Growth effects of uniparental disomies and the conflict theory of genomic imprinting

A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region

We describe a complex imprinted locus in chromosome 15q11-q13 that encodes two genes, ZNF127 and ZNF127AS. The ZNF127 gene encodes a protein with a RING (C3HC4) zinc-finger and multiple C3H zinc-finger motifs, the former being closely related to a protein from variola major virus, the smallpox etiological agent. These motifs allow prediction of ZNF127 function as a ribonucleoprotein. The intronless ZNF127 gene is expressed ubiquitously, but the entire coding sequence and 5' CpG island overlaps a second gene, ZNF127AS, that is transcribed from the antisense strand with a different transcript size and pattern of expression. Allele-specific analysis shows that ZNF127 is expressed only from the paternal allele. Consistent with this expression pattern, in the brain the ZNF127 5' CpG island is completely unmethylated on the paternal allele but methylated on the maternal allele. Analyses of adult testis, sperm and fetal oocytes demonstrates a gametic methylation imprint with unmethylated paternal germ cells. Recent findings indicate that ZNF127 is part of the coordinately regulated imprinted domain affected in Prader-Willi syndrome patients with imprinting mutations. Therefore, ZNF127 and ZNF127AS are novel imprinted genes that may be associated with some of the clinical features of the polygenic Prader-Willi syndrome.

Genomic imprinting and cancer

Although we inherit two copies of all genes, except those that reside on the sex chromosomes, there is a subset of these genes in which only the paternal or maternal copy is functional. This phenomenon of monoallelic, parent-of-origin expression of genes is termed genomic imprinting. Imprinted genes are normally involved in embryonic growth and behavioral development, but occasionally they also function inappropriately as oncogenes and tumor suppressor genes. The evidence that imprinted genes play a role in carcinogenesis will be discussed in this review. Additional information about imprinted genes can be found on the Genomic Imprinting Website at: (http://www.geneimprint.com).

Do we understand the evolution of genomic imprinting?

The conflict theory is the only hypothesis to have attracted any critical attention for the evolution of genomic imprinting. Although the earliest data appeared supportive, recent systematic analyses have not confirmed the model's predictions. The status of theory remains undecided, however, as post-hoc explanations can be provided as to why these predictions are not borne out.

Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor

The repeatability of patterns of variation in Ka/Ks and Ks is expected if such patterns are the result of deterministic forces. We have contrasted the molecular evolution of the mammalian insulin-like growth factor type II receptor (Igf2r) in the mouse-rat comparison with that in the human-cow comparison. In so doing, we investigate explanations for both the evolution of genomic imprinting and for Ks variation (and hence putatively for mutation rate evolution). Previous analysis of Igf2r, in the mouse-rat comparison, found Ka/Ks patterns that were suggested to be contrary to those expected under the conflict theory of imprinting. We find that Ka/Ks variation is repeatable and hence confirm these patterns. However, we also find that the molecular evolution of Igf2r signal sequences suggests that positive selection, and hence conflict, may be affecting this region. The variation in Ks across Igf2r is also repeatable. To the best of our knowledge this is the first demonstration of such repeatability. We consider three explanations for the variation in Ks across the gene: (1) that it is the result of mutational biases, (2) that it is the result of selection on the mutation rate, and (3) that it is the product of selection on codon usage. Explanations 2 and 3 predict a Ka-Ks correlation, which is not found. Explanation 3 also predicts a negative correlation between codon bias and Ks, which is also not found. However, in support of explanation 1 we do find that in rodents the rate of silent C --> T mutations at CpG sites does covary with Ks, suggesting that methylation-induced mutational patterns can explain some of the variation in Ks. We find evidence to suggest that this CpG effect is due to both variation in CpG density, and to variation in the frequency with which CpGs mutate. Interestingly, however, a GC4 analysis shows no covariance with Ks, suggesting that to eliminate methyl-associated effects CpG rates themselves must be analyzed. These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations.

Sex and conflict

Evolutionary conflict occurs when the deterministic spread of an allele lowers the fitness either of its bearer or of other individuals in the population, leading to selection for suppressors. Sex promotes conflict because associations between alleles are temporary. Differing selection on males and females, sexual selection, and differences in transmission patterns between classes of nuclear and cytoplasmic genes can all give rise to conflict. Inert Y chromosomes, uniparental inheritance of cytoplasmic genes, mating strains and sexes, and many features of sexual behavior may have evolved in part as a result of evolutionary conflict. Estimates of its quantitative importance, however, are still needed.

Parent-of-origin effects on seed development in Arabidopsis thaliana

Many flowering plants are polyploid, but crosses between individuals of different ploidies produce seeds that develop abnormally and usually abort. Often, seeds from interploidy crosses develop differently depending on whether the mother or father contributes more chromosome sets, suggesting that maternal and paternal genomes are not functionally equivalent. Here we present the first cytological investigation of seed development following interploidy crosses in Arabidopsis thaliana. We find that crosses between diploid and tetraploid plants in either direction, resulting in double the normal dose of maternal or paternal genomes in the seed, produce viable seeds containing triploid embryos. However, development of the seed and in particular the endosperm is abnormal, with maternal and paternal genomic excess producing complementary phenotypes. A double dose of maternal genomes with respect to paternal contribution inhibits endosperm development and ultimately produces a smaller embryo. In contrast, a double dose of paternal genomes promotes growth of the endosperm and embryo. Reciprocal crosses between diploids and hexaploids, resulting in a triple dose of maternal or paternal genomes, produce seeds that begin development with similar but more extreme phenotypes than those with a double dose, but these invariably abort. One explanation of our observations is that seeds with maternal or paternal excess contain different doses of maternally or paternally expressed imprinted loci affecting endosperm development.

The conflict theory of genomic imprinting: how much can be explained?

In some mammalian genes, paternally and maternally derived alleles are expressed differently: this phenomenon is called genomic imprinting. Several-explanations have been proposed for the observed patterns of genomic imprinting, but the most successful explanation is the genetic conflict hypothesis--natural selection operating on the gene expression produces the parental origin-dependent gene expression--because the paternally derived allele tends to be less related to the siblings of the same mother than the maternal allele and hence the paternal allele should evolve to be more aggressive in obtaining maternal resources. The successes and failures of this argument have been examined in explaining the observed patterns of genomic imprinting in mammals. After a brief summary of the observations with some examples, a quantitative genetic model describing the evolution of the cis-regulating element of a gene affecting the maternal resource acquisition was presented. The model supports the verbal argument that the growth enhancer should evolve to show imprinting with the paternal allele expressed and the maternal allele inactive, whereas a growth suppressor gene tends to have an inactive paternal allele and an active maternal allele. There are four major problems of the genetic conflict hypothesis. (1) Some genes affect embryonic growth but are not imprinted (e.g., Igf1), which can be explained by considering recessive, deleterious mutations on the coding regions, (2) A gene exists that shows the pattern that is a perfect reversal (Mash2), which is needed for placental growth, and yet has an active maternal allele and an inactive paternal allele. This can be explained if the overproduction of this gene causes dose-sensitive abortion to occur in early gestation. (3) Paternal disomies are sometimes smaller than normal embryos. This is a likely outcome of evolution if imprinted genes control the allocation between placenta and embryo by modifying the cell developmental fate. (4) Genes on X chromosomes do not follow the predictions of the genetic conflict hypothesis. For genes on X chromosomes, two additional forces of natural selection (sex differentiation and dosage compensation) cause genomic imprinting, possibly in the opposite direction. Available evidence suggests that these processes are stronger than the natural selection caused by female multiple mating. Finally, the same formalism of evolution can handle an alternative nonconflict hypothesis: genomic imprinting might have evolved because it reduces the risk of the spontaneous development of parthenogenetic embryo, causing a serious threat to the life of the mother (ovarian time bomb hypothesis). This hypothesis can also explain major patterns of genomic imprinting. In conclusion, the genetic conflict hypothesis is very successful in explaining the observed patterns of imprinting for autosomal genes and probably is the most likely evolutionary explanation for them. However, for genes on X chromosomes, other processes of natural selection are more important. Considering that a nonconflict hypothesis can also explain the patterns in principle, we need a quantitative estimate of various parameters, such as the rate of dose-dependent abortion, the degree of female promiscuity, and the rate of spontaneous development of the parthenogenetic embryo, in order to make judgments on the relative importance of different forces of natural selection to form genomic imprinting.

Chromosomal imprinting in plants

Chromosomal imprints in the broadest sense can arise in somatic as well as germline cells. They can be imposed through the modification of chromosomal proteins or by the modification of chromosomal DNA, and they typically effect the expression of nearby genes. Modification enzymes--such as histone deacetylases and cytosine methyltransferases, as well as chromatin components--are known to play this role in animals and many of these same enzymes and components have been found in plants. Transposable elements are subject to chromosomal imprinting and may play a fundamental role in this process in plant and other eukaryotic genomes.