inheritable epigenetic information [3]. They injected RNA extract from the sperm of traumatized males into fertilized eggs of wild-type females. The resulting offspring expressed similar behavioral alterations as their fathers, showing that sperm RNA is likely a carrier of a transmissible epigenetic signal. However, additional mechanisms may also be involved. “Non-coding RNAs are not altered in sperm of the progeny”, Mansuy explained. “But since the phenotype does persist in the third generation, we believe the change in RNA in sperm is transferred to another likely more stable form of epigenetic mark”.
E
nvironmental information can leave epigenetic marks that are relayed to the next and even further generations. However, the resulting phenotypes are not necessarily useful adaptations to the environment, as one would expect in a truly
ª 2014 The Author
EMBO reports
Lifestyle in the sperm
Lamarckian evolution. “Stress can, in some conditions, improve behavioral flexibility”, Mansuy commented. But this is rather the exception than the rule. In general terms, depression and impaired memory can hardly be called a useful adaptation. Similarly, the metabolic changes in Rando’s feeding paradigm are not unambiguously adaptive. “Whether or not the offspring of starved mice are better adapted to starvation has not been analyzed”, he said. The extent to which useful adaptations can be inherited epigenetically may depend on what Rando calls the “bandwidth” of epigenetic information in sperm. “You can imagine two extremes”, Rando explained. “One extreme is that sperm carry an infinite amount of environmental information. Every methylation site could carry one bit of information and, in terms of RNA profile, the high-dimensional complexity of the transcriptome could be used. The alternative is that sperm transmit some blunt measure of quality of life: Life was terrible, life was ok, life was great”. And there is, according to Rando, a good reason to lean toward the latter interpretation: Different paradigms produce an overlapping set of phenotypes in the progeny. “You might find metabolic phenotypes in a parental stress paradigm or behavioral phenotypes in nutritional paradigms”, Rando said. Whatever causes these epigenetic effects might be more related to sperm quality than to adaptive traits.
......................................................
“Disease risk may therefore
not only depend on our own genes and environmental exposure, but also on environmental exposure of our parents” ...................................................... However, a recent discovery seems to contradict this view. Brian Dias and Kerry Ressler at Emory University in Atlanta, Georgia, USA, reported that mice can inherit olfactory memories from their fathers [4]. They trained mice to fear specific odors by associating them with mild foot shocks and showed that the offspring of these mice—children and grandchildren—were also more sensitive to that particular smell. “It will certainly be important to see other examples in the same domain. But if this proves to be the
first of many papers, that would demonstrate high-dimensional information transfer”, Rando commented. To date, however, data are sparse and there is a good portion of skepticism. In addition, the concept of inheritance of memory raises questions. “If things learned by a grandfather would be inherited in a substantial manner, this would have been noticed by now”, Mansuy noted. Inherited memories or not, it is becoming increasingly accepted among the scientific community that at least some environmental information can be passed on to offspring. This is an important insight for clinical research as human and rodent studies have shown that disease risk may not only depend on an individual’s genetic setup and environment, but also on the environment of his or her ancestors. Many complex diseases have a strong heritable component. Although genomewide association studies have successfully identified hundreds of variants that are associated with disease risks, these variants only explain a small portion of the observed heritability, which has been referred to as “missing heritability”. According to Mansuy, epigenetic inheritance could provide an explanation for this puzzle. “Today, many people agree that epigenetic inheritance largely contributes to diseases like depression, personality disorder, even Alzheimer’s disease”, she said.
I
n searching for potential mechanisms of multigenerational epigenetic inheritance, an obvious place to look is in C. elegans. In 1998, Andrew Fire, then working at the Carnegie Institution of Washington in Baltimore, Maryland, USA, and Craig Mello, who was at the University of Massachusetts Cancer Center in Worcester, USA, published a seminal paper on a process called RNA interference (RNAi), for which they were later awarded the Nobel Prize. Short pieces of double-stranded RNA, they found, can silence specific target genes. And these interference effects, as Fire and Mello mention in their original publication, “can persist well into the next generation, even though many endogenous RNA transcripts are rapidly degraded in the early embryo” [5]. In 2012—more than 15 years after the Nobel Prize-winning publication—the research groups of Craig Mello and Eric Miska, a molecular geneticist at the University of Cambridge, UK, published a set of
EMBO reports Vol 15 | No 12 | 2014
1235
Published online: November 8, 2014
EMBO reports
papers that shed further light on the underlying mechanisms. “We found a nuclear RNAi pathway that seems to make this multi-generational inheritance possible”, Miska said. The researchers unraveled a silencing machinery that is guided to nascent RNA transcripts at specific loci by small RNAs, where it modulates chromatin structure to shut down genes [6]. In addition, when the scientists induced silencing using piRNAs—a germline-specific set of small RNAs—instead of external RNAs, they generated a very strong silencing effect. “We call this paramutation”, Miska said, named after a stable inheritance mechanism of epigenetic marks in plants. “This seems to be the first example in animals”, he added.
......................................................
“Although it seems conceiv-
able that the RNAi and piRNA pathways could transmit environmental adaptions across several generations, it is still not clear if this happens in nature” ...................................................... Similar to mice and humans, most chromatin marks are erased during germline development in C. elegans. Accordingly, Miska thinks that RNA is the most likely candidate to carry information from one generation to the next. “Our model is that small RNA is inherited and then these molecules re-establish a certain chromatin mark”, he said. This idea is in line with a previous study by Andrew Fire and colleagues who showed that the genomic locus is not required to pass RNAi-induced silencing from parents to offspring; all you need is some diffusible substance in the sperm. If small RNA can transmit information across generations, what is the nature of this information? Does it include environmental cues? Feeding worms RNA to silence genes in laboratory experiments can hardly be called an environmental cue, as Miska conceded. “That would be cheating a little bit, although I’d love to see it as an environmental cue”, he said. Starvation, a temperature change, infections, or behavioral experiences would be more typical environmental changes encountered by a worm in real life. Several laboratories have developed paradigms in C. elegans to investigate the
1236
EMBO reports Vol 15 | No 12 | 2014
Lifestyle in the sperm
transgenerational inheritance of such environmentally induced traits. Some reports show that an antiviral RNAi response can be inherited to the next generation. In addition, the inheritance of an acquired olfactory behavior has been described and starvation has been shown to trigger the expression of small RNAs that are inherited to the next generation. But in most of these cases, there are still open questions: Is the nuclear RNAi machinery discovered by the Miska and Mello laboratories really involved? Do inherited RNA expression profiles reflect useful physiological adaptations? Is the phenotype stably transmitted over several generations? None of the studies can answer all of the questions. Although it seems conceivable that the RNAi and piRNA pathways could transmit environmental adaptions across several generations, it is still not clear whether this happens in nature. Just like in mammals, the question of “bandwidth” arises. How specific is the information that is inherited across generations? Even though the system could potentially carry a lot of information, this does not imply that all of it is used. Again, epigenetic inheritance could be refined to some gross evaluation of life’s quality: “environment is bad, better warn the kids”, as Miska described it.
W
hile there is massive epigenetic reprogramming in embryonic and germline development in mammals, this is not the case in plants where, accordingly, epigenetic inheritance is much more common. To investigate the impact of heritable epigenetic variation, Frank Johannes, a specialist in population epigenetics and epigenomics at the University of Groningen, the Netherlands, in collaboration with researchers from Paris, created so-called “epigenetic recombinant inbred lines” of Arabidopsis. These lines are genetically equal, but show different methylation patterns. “In this experimental system, certain methylation changes can be stably inherited for many generations”, Johannes said. Moreover, plant lines with different methylation patterns also show different phenotypes. They vary in flowering time, plant height, fruit size, and other traits. In a recent study [7], Johannes and his colleagues determined specifically which of the differentially methylated regions in the plant genome cause variation in flowering time and root length. “This has really been the
Katrin Weigmann
first systematic demonstration that DNA methylation across the genome can affect complex traits in a heritable way”, he said. Whereas phenotypic diversity within populations is commonly attributed to genetic variation, these results show that epigenetic changes also contribute.
......................................................
“. . . even if epimutations are
not environmentally induced, epigenetics may play an important role in evolution” ...................................................... Plants have a wide scope of options for epigenetic regulation, including a unique epigenetic pathway, RNA-directed DNA methylation, where small RNAs guide changes to the chromatin. But are such mechanisms used to pass environmentally induced traits to the next generation? “This is a bit of a controversial area of research”, Johannes said. “Some studies have investigated the effect of environmental treatments on the methylome and whether changes that are induced would persist over multiple generations. It turns out that evidence for this is quite limited”, he said. “As of now it seems the environment is not ‘strong’ enough to induce lasting methylation changes. But there is certainly more room for investigation”.
N
onetheless, even if epimutations are not environmentally induced, epigenetics may play an important role in evolution. To understand how a population adapts to environmental changes, scientists have long used genetic models of evolution. One parameter that often enters into such models is the mutation rate. But, according to Johannes, the epimutation rate should also be considered. “We already know that the epimutation rate, at least at individual cytosines, is actually much higher than the genetic mutation rate. There is a much higher probability to come up with a potentially favorable epiallele, which may facilitate adaptation. This makes the system much less constrained”, he said. As plants are sessile organisms that cannot move to a more favorable environment, one can easily imagine how a faster adaptation rate can be particularly profitable for them. But epigenetic changes are also more likely to undergo reversion. Epigenetics may play an important role in the initial steps
ª 2014 The Author
Published online: November 8, 2014
Katrin Weigmann
toward adaptation, but advantageous phenotypic traits ultimately need to be fixed by changes to the genome. “Theoretical modeling shows that a population can be rapidly brought to an adaptive peak through a series of epimutations, and that subsequent genetic mutations can produce favorable alleles that stabilize the population around the peak. Of course, these processes are largely hypothetical and what the epigenetics community needs is further experimental data to support such theoretical insights”, Johannes explained. Epigenetic inheritance is an intriguing mechanism with important implications, as epigenetic changes inherited from our ancestors may impact on metabolic and psychiatric disorders. In addition, the inheritance of epigenetic marks in plants can affect complex traits, and epimutation rates could be an important concept for evolutionary models. As yet, however, there is little evidence that epigenetic inheritance could provoke directed evolution, as proposed by Lamarck. It is questionable, using Rando’s words, whether the
ª 2014 The Author
EMBO reports
Lifestyle in the sperm
“bandwidth” of epigenetic information is broad enough to afford the stable inheritance of detailed environmental information through the epigenetic code over many generations. There are a handful of reports about inherited environmental adaptions that do point to significant bandwidth, but the experiments reported have not yet been repeated independently and the data have not yet convinced the majority of the scientific community. “It’s like seeing a unicorn in the garden”, Miska said. “If you see one you better have a lot of evidence that it is true”. To date, this evidence is still lacking.
References 1.
2.
3.
Gapp K, Jawaid A, Sarkies P, Bohacek J, Pelczar P, Prados J, Farinelli L, Miska E, Mansuy IM (2014) Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat Neurosci 17: 667 – 669
4.
Dias BG, Ressler KJ (2014) Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci 17: 89 – 96
5.
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806 – 811
6.
Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, Cording AC, Doebley AL, Goldstein
Pennisi E (2013) Plant biology. Evolution
LD, Lehrbach NJ, Le Pen J et al (2012) piRNAs
heresy? Epigenetics underlies heritable plant
can trigger a multigenerational epigenetic
traits. Science 341: 1055
memory in the germline of C. elegans. Cell 150:
Carone BR, Fauquier L, Habib N, Shea JM, Hart
88 – 99
CE, Li R, Bock C, Li C, Gu H, Zamore PD et al (2010) Paternally induced transgenerational
7.
Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E,
environmental reprogramming of metabolic
Hospital F, Aury JM, Wincker P et al (2014)
gene expression in mammals. Cell 143:
Mapping the epigenetic basis of complex
1084 – 1096
traits. Science 343: 1145 – 1148
EMBO reports Vol 15 | No 12 | 2014
1237
Published online: November 8, 2014
Science & Society
Lifestyle in the sperm There is growing evidence that epigenetic marks can be inherited. But what is the nature of the information they store and over how many generations do they prevail? Katrin Weigmann
M
ore than 200 years ago, JeanBaptiste Lamarck (1744–1829) proposed a theory for the major question in biology: How do organisms change over time to adapt to their environment and create new species? Lamarck reasoned that if an organism changes to better adapt to its environment, these changes would be passed on to its offspring, and this would explain changes over generations. He was eventually refuted, however, by Charles Darwin’s theory of evolution by natural selection, and Gregor Mendel’s genetics, which explained how random mutations, not adaptive changes, generate diversity. The discovery of the structure of DNA, which mechanistically explained inheritance and mutations, finally moved Lamarck’s theory to the huge pile of disproven scientific hypotheses. Recent research has re-opened a debate about Lamarck, however, as so-called epigenetic inheritance—based on reports that stress, nutrition, toxins, and infections not only affect an individual’s behavior, body weight, and health and defense system, but also that of its offspring—goes some way to rehabilitating his theory. “A Revolution in Evolution: A Return to Lamarck?” wrote Gregg Henriques, Professor of Psychology at James Madison University, in December last year on the blog of Psychology Today (http://www.psychologytoday.com/), while Science magazine asked whether the discovery that epigenetic changes can be inherited is “evolutionary heresy” [1]. In reality, epigenetics does not really challenge our basic model of evolutionary inheritance, founded on the work of Darwin and Mendel, but it does add some important features to the
model, and research into epigenetics and whether such epigenetic marks are heritable is expanding rapidly.
G
enerally, epigenetics is the study of heritable changes in gene regulation that are not a result of changes to the underlying DNA sequence. Mechanisms that produce such changes include chemical modifications to the DNA, such as DNA methylation, or to proteins associated with the DNA (such as histone modification), but also other factors, most notably non-coding RNAs. Epigenetic processes play a central role in cell development and explain how the same genome can give rise to many different cell types; how these cells maintain their identity throughout life; and how this information is passed on to daughter cells. Two recent developments have contributed to the growing interest in epigenetic inheritance. First, it has become clear that environmental factors—such as toxins, nutrition, or stressful experiences—can leave their marks on the epigenome, permanently altering gene expression and impacting on health, disease, and behavior many years later. Second, and even more fascinating, epigenetic changes can be inherited across generations, despite the fact that nearly all epigenetic marks are thought to be erased during gametogenesis and in early embryonic development in a process called “epigenetic reprogramming”. But to prove Lamarck right, epigenetic inheritance would have to meet a number of additional criteria. Do epigenetic changes induced by the environment reflect beneficial adaptations to the environment? And if so, are these changes inherited over many generations in an
epigenetic fashion or are they eventually fixed into the genome itself to play a role in evolution? The best evidence for the inheritance of environmentally induced traits in humans comes from epidemiological studies of the so-called Dutch hunger winter and the ¨ verkalix cohort. During the winter of O 1944–1945, the German-occupied part of the Netherlands suffered a devastating famine. Women who were pregnant during that winter gave birth to children who developed a number of clinical disorders, and their grandchildren also suffered from ¨ verkalix is a remote commupoor health. O nity in northern Sweden for which detailed accounts of harvests, births, and deaths are available. Tracing back family trees, researchers have found correlations between food availability during the prepuberty years of grandparents and the mortality risk of subsequent grandchildren. These studies suggest that starvation during critical periods of development—fetal development and early adolescence— induces epigenetic changes in the germline that persist to the children and possibly grandchildren.
O
f course, these studies are merely observational and retrospective and carry the risk of possible bias and confounding factors. However, several recent rodent studies further support the idea that acquired traits can be transmitted across generations. Most of these studies have focused on the inheritance from fathers rather than mothers to rule out maternal effects that are not germline specific, such as in utero embryonic development or maternal care after birth. For
Freelance journalist in Oldenburg, Germany. E-mail: [email protected] DOI 10.15252/embr.201439759 | Published online 8 November 2014
ª 2014 The Author
EMBO reports Vol 15 | No 12 | 2014
1233
Published online: November 8, 2014
EMBO reports
example, a high-fat diet in male rats induced adiposity, impaired glucose tolerance, and insulin sensitivity in their female offspring, along with an altered expression of pancreatic islet genes. The sperm of pre-diabetic male mice had altered methylation patterns, and their offspring showed increased glucose intolerance. In addition, the progeny of male
1234
EMBO reports Vol 15 | No 12 | 2014
Lifestyle in the sperm
mice that had been fed a low-protein diet exhibited altered expression of genes involved in lipid and cholesterol metabolism [2]. Oliver Rando, a molecular biologist at the University of Massachusetts Medical School in Worcester, USA, and lead author of the low-protein study, is looking for the mechanisms behind this effect. Together with his
Katrin Weigmann
colleagues, he has initiated an epigenomewide mapping of histone modification, cytosine methylation, and small RNAs. Although the researchers see at least some changes in all three types of marks, some seem to be more promising than others. “As a guess, I am most optimistic about the small RNAs. But the cytosine methylation changes we find are also appealing to us
ª 2014 The Author
Published online: November 8, 2014
Katrin Weigmann
because they occur at regions that escape demethylation at fertilization”, Rando said. In addition to nutrition, scientists are also investigating other examples of epigenetic inheritance. Isabelle Mansuy, a neuroscientist at the University Zu¨rich and the Swiss Federal Institute of Technology in Zu¨rich, Switzerland, has demonstrated that early postnatal trauma in mice can affect behavior across generations. In her experiments, she separates newborn mice from their mothers at unpredictable times every day for 2 weeks. “The effect is quite dramatic”, Mansuy said, “it severely alters the animals’ behavior”. When the pups become adult, they suffer from depression, loss of behavioral control, impaired cognitive functions, and social skills. These symptoms, along with the altered expression of several genes, including stressrelated genes, are transmitted to the progeny for several generations.
......................................................
“The extent to which useful adaptations can be inherited epigenetically may depend on what Rando calls the “bandwidth” of epigenetic information in sperm” ...................................................... In a recent article, Mansuy and her colleagues identified small non-coding RNAs as potential mediators of inheritable epigenetic information [3]. They injected RNA extract from the sperm of traumatized males into fertilized eggs of wild-type females. The resulting offspring expressed similar behavioral alterations as their fathers, showing that sperm RNA is likely a carrier of a transmissible epigenetic signal. However, additional mechanisms may also be involved. “Non-coding RNAs are not altered in sperm of the progeny”, Mansuy explained. “But since the phenotype does persist in the third generation, we believe the change in RNA in sperm is transferred to another likely more stable form of epigenetic mark”.
E
nvironmental information can leave epigenetic marks that are relayed to the next and even further generations. However, the resulting phenotypes are not necessarily useful adaptations to the environment, as one would expect in a truly
ª 2014 The Author
EMBO reports
Lifestyle in the sperm
Lamarckian evolution. “Stress can, in some conditions, improve behavioral flexibility”, Mansuy commented. But this is rather the exception than the rule. In general terms, depression and impaired memory can hardly be called a useful adaptation. Similarly, the metabolic changes in Rando’s feeding paradigm are not unambiguously adaptive. “Whether or not the offspring of starved mice are better adapted to starvation has not been analyzed”, he said. The extent to which useful adaptations can be inherited epigenetically may depend on what Rando calls the “bandwidth” of epigenetic information in sperm. “You can imagine two extremes”, Rando explained. “One extreme is that sperm carry an infinite amount of environmental information. Every methylation site could carry one bit of information and, in terms of RNA profile, the high-dimensional complexity of the transcriptome could be used. The alternative is that sperm transmit some blunt measure of quality of life: Life was terrible, life was ok, life was great”. And there is, according to Rando, a good reason to lean toward the latter interpretation: Different paradigms produce an overlapping set of phenotypes in the progeny. “You might find metabolic phenotypes in a parental stress paradigm or behavioral phenotypes in nutritional paradigms”, Rando said. Whatever causes these epigenetic effects might be more related to sperm quality than to adaptive traits.
......................................................
“Disease risk may therefore
not only depend on our own genes and environmental exposure, but also on environmental exposure of our parents” ...................................................... However, a recent discovery seems to contradict this view. Brian Dias and Kerry Ressler at Emory University in Atlanta, Georgia, USA, reported that mice can inherit olfactory memories from their fathers [4]. They trained mice to fear specific odors by associating them with mild foot shocks and showed that the offspring of these mice—children and grandchildren—were also more sensitive to that particular smell. “It will certainly be important to see other examples in the same domain. But if this proves to be the
first of many papers, that would demonstrate high-dimensional information transfer”, Rando commented. To date, however, data are sparse and there is a good portion of skepticism. In addition, the concept of inheritance of memory raises questions. “If things learned by a grandfather would be inherited in a substantial manner, this would have been noticed by now”, Mansuy noted. Inherited memories or not, it is becoming increasingly accepted among the scientific community that at least some environmental information can be passed on to offspring. This is an important insight for clinical research as human and rodent studies have shown that disease risk may not only depend on an individual’s genetic setup and environment, but also on the environment of his or her ancestors. Many complex diseases have a strong heritable component. Although genomewide association studies have successfully identified hundreds of variants that are associated with disease risks, these variants only explain a small portion of the observed heritability, which has been referred to as “missing heritability”. According to Mansuy, epigenetic inheritance could provide an explanation for this puzzle. “Today, many people agree that epigenetic inheritance largely contributes to diseases like depression, personality disorder, even Alzheimer’s disease”, she said.
I
n searching for potential mechanisms of multigenerational epigenetic inheritance, an obvious place to look is in C. elegans. In 1998, Andrew Fire, then working at the Carnegie Institution of Washington in Baltimore, Maryland, USA, and Craig Mello, who was at the University of Massachusetts Cancer Center in Worcester, USA, published a seminal paper on a process called RNA interference (RNAi), for which they were later awarded the Nobel Prize. Short pieces of double-stranded RNA, they found, can silence specific target genes. And these interference effects, as Fire and Mello mention in their original publication, “can persist well into the next generation, even though many endogenous RNA transcripts are rapidly degraded in the early embryo” [5]. In 2012—more than 15 years after the Nobel Prize-winning publication—the research groups of Craig Mello and Eric Miska, a molecular geneticist at the University of Cambridge, UK, published a set of
EMBO reports Vol 15 | No 12 | 2014
1235
Published online: November 8, 2014
EMBO reports
papers that shed further light on the underlying mechanisms. “We found a nuclear RNAi pathway that seems to make this multi-generational inheritance possible”, Miska said. The researchers unraveled a silencing machinery that is guided to nascent RNA transcripts at specific loci by small RNAs, where it modulates chromatin structure to shut down genes [6]. In addition, when the scientists induced silencing using piRNAs—a germline-specific set of small RNAs—instead of external RNAs, they generated a very strong silencing effect. “We call this paramutation”, Miska said, named after a stable inheritance mechanism of epigenetic marks in plants. “This seems to be the first example in animals”, he added.
......................................................
“Although it seems conceiv-
able that the RNAi and piRNA pathways could transmit environmental adaptions across several generations, it is still not clear if this happens in nature” ...................................................... Similar to mice and humans, most chromatin marks are erased during germline development in C. elegans. Accordingly, Miska thinks that RNA is the most likely candidate to carry information from one generation to the next. “Our model is that small RNA is inherited and then these molecules re-establish a certain chromatin mark”, he said. This idea is in line with a previous study by Andrew Fire and colleagues who showed that the genomic locus is not required to pass RNAi-induced silencing from parents to offspring; all you need is some diffusible substance in the sperm. If small RNA can transmit information across generations, what is the nature of this information? Does it include environmental cues? Feeding worms RNA to silence genes in laboratory experiments can hardly be called an environmental cue, as Miska conceded. “That would be cheating a little bit, although I’d love to see it as an environmental cue”, he said. Starvation, a temperature change, infections, or behavioral experiences would be more typical environmental changes encountered by a worm in real life. Several laboratories have developed paradigms in C. elegans to investigate the
1236
EMBO reports Vol 15 | No 12 | 2014
Lifestyle in the sperm
transgenerational inheritance of such environmentally induced traits. Some reports show that an antiviral RNAi response can be inherited to the next generation. In addition, the inheritance of an acquired olfactory behavior has been described and starvation has been shown to trigger the expression of small RNAs that are inherited to the next generation. But in most of these cases, there are still open questions: Is the nuclear RNAi machinery discovered by the Miska and Mello laboratories really involved? Do inherited RNA expression profiles reflect useful physiological adaptations? Is the phenotype stably transmitted over several generations? None of the studies can answer all of the questions. Although it seems conceivable that the RNAi and piRNA pathways could transmit environmental adaptions across several generations, it is still not clear whether this happens in nature. Just like in mammals, the question of “bandwidth” arises. How specific is the information that is inherited across generations? Even though the system could potentially carry a lot of information, this does not imply that all of it is used. Again, epigenetic inheritance could be refined to some gross evaluation of life’s quality: “environment is bad, better warn the kids”, as Miska described it.
W
hile there is massive epigenetic reprogramming in embryonic and germline development in mammals, this is not the case in plants where, accordingly, epigenetic inheritance is much more common. To investigate the impact of heritable epigenetic variation, Frank Johannes, a specialist in population epigenetics and epigenomics at the University of Groningen, the Netherlands, in collaboration with researchers from Paris, created so-called “epigenetic recombinant inbred lines” of Arabidopsis. These lines are genetically equal, but show different methylation patterns. “In this experimental system, certain methylation changes can be stably inherited for many generations”, Johannes said. Moreover, plant lines with different methylation patterns also show different phenotypes. They vary in flowering time, plant height, fruit size, and other traits. In a recent study [7], Johannes and his colleagues determined specifically which of the differentially methylated regions in the plant genome cause variation in flowering time and root length. “This has really been the
Katrin Weigmann
first systematic demonstration that DNA methylation across the genome can affect complex traits in a heritable way”, he said. Whereas phenotypic diversity within populations is commonly attributed to genetic variation, these results show that epigenetic changes also contribute.
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“. . . even if epimutations are
not environmentally induced, epigenetics may play an important role in evolution” ...................................................... Plants have a wide scope of options for epigenetic regulation, including a unique epigenetic pathway, RNA-directed DNA methylation, where small RNAs guide changes to the chromatin. But are such mechanisms used to pass environmentally induced traits to the next generation? “This is a bit of a controversial area of research”, Johannes said. “Some studies have investigated the effect of environmental treatments on the methylome and whether changes that are induced would persist over multiple generations. It turns out that evidence for this is quite limited”, he said. “As of now it seems the environment is not ‘strong’ enough to induce lasting methylation changes. But there is certainly more room for investigation”.
N
onetheless, even if epimutations are not environmentally induced, epigenetics may play an important role in evolution. To understand how a population adapts to environmental changes, scientists have long used genetic models of evolution. One parameter that often enters into such models is the mutation rate. But, according to Johannes, the epimutation rate should also be considered. “We already know that the epimutation rate, at least at individual cytosines, is actually much higher than the genetic mutation rate. There is a much higher probability to come up with a potentially favorable epiallele, which may facilitate adaptation. This makes the system much less constrained”, he said. As plants are sessile organisms that cannot move to a more favorable environment, one can easily imagine how a faster adaptation rate can be particularly profitable for them. But epigenetic changes are also more likely to undergo reversion. Epigenetics may play an important role in the initial steps
ª 2014 The Author
Published online: November 8, 2014
Katrin Weigmann
toward adaptation, but advantageous phenotypic traits ultimately need to be fixed by changes to the genome. “Theoretical modeling shows that a population can be rapidly brought to an adaptive peak through a series of epimutations, and that subsequent genetic mutations can produce favorable alleles that stabilize the population around the peak. Of course, these processes are largely hypothetical and what the epigenetics community needs is further experimental data to support such theoretical insights”, Johannes explained. Epigenetic inheritance is an intriguing mechanism with important implications, as epigenetic changes inherited from our ancestors may impact on metabolic and psychiatric disorders. In addition, the inheritance of epigenetic marks in plants can affect complex traits, and epimutation rates could be an important concept for evolutionary models. As yet, however, there is little evidence that epigenetic inheritance could provoke directed evolution, as proposed by Lamarck. It is questionable, using Rando’s words, whether the
ª 2014 The Author
EMBO reports
Lifestyle in the sperm
“bandwidth” of epigenetic information is broad enough to afford the stable inheritance of detailed environmental information through the epigenetic code over many generations. There are a handful of reports about inherited environmental adaptions that do point to significant bandwidth, but the experiments reported have not yet been repeated independently and the data have not yet convinced the majority of the scientific community. “It’s like seeing a unicorn in the garden”, Miska said. “If you see one you better have a lot of evidence that it is true”. To date, this evidence is still lacking.
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