INSIGHT REVIEW NATURE Vol 447 24 May 2007 fertilization, the repressive epigenetic marks might need to be removed involve pre-existing histone marks". After fertilization, the methylation for transcriptional activation of these genes and correct early lineage of imprinted-gene DMRs is maintained by DNmTlo( the oocyte form development to take place(discussed later) of DNMTI) for one division cycle during very early pre-implantation developmentand then by DNMTls(the somatic form of DNMTI)in Stability for transposon silencing and imprinting embryonic and adult tissues In contrast to developmental genes, which need to be epigenetically Imprinted genes can be directly silenced by methylation of DMrs gulated with flexibility, transposons(if possible)need to be silenced (which often contain CpG islands )that overlap the promoter. More fre- rent them from moving around in the genome and potentially causing a single dMr that is methylated in the germ line and is responsible for utations". Therefore, many transposon families are both methyl- regulating gene silencing in the rest of the cluster. So far, there are two ted themselves and marked by repressive histone modifications distinct models for how, after fertilization, imprinted genes are silenced uch as H3K9 methylation), and these marks are important for the through the action of nearby unmethylated DMRs. First, the DRover heritable silencing of transposons. Some transposon families(such as laps the promoter of a long, non-coding, unspliced, nuclear RNA ntracisternal A particles; IAPs)are also resistant to the erasure of Dna The presence of the unmethylated and expressed copy of the non-coding methylation in the zygote and in PGCs, possibly resulting in epigenetic RNA results in the silencing of linked genes, a process that involves inheritance across generations(discussed later) repressive histone modifications. It is unclear how the presence of the Imprinted genes are a class of mammalian genes with possible non-coding RNA leads to gene silencing in cis. In one model, repressive mechanistic relationships to transposons in that CpG islands in their complexes(for example, PRCs)might be targeted during transcription promoters become methylated and in that silencing relies on long- Alternatively, the RNA might coat the region to be inactivated, sim term epigenetic stability In imprinted genes(and transposons), DNA larly to how Xist RNA(inactive X-specific transcripts)coats the inactive methylation is introduced during either oogenesis or spermatogenesis, Xchromosome. This might establish a physical structure from which by the de novo methyltransferase DNA methyltransferase 3A(DNMT3A) RNA polymerase II( Pol II)is excluded, resulting in transcriptional and its cofactor DNMT3-like(DNMT3L)(Fig 3a). How particular silencing(Fig. 3b). In one case of silencing mediated by an imprinted imprinted genes are selected for de novo methylation during oogenesis non-coding RNA, the developmental kinetics of inactivation are mark or spermatogenesis is not understood, although this targeting could edly similar to those of imprinted X-chromosome inactivation. Both a Acquisition of dna methylation in germ cells Immature gamete DNMT b Silencing of the X chromosome and im Embryonic lineage d methyltransferase? Differentiated 想8 Extra-embryonic lineage Figure 3 Developmental regulation of imprinting and X-chromosome adjacent genes as a consequence of the physical exclusion of pol ll and the inactivation. a, During germ-cell development, selected imprinted genes acquisition of histone modifications and/or DNA methylation, depending and transposons become methylated. This process depends on de novo the embryonic lineage. DNA methylation stabilizes gene silencing methyltransferases such as DNMT3A and its cofactor DNMT3L. It in embryonic tissues but is less important in extra-embryonic tissues, is possible that the targeting of DNA methylation requires arginine where PRC-mediated silencing might predominate. This mechanism of arried out by PRMT7. Mature male germ cells postzygotic gene silencing occurs in X-chromosome inactivation and in have chromatin that is largely based on non-histone proteins known as some forms of autosomal gene imprinting H3K9 methylation is shown tamines(dark pink); this alters the packaging of the DNA. b, Expression in green, H3K27 methylation in yellow, histone arginine methylation in of non-coding RNAs(wavy blackline) in cis can result in the silencing of pink and DNA methylation in red. 28 @2007 Nature Publishing Groupfertilization, the repressive epigenetic marks might need to be removed for transcriptional activation of these genes and correct early lineage development to take place (discussed later). Stability for transposon silencing and imprinting In contrast to developmental genes, which need to be epigenetically regulated with flexibility, transposons (if possible) need to be silenced completely and stably (at least from the perspective of the host) to pre￾vent them from moving around in the genome and potentially causing mutations22. Therefore, many transposon families are both methyl￾ated themselves and marked by repressive histone modifications (such as H3K9 methylation), and these marks are important for the heritable silencing of transposons. Some transposon families (such as intracisternal A particles; IAPs) are also resistant to the erasure of DNA methylation in the zygote and in PGCs, possibly resulting in epigenetic inheritance across generations (discussed later). Imprinted genes are a class of mammalian genes with possible mechanistic relationships to transposons23, in that CpG islands in their promoters become methylated and in that silencing relies on long￾term epigenetic stability. In imprinted genes (and transposons), DNA methylation is introduced during either oogenesis or spermatogenesis, by the de novo methyltransferase DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3-like DNMT3L)24,25 (Fig. 3a). How particular imprinted genes are selected for de novo methylation during oogenesis or spermatogenesis is not understood, although this targeting could involve pre-existing histone marks26. After fertilization, the methylation of imprinted-gene DMRs is maintained by DNMT1o (the oocyte form of DNMT1) for one division cycle during very early pre-implantation development27 and then by DNMT1s (the somatic form of DNMT1) in embryonic and adult tissues28. Imprinted genes can be directly silenced by methylation of DMRs (which often containCpG islands) that overlap the promoter. More fre￾quently, however, imprinted genes occur in clusters, and there is usually a single DMR that is methylated in the germ line and is responsible for regulating gene silencing in the rest of the cluster. So far, there are two distinct models for how, after fertilization, imprinted genes are silenced through the action of nearby unmethylated DMRs. First, the DMR over￾laps the promoter of a long, non-coding, unspliced, nuclear RNA29,30. The presence of the unmethylated and expressed copy of the non-coding RNA results in the silencing of linked genes, a process that involves repressive histone modifications31,32. It is unclear how the presence of the non-coding RNA leads to gene silencing in cis. In one model, repressive complexes (for example, PRCs) might be targeted during transcription33. Alternatively, the RNA might ‘coat’ the region to be inactivated, simi￾larly to how Xist RNA (inactive X-specific transcripts) coats the inactive X chromosome31,34. This might establish a physical structure from which RNA polymerase II (Pol II) is excluded, resulting in transcriptional silencing35 (Fig. 3b). In one case of silencing mediated by an imprinted non-coding RNA, the developmental kinetics of inactivation are mark￾edly similar to those of imprinted X-chromosome inactivation. Both Acquisition of DNA methylation in germ cells Silencing of the X chromosome and imprinted genes a b Immature gamete Mature gamete DNMT DNMT Histone methyltransferase? Pluripotent cell PRC Differentiated cells Embryonic lineage Extra-embryonic lineage PRMT7? Pol II Pol II Pol II Figure 3 | Developmental regulation of imprinting and X-chromosome inactivation. a, During germ-cell development, selected imprinted genes and transposons become methylated. This process depends on de novo methyltransferases such as DNMT3A and its cofactor DNMT3L. It is possible that the targeting of DNA methylation requires arginine methylation of histones, carried out by PRMT7. Mature male germ cells have chromatin that is largely based on non-histone proteins known as protamines (dark pink); this alters the packaging of the DNA. b, Expression of non-coding RNAs (wavy black line) in cis can result in the silencing of adjacent genes as a consequence of the physical exclusion of Pol II and the acquisition of histone modifications and/or DNA methylation, depending on the embryonic lineage. DNA methylation stabilizes gene silencing in embryonic tissues but is less important in extra-embryonic tissues, where PRC-mediated silencing might predominate. This mechanism of postzygotic gene silencing occurs in X-chromosome inactivation and in some forms of autosomal gene imprinting. H3K9 methylation is shown in green, H3K27 methylation in yellow, histone arginine methylation in pink and DNA methylation in red. 428 INSIGHT REVIEW NATURE|Vol 447|24 May 2007 ￾
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