Specific differentially methylated domain sequences direct the maintenance of methylation at imprinted genes

Landmark features of imprinted genes are differentially methylated domains (DMDs), in which one parental allele is methylated on CpG dinucleotides and the opposite allele is unmethylated. Genetic experiments in the mouse have shown that DMDs are required for the parent-specific expression of linked clusters of imprinted genes. To understand the mechanism whereby the differential methylation is established and maintained, we analyzed a series of transgenes containing DMD sequences and showed that imperfect tandem repeats from DMDs associated with the Snurf/Snrpn, Kcnq1, and Igf2r gene clusters govern transgene imprinting. For the Igf2r DMD the minimal imprinting signal is two unit copies of the tandem repeat. This imprinted transgene behaves identically to endogenous imprinted genes in Dnmt1o and Dnmt3L mutant mouse backgrounds. The primary function of the imprinting signal within the transgene DMD is to maintain, during embryogenesis and a critical period of genomic reprogramming, parent-specific DNA methylation states established in the germ line. This work advances our understanding of the imprinting mechanism by defining a genomic signal that dependably perpetuates an epigenetic state during postzygotic development.     

Genomic imprinting in mammals-epigenetic parental memories

Genomic imprinting is an epigenetic phenomenon that brings the difference of expression between paternally or maternally derived alleles and is specific for mammals in vertebrates. This imprint is established in the parental germlines and then inherited to the next generation to regulate expression of imprinted genes that are essential to support proper embryonic development. More than one hundred imprinted genes have been identified in mice and humans. Some are essential for embryonic development, especially placental formation, and others regulate metabolism, behavior and physiological functions. In humans, disruption of genomic imprinting causes several diseases, including cancer. Recently, the molecular mechanisms of genomic imprinting are getting clarified. How do parents regulate gene expression of their children? Why and how is genomic imprinting evolved in mammals? The review offers a handful of recent progress in this area.     

Parental genomic imprinting in plants: significance for reproduction

Parental genomic imprinting is an epigenetic phenomenon causing the expression of a gene from one of the two parental alleles. Imprinting has been identified in plants and mammals. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin dependent expression of imprinted genes. We review the mechanisms and functions of imprinting in plants. We further describe the significance of imprinting for reproduction and discuss potential models for its evolution.     

Convergent evolution of genomic imprinting in plants and mammals

Parental genomic imprinting is characterized by the expression of a selected panel of genes from one of the two parental alleles. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin-dependent expression of imprinted genes. Because similar epigenetic marks have been recruited independently in plants and mammals, the only organisms in which imprinted gene loci have been identified so far, this phenomenon represents a case for convergent evolution. Here we discuss the emerging parallels in imprinting in both taxa. We also describe the significance of imprinting for reproduction and discuss potential models for its evolution.     

A maternal-offspring coadaptation theory for the evolution of genomic imprinting

Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother–offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but a prevailing view has emerged that holds that genomic imprinting is a consequence of conflict between maternal and paternal gene copies over maternal investment. However, many imprinting patterns and the apparent overabundance of maternally expressed genes remain unexplained and may be incompatible with current theory. Here we demonstrate that sole expression of maternal gene copies is favored by natural selection because it increases the adaptive integration of offspring and maternal genomes, leading to higher offspring fitness. This novel coadaptation theory for the evolution of genomic imprinting is consistent with results of recent studies on epigenetic effects, and it provides a testable hypothesis for the origin of previously unexplained major imprinting patterns across different taxa. In conjunction with existing hypotheses, our results suggest that imprinting may have evolved due to different selective pressures at different loci.     

A Maternal–Offspring Coadaptation Theory for the Evolution of Genomic Imprinting

Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother–offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but a prevailing view has emerged that holds that genomic imprinting is a consequence of conflict between maternal and paternal gene copies over maternal investment. However, many imprinting patterns and the apparent overabundance of maternally expressed genes remain unexplained and may be incompatible with current theory. Here we demonstrate that sole expression of maternal gene copies is favored by natural selection because it increases the adaptive integration of offspring and maternal genomes, leading to higher offspring fitness. This novel coadaptation theory for the evolution of genomic imprinting is consistent with results of recent studies on epigenetic effects, and it provides a testable hypothesis for the origin of previously unexplained major imprinting patterns across different taxa. In conjunction with existing hypotheses, our results suggest that imprinting may have evolved due to different selective pressures at different loci.     

印记基因DLK1的研究进展

在哺乳动物中,有一部分特别的基因,它们由于受到印迹而只表达单一亲本的基因,这种表观遗传的修饰现象就是基因组印记,这有别于经典的孟德尔遗传学定律。DNA甲基化是一种重要的表观遗传修饰,主要的修饰部位发生在DNA的CpG岛。它参与了细胞分化,基因组稳定性、基因印记等多种细胞生物学过程,基因印迹的建立和维持是胚胎正常发育的基础,这一过程的实现有赖于各种DNA甲基化转移酶的精确表达和密切的配合。已发现在哺乳动物的基因组中存在着许多的印记基因,DLK1基因为父系表达母源沉默的印记基因,它的表达同样受到DNA甲基化的调节,它首先在神经母细胞瘤发现并克隆,定位于人类染色体14q32,属于表皮生长因子样超家族的成员之一,约有6个外显子。研究表明,DLK1基因在胚胎肝、早期肌肉组织以及造血干细胞等组织中均有表达,人DLK1基因全长1557bp,编码序列含有1152核苷酸,编码383个氨基酸残基,在人、小鼠、绵羊都存在保守序列,它参与多种细胞的增殖、分化并且与相关肿瘤的发生发展有着密切的关系,印迹基因的印迹异常与肿瘤的易感性及发生发展有重要的关系,本文就国内外DLK1基因的研究进展做一综述。     

印记基因DLK1的研究进展

在哺乳动物中,有一部分特别的基因,它们由于受到印迹而只表达单一亲本的基因,这种表观遗传的修饰现象就是基因组印记,这有别于经典的孟德尔遗传学定律。DNA甲基化是一种重要的表观遗传修饰,主要的修饰部位发生在DNA的CpG岛,它参与了细胞分化,基因组稳定性、基因印记等多种细胞生物学过程,基因印迹的建立和维持是胚胎正常发育的基础,这一过程的实现有赖于各种DNA甲基化转移酶的精确表达和密切的配合。已发现在哺乳动物的基因组中存在着许多的印记基因,DLK1基因为父系表达母源沉默的印记基因,它的表达同样受到DNA甲基化的调节,它首先在神经母细胞瘤发现并克隆,定位于人类染色体14q32,属于表皮生长因子样超家族的成员之一,约有6个外显子。研究表明,DLK1基因在胚胎肝、早期肌肉组织以及造血干细胞等组织中均有表达,人DLK1基因全长1557bp,编码序列含有1152核苷酸,编码383个氨基酸残基,在人、小鼠、绵羊都存在保守序列,它参与多种细胞的增殖、分化并且与相关肿瘤的发生发展有着密切的关系,印迹基因的印迹异常与肿瘤的易感性及发生发展有重要的关系,本文就国内外DLK1基因的研究进展做一综述。     

A DNA methylation imprint, determined by the sex of the parent, distinguishes the angelman and Prader-Willi syndromes

The Angelman (AS) and Prader-Willi (PWS) syndromes are two clinically distinct disorders that are caused by a differential parental origin of chromosome 15q11-q13 deletions. Both also can result from uniparental disomy (the inheritance of both copies of chromosome 15 from only one parent). Loss of the paternal copy of 15q11-q13, whether by deletion or maternal uniparental disomy, leads to PWS, whereas a maternal deletion or paternal uniparental disomy leads to AS. The differential modification in expression of certain mammalian genes dependent upon parental origin is known as genomic imprinting, and AS and PWS represent the best examples of this phenomenon in humans. Although the molecular mechanisms of genomic imprinting are unknown, DNA methylation has been postulated to play a role in the imprinting process. Using restriction digests with the methyl-sensitive enzymes HpaII and HhaI and probing Southern blots with several genomic and cDNA probes, we have systematically scanned segments of 15q11-q13 for DNA methylation differences between patients with PWS (20 deletion, 20 uniparental disomy) and those with AS (26 deletion, 1 uniparental disomy). The highly evolutionarily conserved cDNA, DN34, identifies distinct differences in DNA methylation of the parental alleles at the D15S9 locus. Thus, DNA methylation may be used as a reliable, postnatal diagnostic tool in these syndromes. Furthermore, our findings demonstrate the first known epigenetic event, dependent on the sex of the parent, for a locus within 15q11-q13. We propose that expression of the gene detected by DN34 is regulated by genomic imprinting and, therefore, that it is a candidate gene for PWS and/or AS.     

Genomic imprinting and epigenetic reprogramming: unearthing the garden of forking paths

Genomic imprinting, an epigenetic form of gene regulation, determines the parent-dependent gene expression of marked or imprinted genes during gametogenesis and embryonic development. Imprinting involves differential allele DNA methylation in one sex cell lineage but not in the other. Egg and sperm each contributes the same DNA sequences to the zygote but epigenetic imprinting of a subset of genes determines that only one of the parent alleles are expressed relative to the parental origin. Primordial germ cells inherit biallelically imprinted genes from maternal and paternal origin and erase their imprints to start de novo monoallelic imprinting during gametogenesis. Epigenetic paternalization is an ongoing process in the mitotically-dividing spermatogonial stem cell and derived meiotically-dividing spermatocyte progeny to endow sperm with imprinted alleles. Epigenetic maternalization is restricted to the oocyte growth phase of folliculogenesis and is unrelated to DNA replication since it takes place while the oocyte remains in the diplotene stage of meiotic prophase I. Sperm and oocyte genomic methylation patterns depend on the activity of DNA methyltransferases (Dnmt). A variant of Dnmt1, designated Dnmt1o, accumulates in oocyte nuclei during the follicular growth phase. Dnmt3L, an isoform of Dnmt3a and Dnmt3b, but lacking enzymatic activity, interacts with Dnmt2a and Dnmt3b and is required for spermatogenesis. In the mouse early zygote, the male pronucleus is demethylated within 4 h of fertilization. Global demethylation takes place gradually up to the morula stage. In the blastocyst, de novo methylation is reestablished in the inner cell mass but not in the trophectoderm. Both the significance of genomic imprinting and the severe developmental defects caused by disrupted Dnmt activity, point to a need for a better understanding of the causes of low cloning efficiency by somatic nuclear transfer to enucleated ovulated oocyte.     

Conflict theory of genomic imprinting in mammals

In mammals, some embryonic genes are expressed differently depending on whether they are inherited from the sperm or egg, a phenomenon known as genomic imprinting. The information on the parental origin is transmitted by an epigenetic mark. Both the molecular mechanisms and evolutionary processes of genomic imprinting have been studied extensively. Here, I illustrate the simplest evolutionary dynamics of imprinting evolution based on the “conflict theory,” by considering the evolution of a gene encoding an embryonic growth factor controlling the maternal resource supply. It demonstrates that (a) the autosomal genes controlling placenta development to modify maternal resource acquisition may evolve a strong asymmetry of gene expression, provided the mother has some chance of accepting multiple males. (b) The genomic imprinting may not evolve if there is a small fraction of recessive deleterious mutations on the gene. (c) The growth-enhancing genes should evolve to paternally expressed, while the growth-suppressing genes should evolve to maternally expressed. (d) The X-linked genes also evolve genomic imprinting, but the main evolutionary force is the sex difference in the optimal embryonic size. I discuss other aberrations that can be explained by the modified versions of the basic model.     

Etablissement de l’empreinte parentale dans la lignée germinale. Conséquences pour la prise en charge en AMP

Genomic imprinting is an epigenetic phenomenon in eutherian mammals that results in the differential expression of the paternally and maternally inherited alleles of a gene. Imprinted genes are necessary for normal mammalian development. Parental specific epigenetic modifications are imprinted on a subset of genes in the mammalian genome during germ cell maturation. Imprinting involves both cytosine methylation within CpG islands and changes in chromatin structure. All such epigenetic modifications are potentially reversible and can be erased. After the erasure step, new parental imprints are initiated, resulting in reintroduction of sex-specific imprints in the male and female germ line. Although the function of genomic imprinting is not clear, it has been proposed that it evolved in mammals to regulate intrauterine growth and mammalian development. If the epigenotype of individual gametes is directly correlated with their later developmental capacities, genomic imprinting would have important practical implications in reproductive medicine for the use of embryos derived from assisted reproduction.     

基因组印记研究进展

基因组印记是由于父源或母源的等位基因受到“标记”而发生的不符合孟德尔遗传定律的特殊遗传现象。父源或母源的等位基因通过某种特异的基因修饰机制,如DNA甲基化,非编码RNA的调节作用和组蛋白修饰等,抑制另一拷贝的表达。哺乳动物中的基因印记影响着其生长发育,正常印记模式的改变在临床上会引起许多疾病。文章总结了自印记现象被发现后二十几年来的研究进展,包括印记的发生机制、发生途径、进化方式和起源理论。目前对基因印记的了解还不完全,后基因组技术的发展也许能够促进对其分子机制的进一步揭示。     

Genomic imprinting: parental influence on the genome

Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions--imprints--that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various disease syndromes. The study of imprinting also provides new insights into epigenetic gene modification during development.     

基因组印记与疾病研究进展

基因组印记是一种特别的非孟德尔遗传现象,即来自双亲的等位基因在子代中的差异性表达,是遗传后的基因调控方式,主要与基因组甲基化模式有关,包括去甲基化、重新甲基化及甲基化维持三个过程。印记基因主要通过对启动子、边界元件及非编码RNA的作用来调控基因表达。基因组印记异常与一些先天性疾病相关,也与肿瘤发生和易感性有关,     

Genomic imprinting in plants

Genomic imprinting attracted particular attention in the 1980’s following the discovery that the parental origin of genetic information is essential for normal development of eutherians,1,2 for review see.3 The term imprinting was first introduced in the 1960s to describe the elimination of the paternal chromosomes during spermatogenesis in the Sciarid fly.4?6Today the term genomic imprinting mainly refers to parent?of?origin specific effects distinguishing each parental genome which can be regarded as memories, or “imprints”.7,8 Breaking the rules of Mendel, genomic imprinting is an epigenetic phenomenon per se. Epigenetics is currently defined as the study of mitotically or meiotically heritable changes in gene expression without any change in DNA sequence9,10 and it is intimately linked to the study of inheritance of chromatin states.11 Gene imprinting currently refers to differential expression of autosomal genes according to their parent of origin.12The phenomenon of genomic imprinting explains several cases of parent?specific human disorders.13 To date over 80 imprinted genes have been described in mammals14 and their parent?of?origin specific expression can correlate with changes in DNA methylation patterns, antisense noncoding RNAs and chromatin folding.3 Epigenetic imprints can either activate or silence the “imprinted” allele, and hence imprinting can be associated with either an expressed or silenced allele.15 In mammals, the number of paternally expressed imprinted genes is almost equivalent to the number of maternally expressed genes and the imprinted status can differs according to tissue, developmental stage and species. It is then crucial for our understanding to clearly indicate the status of imprinting (i.e., paternally or maternally expressed) and the context (e.g., species, developmental stage, tissue).