The latest conference of Abcam took place in Churchill College in Cambridge on April 11-12th. The different presentations covered non-coding RNA and transgenerational inheritance. Below you find some summaries to let you share in the incredible developments in this emerging area.
Engineering Epigenetically Modified Plants
Most eukaryotes contain small regulatory RNAs (sRNAs), typically 21-24 nucleotides long, which are potent regulators of gene expression. This gene silencing process is known as RNA silencing or RNA interference (RNAi) and in plants and nematodes, it is associated with the production of a mobile signal that can travel from cell-to-cell and over long distances.
Some of the RNAs target RNA molecules and interfere via RNA cleavage, translational repression or mRNA destabilization. In plants the posttranscriptional mechanism is involved in defense against RNA viruses. Other sRNAs participate in more complex epigenetic systems affecting chromatin or they act as part of an RNA signal that moves between cells. The chromatin effects play a role in defense against DNA viruses and transposable elements.
David Baulcombe from the University of Cambridge revealed their recent work on how small RNAs mediate epigenetic modification of plant genomes when hybrids are produced or when a plant of one genotype is grafted onto another.
piRNA and Transposon Silencing
The process of transposon silencing is of fundamental importance for genome integrity and germ cell development. Piwi-interacting RNAs (piRNAs), a gonad-specific class of small RNAs (25-30 nucleotides long), provide protection against these transposons, ensuring genome integrity and fertility.
Mechanisms of piRNA biogenesis are largely unclear, but two models summarize our current knowledge. Primary processing of long single-stranded precursors results in the generation of primary piRNAs. Secondary biogenesis takes place via a ‘ping-pong’-cycle; a feed-forward amplification loop where secondary piRNAS are generated using primary piRNAs as initial guides.
Ramesh S. Pillai from EMBL in Grenoble identified a Tudor and helicase domain-containing protein, Tdrd12, as a novel component of the secondary piRNA biogenesis machinery in mice. Tdrd12 function is proposed to act as a molecular scaffold that dynamically bridges the association between Piwi proteins engaged in piRNA amplification.
Donal O’Carroll from EMBL in Monterotondo, investigated the function of Mili in spermatogenesis. The murine Piwi protein Mili is required to establish epigenetic transposon silencing during male germ cell development. They found that Mili-mediated piRNA amplification is selectively required for LINE1, but not intracisternal A particle, silencing. Multiple epigenetic mechanisms enforce LINE1 silencing during adult spermatogenesis, such as H3K9 dimethylation and DNA methylation.
Isabelle Mansuy from the Brain Research institute in Switzerland investigated the role of small non-coding RNAs in sperm and their link to the inheritance of the effect of early traumatic stress in mice. Using a mouse model of early postnatal stress (severe behavioral and metabolic impairments), they found that early stress alters the expression of multiple sncRNAs in sperm of adult males. Alterations were also observed in the brain and serum of stressed adult males, and in the brain of their progeny, suggesting transgenerational transmission. Moreover, after injecting sperm RNAs from stressed males into fertilized mouse oocytes, some of the behavioral and metabolic symptoms were reproduced.
René Ketting from the Hubrecht Institute in the Netherlands recently demonstrated that in zebrafish maternally inherited piRNAs can have a long lasting effect on piRNA expression profiles in offspring. In addition maternally provided Piwi-piRNA complexes can be stable for weeks and play a role in germ cell maintenance.
Transgenerational RNAi inheritance in Caenorhabditis elegans
Scott Kennedy from the Laboratory of Genetics of the University of Wisconsin-Madison explored how epigenetic information is inherited using the model organism Caenorhabditis elegans, wherein RNA interference can be inherited for more than five generations. They conducted a genetic screen for nematodes defective in transmitting RNAi silencing to future generations and identified the heritable RNAi defective 1 (hrde-1) gene. Hrde-1 encodes an Argonaute protein that associates with small interfering RNAs in germ cells.
They found that during the normal course of reproduction, endogenously expressed small RNAs direct nuclear gene silencing in germ cells. In hrde-1 deficient animals, germline silencing is lost. These data have led to the proposition that C. elegans uses the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to regulate important biological processes.
Oded Rechavi from The Life Sciences Faculty in Tel Aviv, Israel, showed that C. elegans inherit antiviral resistance through transgenerational transmission of small RNAs, which mediate RNA interference. Artificially generated viral infection models previously showed that C. elegans can fight viruses by processing the viral dsRNA trigger into virus-derived small interfering RNAs (viRNAs) to guide specific viral immunity by Argonaute-dependent RNAi.
Rechavi showed that an episode of viral expression is memorized in the form of small viRNA molecules that are transmitted through many ensuing generations in the absence of the genetic template and even in the absence of a functional small RNA-generating machinery. These inherited viRNA molecules protect ensuing generations from the virus by silencing the expression of the viral genome. They therefore provide evidence for transgenerational transmittance of extrachromosomal information, and suggest a biologically relevant context in which such extrachromosomal information provides a benefit of potential evolutionary relevance to an organism.
Intergenerational epigenetic inheritance after in utero undernutrition
Elisabeth Radford from the University of Cambridge analysed the role of imprinted genes in multiple tissues of a murine model of the developmental origins of health and disease using microarrays and quantitative RT-PCR. Imprinted genes have been shown to regulate the development of key metabolic organs, and are therefore good candidates to play a role in the developmental origins of health and disease. They are functionally monoallelic and have been hypothesized to be particularly vulnerable to environmental perturbation.
Deregulation of germ cell epigenetic reprogramming of imprinted control elements may be involved in phenotypic inheritance by the next generation. Elisabeth Radford proposed the opposite hypothesis that imprinted genes may be more tightly safeguarded from perturbation due to their multiple layers of epigenetic regulation.
With genome-wide and candidate based data she showed us that neither of these hypotheses is true. Imprinted genes as a class are neither more susceptible nor protected from expression changes, but a subset of imprinted genes may be involved in the adaptation of the conceptus. Imprints in the developing germline are not affected and imprinted genes are largely stable in the second generation. However, she proposed that the selective dosage modulation of certain imprimted genes plays an important role in the adaptive foetal response to in utero nutritional scarcity.
Our understanding of transgenerational epigenetic effects is emerging. This conference highlighted the complex mixture of mechanisms that are involved in different organisms. There are several well-studied examples of stable inherited epialleles in plans. Research in Caenorhabditis elegans also illustrated transgenerational epigenetic inheritance. The impact of the environment has been observed to extend over multiple generations in mammals, there is evidence for intergenerational inheritance, but the importance and underlying mechanism of transgenerational inheritance remains a fundamental question.
**EpiGenie would like to express our thanks to Anne Rochtus, who’s a PhD student Center for Molecular and Vascular Biology in Leuven, Belgium for covering this event for us.