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School of Biomedical and Clinical Laboratory Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
Correspondence should be addressed to N Spears; Email: Norah.Spears{at}ed.ac.uk
| Abstract |
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| What is genomic imprinting? |
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Within the mammalian genome, the majority of cytosine residues found as CpG dinucleotides (i.e. those cytosines positioned next to a guanine residue) have a methyl group added to their carbon 5 position (Costello & Plass 2001). It is this addition of the methyl group, referred to as DNA methylation, that is proposed as the key mechanism (certainly the best studied mechanism) regulating imprinting. It is important to point out, however, that the majority of methylated DNA in the genome is not concerned with genomic imprinting. Heavy methylation of DNA results in a more condensed structure which is resistant to transcription. Thus, if an animal inherits a methylated copy of a gene from its mother and a non-methylated copy from its father, the maternal copy will have its transcription repressed leaving the paternal copy as the only active gene. DNA methylation is an epigenetic modification which can be inherited in a stable manner but is also reversible, allowing gender specific patterns to be initiated in germ cells.
| Why did genomic imprinting evolve? |
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An alternative theory to account for the presence of imprinted genes within the genome is the evolvability model (Beaudet & Jiang 2002). This predicts that species which have genomic imprinting are more able to evolve in response to environmental pressures, as they can induce rapid changes by altering which of the two alleles is silenced and which is expressed. An individual organism can carry an allele which promotes growth that, while imprinted, has no phenotypic effects. Thus, if increased growth becomes advantageous, the relevant allele is already present in the gene pool: by rapid reversal of the imprinting, the allele can be expressed. There is also the ovarian time bomb concept which proposes that genomic imprinting evolved to protect the female from ovarian disease: Varmuza & Mann (1994) hypothesised that imprinting could limit the level of growth and development of any parthenogenetic embryos within the ovary, thereby preventing malignant trophoblast formation.
| How are DNA methylation patterns regulated? |
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Laying down of methylation patterns
To allow reprogramming of the germ cell, the genome must undergo demethylation (as described later). Once the initial imprints have been removed the appropriate new pattern must be established, thus ensuring that the paternal- and maternal-specific imprints are laid down in the sperm and oocyte respectively. The enzymes which are capable of laying down the new methyl groups onto previously unmethylated DNA are from the Dnmt3 family. Members of this family which have active transmethylase activity are Dnmt3a and Dnmt3b, which share a high degree of sequence homology but have been shown to have different expression patterns and timing through development. The third member of this family, Dnmt3l, shares sequence homology with the other enzymes but is missing the catalytic domain needed to add methyl groups onto DNA. After both examining the localisation of this protein and using mice with a disrupted Dnmt3l gene, a role in the establishment of maternal imprints in the oocyte has been hypothesised for this enzyme, as discussed below.
Maintenance of methylation
When a methyl group is added onto already hemi-methylated DNA during cell replication (necessary if the daughter cells are to maintain the methylation pattern of the cell undergoing mitosis), the process is termed maintenance methylation. Dnmt1 has the primary responsibility for maintaining the methylation status of DNA. The most common form of this methyltransferase is that found in all somatic cells, Dnmt1s, and has been shown to be vital for development. In addition, there are two splice variants identified which are specific to the germ cells and early embryo. Dnmt1p is found in pachytene spermatocytes whilst Dnmt1o is only identifiable in the oocyte and pre-implantation embryo. It is not until embryonic day 7 (E7) that the embryo is capable of producing full-length Dnmt1s protein.
Interestingly, although Dnmt1 has been identified as the main maintenance methylase in vivo, studies in vitro have shown that this enzyme has a higher de novo methylase activity than either Dnmt3a or Dnmt3b. In vivo, Dnmt1 de novo methylase activity has yet to be found, but the possible implications of this in vitro activity should be borne in mind (Howell et al. 2001).
How does methylation lead to repressed gene transcription?
There are two main mechanisms by which the methylation of DNA can prevent the transcription of genes. The first of these is by the methyl group causing direct interference preventing particular transcription factors from binding to methylated DNA (Iguchi-Ariga & Schaffner 1989). The second mechanism results from methyl-binding domain proteins (MBDs) binding to methylated DNA.
Of the MBDs identified to date, MBD1 to MBD3 and methyl CpG-binding protein 2 (MeCP2) are involved in transcriptional repression (Nan et al. 1997, Fujita et al. 1999, Ng et al. 1999), while MBD4 is thought to have a role as a mismatch repair protein (Hendrich et al. 1999). MBD1 and MeCP2 both contain transcriptional repression domains which act via histone deacetylases (HDACs). HDACs cause local deacetylation of the histone tails which, in turn, results in remodelling of the chromatin into a more condensed structure that is resistant to transcription (Taunton et al. 1996). MBD1 mediates transcriptional repression through recruitment of a histone methylase capable of binding HDACs (Ng et al. 2000, Fujita et al. 2003), while MeCP2 acts to bind a co-repressor complex containing an HDAC (Jones et al. 1998, Nan et al. 1998), although MeCP2 has also been shown to cause transcription repression in the absence of HDAC activity (Nan et al. 1998, Yu et al. 2000). MBD2 and MBD3 are both components of a large protein complex, MeCP1 (Feng & Zhang 2001). MeCP1 binds methylated DNA in a non-sequence-specific manner. The binding of MeCP1 to methylated DNA is due to the presence of MBD2 in the complex (Ng et al. 1999). Interestingly, the mammalian form of MBD3 appears not to bind directly to methylated DNA (Hendrich & Bird 1998). The MeCP1 complex binds methylated DNA less tightly than MeCP2, which suggests that long-term transcriptional repression may be maintained by the permanent binding of MeCP2, with more transient transcriptional silencing determined by the binding of the MeCP1 complex (Ng et al. 1999). In addition to the MBD family, there is a further binding protein termed Kaiso which is capable of methylation-dependent repression of gene transcription. Although it is not an MBD-containing protein, it is capable of binding to methylated DNA via its zinc finger (Prokhortchouk et al. 2001). Kaiso has been shown to be a vital component of amphibian development; blocking translation of this protein is lethal (Ruzof et al. 2004) but the extent of its role in mammalian systems has yet to be established. Methylation-dependent transcriptional repression is covered by many good reviews such as Wade (2001) and Li (2002).
Transgenic studies show that mice lacking MBD1 have no observable phenotype, although problems within the nervous system are evident at the molecular level (Zhao et al. 2003). Mbd2 knockout (KO) mice are also viable, although they exhibit impaired maternal behaviour (Hendrich et al. 2001). Mbd3 null mutations are embryo lethal (Hendrich et al. 2001). The abnormal phenotype of Mecp2 KO mice develops from several weeks of age and is lethal by 8 weeks of age, with all known abnormalities having their origin in the nervous system (Guy et al. 2001). The fact that Mbd1, Mbd2 and Mbd3 KO mice have no apparent phenotype outside of the nervous system suggests that there is a degree of redundancy within the MBD-mediated system of transcription control. Although a double KO of Mbd2 and Mecp2 has demonstrated that both these proteins function in separate pathways, this does not rule out co-operation between other members of the MBD family (Guy et al. 2001).
| Genomic imprinting in germ cells and embryos |
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| Oocyte development |
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| Sperm development |
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The resumption of mitotic division of male germ cells at puberty coincides with an increase in the level of Dnmt1 within the spermatocytes. During the early stages of meiosis the level of Dnmt1s in spermatocytes is high but a reduction in the level of the Dnmt1 enzyme has been observed in pachytene stage spermatocytes (Jue et al. 1995). This is due to the expression of an alternatively spliced version, Dnmt1p, which does not appear to be translated. Although Dnmt1s within the sperm is normally found in both the nucleus and the cytoplasm, it is concentrated at nuclear foci during some stages of meiosis and it may be that this correlates with the laying down of paternal imprints (Jue et al. 1995). Dnmt3l is expressed in the murine testes from E12.5 in non-dividing prospermatogonia with peak expression seen at the time of birth, after which there is a dramatic postnatal reduction in expression level (Bourchis & Bestor 2004, La Salle et al. 2004). Dnmt3a expression in the testis is raised before birth and during early postnatal life, in contrast to the level of Dnmt3b expression which is lower during embryonic life and rises postnatally (La Salle et al. 2004). Mice lacking Dnmt3l have smaller testes, and by adulthood there are virtually no spermatozoa present, resulting in sterile animals (Hata et al. 2002). Dnmt3l is required if normal meiosis and silencing of retrotransposons is to occur (Bourchis & Bestor 2004). The loss of Dnmt3a results in a similar although less extreme phenotype than that seen in the Dnmt3l KO mouse (Hata et al. 2002). More recently, the male Dnmt3a conditional KO was created, with no germ cell Dnmt3a expression but with somatic cell levels maintained (Kaneda et al. 2004). Spermatogenesis is severely impaired in these mice so that by 11 weeks of age there are no spermatozoa in the testis, demonstrating a vital role for Dnmt3a in this process. Offspring from these conditional KO males have errors in the methylation of some paternally imprinted genes.
| Fertilisation and early embryo development |
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In some species (such as the mouse), the paternal genome is actively demethylated immediately after fertilisation (Oswald et al. 2000). The occurrence and degree of this demethylation appears to be species specific, and its regulation is currently unknown. Cross-fertilisation using gametes from several species of animal has shown that, although there are sperm characteristics which affect the degree of demethylation, the main factor determining whether the paternal genome becomes demethylated is oocyte specific (Beaujean et al. 2004). In the search for the factor responsible for this post-fertilisation active demethylation, MBD2 was proposed as a candidate after an in vitro study by Bhattacharya et al.(1999). However, a subsequent study utilising MBD2 / oocytes has found that the rapid demethylation of the paternal genome still occurs in its absence (although this result does not eliminate the possibility of redundancy; Santos et al. 2002). The maternal genome undergoes passive demethylation which is slower to occur and is linked to the replication of DNA in the absence of any maintenance methylase activity. Although the general trend after fertilisation is for non-imprinted sequences to undergo demethylation, there does appear to be some specific incidences of de novo methylation such as the DMRs of the Dnmt1o gene in the one-cell to blastocyst stage embryo (Ko et al. 2005).
Dnmt1o remains localised to the cytoplasm of the embryonic cells at all pre-implantation stages with the exception of the eight-cell embryo. During this stage, the protein has been shown to translocate to the nuclei, where it is thought to play a role in maintaining the methylation level of imprinted genes. Dnmt3a is expressed by pre-implantation embryos and there is no evidence of the protein being excluded from the nucleus at any developmental stage (Ko et al. 2005). Although Dnmt3b is not transcribed in the pre-implantation embryo the protein is present at all stages from the one-cell to the blastocyst stage; while mainly localised to the cytoplasm, it is not fully excluded from the nucleus (Ko et al. 2005).
Until recently, embryos which consisted of two maternal or two paternal genomes were unable to develop to term. Work examining the competence of parthenogenetic embryos found they were able to develop at best until E9.5. By creating an embryo with one set of chromosomes from a fully grown and the other from a non-growing oocyte, Kono et al.(1996) showed that embryo development could be extended to E13.5. It was thought that this increase in the length of time the embryo survived was due to the ability of the non-growing oocyte chromosomes (with, therefore, no female imprints yet laid down) to partially compensate for the lack of a paternally imprinted set of chromosomes. Parthenotes which died at E9.5 and E13.5 had incorrect biallelic expression of the normally monoallelic H19 gene. The most recent work by Kono et al.(2004) has resulted in the birth and survival of a viable parthenote. This was achieved using non-growing oocytes from a transgenic mouse with a 13 kb deletion of H19. The mouse had H19 expression consistent with that normally seen from the paternal genome. As H19 in turn influences the expression of the imprinted Igf2 gene, the embryo had monoallelic expression of both H19 and Igf2 (from the wild-type fully grown oocytes only), as would be the case in normal embryos. The fact that normal embryo development is possible after the female genome is altered to more closely resemble the genomic imprinting pattern of the male genome demonstrates the importance of this mechanism in controlling development, reinforcing the idea that the presence of mammalian genomic imprinting might act as a barrier to parthenogenesis (see above).
| Errors in genomic imprinting |
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The cause of the link between ARTs and imprinting disorders is currently unknown. It could be due to some aspect of the ARTs involved. There is a wide range of different ARTs which are now routinely used within clinics. Techniques might expose one or both of the germ cells to an altered hormonal regime in vivo, a period of time in culture or mechanical manipulation. Any such alterations to the normal environment of the oocyte or sperm could result in changes to some aspect of their imprinting mechanisms. Alternatively, it could be due to some error within the germ cells used, bearing in mind that couples seeking to use ARTs have reduced natural fertility.
The potential problems do not end with the germ cells; the pre-implantation embryo is also often exposed to a period of culture which could again alter the epigenetic reprogramming known to occur at these early stages. One such example is abnormal biallelic H19 expression of mouse embryos cultured in Whittens media (Doherty et al. 2000). It is not just in humans and mice that potential problems with imprinting have been seen. In large domestic mammals such as sheep and cattle, large offspring syndrome (LOS) was identified when embryos had been exposed to some time in culture (Young et al. 1998). Further investigations into LOS in sheep have identified changes in the expression level of the imprinted gene, IGF2R, due to epigenetic changes (Young et al. 2001). Similar overgrowth problems seen in mice and humans are often caused by errors in several imprinted genes including Igf2 and H19 (Eggenschwiler et al. 1997), suggesting that other genes responsible for fetal growth and development could be involved in LOS.
If sperm used for in vitro fertilisation have lowered global methylation levels there is no alteration in either fertilisation rate or in early embryo quality; however, there is a reduction in pregnancy rate, demonstrating the importance of normal gamete DNA methylation on embryo development and ultimately ART outcome (Benchaib et al. 2005). There is recent evidence that sperm obtained from males with low sperm counts due to abnormal spermatogenesis have incorrect genomic imprinting (Marques et al. 2004), although such sperm can then be used, for example, in ICSI. Marques et al.(2004) found that, although the maternal imprints had been erased from all sperm, the paternally methylated H19 gene was under-methylated in some sperm from the oligozoospermia donors. Any embryo derived from one of these hypomethylated sperm could have inappropriate expression of the imprinted H19 and IGF2 genes, the effect of which is not known.
Cloning
Studies investigating the failure of cloned animals have also turned their attention to the role of genomic imprinting. The fact that many of the errors seen in cloned animals have epigenetic causes has been demonstrated by examining the offspring of cloned mice. These cloned mice were obese but this trait was not passed onto the offspring, demonstrating that this was not a genetic error but due to epigenetics. This finding is important as it suggests that, despite any problem in the cloned animals, it is possible that their germ cells are able to correctly undergo genomic imprint reprogramming (Tamashiro et al. 2002). In bovine cloned embryos, it has been found that the levels of methylation in the cells of the embryo are higher than normal at the four-cell and eight-cell stages. Although there is initial demethylation of the donor genome, passive demethylation does not occur to the level seen in normal embryos. In addition to a reduction in the amount of demethylation, there also appears to be inappropriate de novo methylation occurring at early stages of embryo development (Dean et al. 2001). It is also possible that errors in the Dnmt enzymes normally present in the early embryo could account for alterations in methylation seen in these embryos. Analysis of cloned mouse embryos shows inappropriate presence of Dnmt1s within the pre-implantation embryo; this transcript of Dnmt1 is never present in normal embryos. It was also observed that at the eight-cell stage, when Dnmt1o would normally translocate into the nuclei of embryonic cells, some nuclei within each embryo were devoid of any Dnmt1 transcript, suggesting that these cells are unable to maintain normal methylation patterns (Chung et al. 2003).
Disease
In some cases, imprinting errors can occur which, although not embryo lethal, cause abnormal physiological processes and lead to disease. Such diseases can arise when any imprinted gene becomes hypermethylated or hypomethylated. Effects are not always limited to the loss of function of a single gene, as some imprinted genes affect the expression of other genes, such as H19 and IGF2. The linked PraderWilli syndrome (PWS) and AS are examples of disorders that can occur when correct imprinting is lost. A loss of a currently unidentified imprinted gene results in PWS when the deletion is paternally inherited, whereas the same errors cause AS to develop when maternally transmitted (Moncla et al. 1999). Other examples of diseases which result after incorrect imprinting include BWS, SilverRussell syndrome and transient neonatal diabetes.
Disease can also result from defects in mechanisms regulating imprints. One of the key groups of enzymes with a role in genomic imprinting are the Dnmts which are responsible for the addition of methyl groups to the DNA. When problems arise within this aspect of the imprinting mechanism it can lead to disease in the individual. One such example is immunodeficiency, centromeric region instability and facial anomalies syndrome which is a result of a mutation in DNMT3B (for review see Ehrlich 2003).
Another major component of the imprinting mechanism is the family of methyl-binding domain proteins. MeCP2 is a protein which contains a methyl-binding domain. It has a role in controlling the transcription of imprinted genes through its ability to bind to methylated DNA. The importance of this protein for normal development and physiological function is demonstrated by Rett syndrome which occurs when MECP2 is mutated (Amir et al. 1999).
There are some diseases with multiple causes which only in some cases involve errors to the imprinting mechanism or alterations to imprinted genes. Cancer is one such disease, with some cases of cancer being identified as having a cause linked to genomic imprinting while many other incidences of the disease occur because of unrelated problems. In some instances, human tumour cells have been found to overexpress one or more of Dnmt1s, 3a and 3b, with the largest upregulation occurring to Dnmt3b (Robertson et al. 1999). These results support the previous observations of abnormal methylation levels seen in tumour cells. One cancer which demonstrates such raised Dnmt levels is acute myelogenous leukaemia; it may be that this overexpression of the Dnmt enzymes accounts for the hypermethylation and silencing of an important tumour suppressor gene (Mizuno et al. 2001).
| Conclusion |
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| Acknowledgements |
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| Footnotes |
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