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From Genotype to Phenotype. What Do Epigenetics and Epigenomics Tell Us&Quest Heredity (2010) 105, 1–3 & 2010 Macmillan Publishers Limited All rights reserved 0018-067X/10 $32.00 www.nature.com/hdy EDITORIAL From genotype to phenotype. What do epigenetics and epigenomics tell us? Heredity (2010) 105, 1–3; doi:10.1038/hdy.2010.66 (H3K9me3) by histone methyltransferase and hetero- chromatin protein 1. Epigenetic differences within High-throughput sequencing is becoming quicker and natural populations and between various ecotypes have increasingly affordable, and as a result there has been a been linked to variation in DNA methylation (Johannes et al., 2009) and even seem to be directed by small dramatic increase in the number of species of which the interfering RNAs that match to specific genomic regions genomes have been sequenced. This is yielding large (Zhai et al., 2008). Several hundred regions of the DNA of amounts of genomic information that can be used to mammalian genomes have been found to be differen- tackle many questions in genetics and genomics from a tially methylated, with their methylated status depend- comparative perspective: the structure and composition ing on cis-acting factors (Schilling et al., 2009), suggesting of genomes in relation to the environment, how specia- that they may influence the overall phenotype. Indeed, it tion occurs, the processes of domestication, responses to has been clearly shown that deficiencies in DNA stress and so on. However, although classical genetic methylation are deleterious and usually lead to early analyses and the ‘omic’ technologies (transcriptomic, embryo mortality, and that any surviving unmethylated proteomic, metabolomic and so on) will continue to mutants exhibit developmental aberrations of progres- provide important information, new and unexpected sive severity (Mathieu et al., 2007). This indicates that any information may also result from studying epigenetic mutation that leads to the misexpression of genes processes (DNA methylation, histone modifications, involved in epigenetic control will have a major effect RNA interference), which do not change the sequence throughout development and may even lead to the onset of the DNA itself, but modify the way genes are of diseases in adulthood, including some tumors. expressed during development. Analyzing the large For epigenetics to have an important role in popula- amount of data available about epigenomes (genome- tions, epigenetic marks and epigenetic alterations need to wide profiling of DNA methylation and histone mod- be handed down from parents to offspring, and so ifications) is a major challenge involving biologists, transmitted down the generations. In mammals, most bioinformatics specialists and computer biologists, epigenetic marks are erased between generations, but because there is increasing evidence of differences in epigenetic reprogramming occurs early in embryogen- epigenetic patterns between individuals (Lister et al., esis, and it is now clear that this erasure is incomplete. 2009), and even between different tissues and cell types. A good example of epigenetic transmission during Recent research into the contribution of epigenetics to the development and across generations is that of the differential regulation of gene expression, imprinting ‘imprinted genes’. The expression of these genes de- (differential gene expression depending on the parent-of- pends on their parent-of-origin and they produce their origin), gene silencing and the involvement of transpo- effects during embryonic development or later on in sable elements (TEs) in these processes, have all shed development. The mechanisms involved in this imprint- fresh light on the relationships between genotype and ing phenomenon and its evolution are reviewed by phenotype. In this special issue, we provide a selection of Hudson, Kulinski, Huetter and Barlow in the mouse and reviews that covers epigenetic processes occurring at by Koehler and Weinhofer-Molisch in plants. The parent- several different levels and in various organisms. of-origin expression of the imprinting genes is regulated DNA methylation is an epigenetic mark that is often by specific regions known as imprinting control regions associated with histone modifications (methylation, (ICRs). These ICRs acquire their DNA methylation acetylation, phosphorylation and so on), chromatin pattern in the male germline, and the paternal imprint conformation and RNA interference, all of which are is protected against demethylation in the paternal processes that regulate gene transcription during em- genome of the zygote. The methylated imprint is thus bryonic and subsequent development. Gibney and Nolan maintained throughout development (Kacem and Feil, review the overall role of epigenetics in influencing gene 2009) in the somatic cell lineage. One important expression during differentiation and development; characteristic of ICRs is that maternally methylated ICRs Teixeira and Colot then summarize the effects of DNA can exert promoter activity on the paternal allele and methylation in plants, in which cytosines are methylated sometimes silence it. This kind of interallelic talk in all sequence contexts, whereas in animals it is mostly resembles the paramutations that have been reported in CGs that are methylated (Feng et al., 2010; Law and plants and in the mouse, in which the two parent-of- Jacobsen, 2010); Dambacher, Hahn and Schotta present origin alleles can influence each other’s expression. cutting-edge research about the part played by histone These epigenetic modifications are also known to be lysine methylation in regulating development, and transmitted to the offspring. Misexpression of imprinted Rountree and Selker review the impact of DNA genes has been shown to be associated with early methylation on the formation of heterochromatin in embryonic lethality and post-natal development in Neurospora crassa, revealing the close interrelationships mammals, and has recently also been identified in plants that exist between the methylation of histone H3 lysine 9 (Bayer et al., 2009). Around 100 imprinted genes Editorial 2 clustered in 25 genomic regions, have been identified in elements and the specification of chromosomal domains, mice and humans. Hudson, Kulinski, Huetter and the review focuses mainly on the less obvious effects of Barlow show that the different patterns of imprinted ATP-dependent nucleosome remodeling enzymes. These gene expression observed in embryonic tissues and extra- enzymes have been shown to disrupt the ionic associa- embryonic tissues, such as the placenta in mammals, can be tion of DNA with histones in nucleosomes or nucleo- explained by differences in DNA methylation and repres- some assembly intermediates and to endow chromatin sive histone modifications. They conclude that genes with flexibility, allowing it to respond to environmental displaying imprinted expression only in extra-embryonic clues. Finding out how an organism integrates such tissues may be regulated by different epigenetic mechan- chromatin changes into its development promises to yield isms than genes with widespread expression. As Koehler new insights into genotype–environment interactions. and Weinhofer-Molisch describe, plants are known to One important clue to the nature of epigenetic display genomic imprinting in the endosperm, which is phenomena is that they seem to involve TEs. Indeed, not restricted to this tissue but extends to tissues that imprinted genes often contain repeated sequences, such contribute to the next generation. The authors then as TEs, and by recruiting the epigenetic machinery, these summarize the roles of histone methylation and of the sequences could mark the ICRs defined above, thus polycomb group proteins. They suggest mechanisms that determining the epigenetic status of the affected alleles. could explain how epigenetic marks are reprogrammed in Moreover, epigenetic processes involving DNA methyla- gametes. Although this discussion clearly shows that tion–demethylation, histone modifications and RNA imprinted genes have an important role in the develop- interference, are all known to influence the expression mental process, recent studies have also reported differ- of various TEs during development. Because TEs are ential DNA methylation between alleles at nonimprinted known to be able to activate–deactivate various genes loci in human autosomes, which seems to involve about and to regulate host genes differentially during embryo- 10% of all genes (Schilling et al., 2009; Zhang et al., 2009). nic development, as reported in the mouse (Peaston et al., Understanding the exact role of these genes is likely to be 2004), many changes in individual phenotypes are of the utmost relevance for our understanding of how expected. This is consistent with reports that epigenetic genomes are regulated. processes, which often involve the decrease in DNA It is well known that early in female development, in methylation 1 (DDM1) chromatin remodeling protein mammals, one of the two X chromosomes is transcription- that controls TE expression, may contribute to loss of ally silenced, which compensates for the unequal copy fitness in Arabidopsis and to meiotic failure in mouse number of X-linked genes in males and females. Leeb and spermatocytes. It is thus believed that organisms have Wutz summarize the mechanistic concepts in X inactivation developed defense mechanisms, mostly based on inter- that underlie this dosage compensation in mammals. fering RNAs as discussed by Teixeira and Colot, Random X inactivation depends on the noncoding Xist intended to
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