ScienceWeek

GENOME BIOLOGY: ON GENOMIC IMPRINTING

The following points are made by S.T. da Rocha and A.C. Ferguson-Smith (Current Biology 2004 14:R646):

1) Genomic imprinting is a normal form of gene regulation that causes a subset of mammalian genes to be expressed from one of the two parental chromosomes. Some imprinted genes are expressed from the maternally inherited chromosomes and others from the paternally inherited chromosomes. This means that the maternal and paternal genomes are not functionally equivalent and is the reason why both a maternal and a paternal genome are required for normal mammalian development. Genomic imprinting has also been described in plants, where the process is believed to have evolved independently from that in mammals, although aspects of the mechanism of imprinting may be the same in both organisms.

2) The existence of imprinted genes adds another dimension to the patterns of inheritance predicted by Mendelian genetics. For example, imprinting disorders have been described. These exhibit parental origin effects in their patterns of inheritance. In these disorders, males and females are usually equally affected, however the defect is manifest only upon inheritance from a parent of one sex. Inheritance from the parent of the opposite sex does not result in an abnormality because the defective gene may be repressed on the chromosome derived from that parent.

3) Genomic imprinting was identified for the first time in the early 1980s through classic manipulation experiments on mouse embryos. Pronuclear transplantation was used to generate "gynogenetic" or "androgenetic" conceptuses, which, respectively, have two sets of maternal chromosomes and no paternal contribution or vice versa. These embryos fail to develop properly and die before term despite being diploid. Furthermore, the defects presented in androgenones and gynogenones are strikingly different. Gynogenetic embryos die before or at mid-gestation and are growth retarded with poor development of the extra-embryonic tissues. In contrast, androgenetic conceptuses have a more restricted developmental potential. Their embryonic components develop poorly while extra-embryonic tissues are better formed.

4) These embryo reconstitution experiments suggested that maternal and paternal contributions to the developing mammalian embryo are different. It was proposed that a specific "imprinting" of the paternal and maternal genomes occurs during the development of the egg and the sperm, resulting in the requirement of both genomes after fertilization for normal full-term development.

5) During this time, genetic studies were in progress that proved this bi-parental requirement for particular chromosomes and chromosomal regions for normal development. Using chromosomal rearrangements that resulted in ova and sperm containing an imbalance of parental chromosomes, mice with maternal chromosomal duplications and corresponding paternal deficiencies were generated, and vice versa. Imprinting was detected by noting developmental abnormalities in these uniparental disomy/uniparental duplication conceptuses.(1-5)

References (abridged):

1. Beechey, C. (2004). http://www.mgu.har.mrc.ac.uk/research/imprinting/largemap.html

2. Bestor, T.H. (2003). Cytosine methylation mediates sexual conflict. Trends Genet. 19, 185-190

3. Cattanach, B.M. and Kirk, M. (1985). Differential activity of maternally and paternally derived chromosome regions in mice. Nature 315, 496-498

4. de la Casa-Esperon, E. and Sapienza, C. (2003). Natural selection and the evolution of genomic imprinting. Annu. Rev. Genet. 37, 2349-2370

5. Egger, G., Liang, G., Aparicio, A., and Jones, P. (2004). Epigenetics in human disease and prospects for epigenetic therapy. Nature 429, 457-463

Current Biology http://www.current-biology.com

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IMPROVING THE SAFETY OF EMBRYO TECHNOLOGIES: POSSIBLE ROLE OF GENOMIC IMPRINTING

The following points are made by L.E. Young and H.R. Fairburn (Theriogenology 2000 53:627):

1) Although developments in mammalian in vitro embryo technologies have allowed many new clinical and agricultural achievements, their application has been hindered by limitations in the developmental potential of resulting embryos. Low efficiencies of development to the pre-implantation blastocyst stage have been consistently observed in most species, including humans, rabbits, pigs and ruminants. Furthermore, in cattle and sheep a wide range of congenital abnormalities currently termed "Large Offspring syndrome" (LOS) are commonly observed as a result of several embryo culture and manipulation procedures.

2) The authors review the hypothesis that at least some of the problems associated with embryo technologies may result from disruptions in imprinted genes. Several imprinted genes (i.e. genes which express only the maternal or paternal allele) are known to have significant effects on fetal size and survival in other species and are possible candidates for involvement in livestock LOS.

3) Major changes in putative imprinting mechanisms such as DNA methylation of imprinted genes occur in the mouse embryo during pre-implantation development. Alterations in DNA methylation are transmitted with stability through repeated cell cycles such that changes in the embryo may still act at the fetal stages. Thus any disruption in establishment and/or maintenance of imprinting during the vulnerable periods of embryo culture or manipulation is a plausible candidate mechanism for inducing fetal loss and Large Offspring Syndrome. Identification of these disruptions may provide crucial means to improve the success of current procedures.

Theriogenology http://www.sciencedirect.com/web-editions/journal/0093691X

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DNA METHYLATION IN MAMMALIAN EPIGENETICS

The following points are made by P.A. Jones and D. Takai (Science 2001 293:1063):

1) DNA methylation is essential for the development of mammals (1,2), but despite 25 years of work, researchers still do not know exactly why. Recent advances have led to the cloning and preliminary characterization of the three known active DNA cytosine methyltransferases (DNMT1, -3a, and -3b) (3,4) and to a greater understanding of how the methylation signal is interpreted in mammalian cells.

2) The post-synthetic addition of methyl groups to the 5-position of cytosines alters the appearance of the major groove of DNA to which the DNA binding proteins bind. These epigenetic "markers" on DNA can be copied after DNA synthesis, resulting in heritable changes in chromatin structure. Methylation of CpG-rich promoters is used by mammals to prevent transcriptional initiation and to ensure the silencing of genes on the inactive X chromosome, imprinted genes, and parasitic DNAs. The potential role of methylation in tissue-specific gene expression or in the regulation of CpG-poor promoters is less well established. There is also tantalizing evidence that normal chromosome structure may be affected by methylation and that human diseases, including cancer, are caused and impacted by abnormal methylation.

3) CpG dinucleotides, the sites of almost all methylation in mammals, are underrepresented in DNA. Clusters of CpGs, called "CpG islands", are often found in association with genes, most often in the promoters and first exons but also in regions more toward the 3' end (5). The exact definition of a CpG island is evolving. The original suggestion by Gardiner-Garden and Frommer (1987) of a region greater than 200 base pairs (bp) with a high-GC content and an observed/expected ratio for the occurrence of CpG > 0.6, should probably be modified to slightly higher stringency in terms of length and GC content, thus excluding a substantial number of small exonic regions and repetitive parasitic DNAs. The salient property of a CpG island is that it is unmethylated in the germline (and indeed in most somatic tissues), thus ensuring its continued existence in the face of the strong mutagenic pressure of 5-methylcytosine deamination.

4) CpG islands often function as strong promoters and have also been proposed to function as replication origins. Even though these islands are generally not methylated, most investigations on the role of DNA methylation in mammals have focused on CpG islands rather than on the regions in which the majority of methylation is found.

5) In summary: Genes constitute only a small proportion of the total mammalian genome, and the precise control of their expression in the presence of an overwhelming background of noncoding DNA presents a substantial problem for their regulation. Noncoding DNA, containing introns, repetitive elements, and potentially active transposable elements, requires effective mechanisms for its long-term silencing. Mammals appear to have taken advantage of the possibilities afforded by cytosine methylation to provide a heritable mechanism for altering DNA-protein interactions to assist in such silencing. Genes can be transcribed from methylation-free promoters even though adjacent transcribed and nontranscribed regions are extensively methylated. Gene promoters can be used and regulated while keeping noncoding DNA, including transposable elements, suppressed. Methylation is also used for long-term epigenetic silencing of X-linked and imprinted genes and can either increase or decrease the level of transcription, depending on whether the methylation inactivates a positive or negative regulatory element.

References (abridged):

1. E. Li, T. H. Bestor, R. Jaenisch, Cell 69, 915 (1992)

2. M. Okano, D. W. Bell, D. A. Haber, E. Li, Cell 99, 247 (1999)

3. T. Bestor, A. Laudano, R. Mattaliano, V. Ingram, J. Mol. Biol. 203, 971 (1988)

4. M. Okano, S. Xie, E. Li, Nature Genet. 19, 219 (1998)

5. F. Larsen, G. Gundersen, R. Lopez, H. Prydz, Genomics 13, 1095 (1992)

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