Identification and properties of imprinted genes and their control elements

THE INHERITANCE OF COGNITIVE SKILLS: DOES GENOMIC IMPRINTING PLAY A ROLE?

Genomic imprinting refers to the differential expression of a gene based on parental origin. Animal and clinical studies have suggested that genomic imprinting is influential in brain development, with the maternal genome playing a disproportionate role in the development of the cortex. The present study investigated this phenomenon in a nonclinical human population, using intrafamilial correlations. Broadly consistent with predictions, it was found that abilities mediated by frontal, parietal, and temporal lobes, but not occipital lobes, were more closely correlated between children and mothers versus fathers. The implications of these findings for the prevailing theory of the evolution of genomic imprinting, and for the general study of genetics and behavior, are discussed.

Imprinted genes and neuroendocrine function

Imprinted genes are monoallelically expressed in a parent-of-origin dependent manner. Whilst the full functional repertoire of these genes remains obscure, they are generally highly expressed in the brain and are often involved in fundamental neural processes. Besides influencing brain neurochemistry, imprinted genes are important in the development and function of the hypothalamus and pituitary gland, key sites of neuroendocrine regulation. Moreover, imprinted genes may directly modulate hormone-dependent signalling cascades, both in the brain and elsewhere. Much of our knowledge about imprinted gene function has come from studying knockout mice and human disorders of imprinting. One such disorder is Prader-Willi syndrome, a neuroendocrine disorder characterised by hypothalamic abnormalities and aberrant feeding behaviour. Through examining the role of imprinted genes in neuroendocrine function, it may be possible to shed light on the neurobiological basis of feeding and aspects of social behaviour and underlying cognition, and to provide insights into disorders where these functions go awry.

Sequence-based bioinformatic prediction and QUASEP identify genomic imprinting of the KCNK9 potassium channel gene in mouse and human

Genomic imprinting is the epigenetic marking of gene subsets resulting in monoallelic or predominant expression of one of the two parental alleles according to their parental origin. We describe the systematic experimental verification of a prioritized 16 candidate imprinted gene set predicted by sequence-based bioinformatic analyses. We used Quantification of Allele-Specific Expression by Pyrosequencing (QUASEP) and discovered maternal-specific imprinted expression of the Kcnk9 gene as well as strain-dependent preferential expression of the Rarres1 gene in E11.5 (C57BL/6 x Cast/Ei)F1 and informative (C57BL/6 x Cast/Ei) x C57BL/6 backcross mouse embryos. For the remaining 14 candidate imprinted genes, we observed biallelic expression. In adult mouse tissues, we found that Kcnk9 expression was restricted to the brain and also was maternal-specific. QUASEP analysis of informative human fetal brain samples further demonstrated maternal-specific imprinted expression of the human KCNK9 orthologue. The CpG islands associated with the mouse and human Kcnk9/KCNK9 genes were not differentially methylated, but strongly hypomethylated. Thus, we speculate that mouse Kcnk9 imprinting may be regulated by the maternal germline differentially methylated region in Peg13, an imprinted non-coding RNA gene in close proximity to Kcnk9 on distal mouse chromosome 15. Our data have major implications for the proposed role of Kcnk9 in neurodevelopment, apoptosis and tumourigenesis, as well as for the efficiency of sequence-based bioinformatic predictions of novel imprinted genes.

Noncoding RNAs and intranuclear positioning in monoallelic gene expression

Mammalian X inactivation, imprinting, and allelic exclusion are classic examples of monoallelic gene expression. Two emerging themes are thought to be critical for monoallelic expression: (1) noncoding, often antisense, transcription linked to differential chromatin marks on otherwise homologous alleles and (2) physical segregation of alleles to separate domains within the nucleus. Here, we highlight recent progress in identifying these phenomena as possible key regulatory mechanisms of monoallelic expression.

Genomic imprinting in mammals: emerging themes and established theories

The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies

Genomic imprinting refers to a specialized form of epigenetic gene regulation whereby the expression of a given allele is dictated by parental origin. Defining the extent and distribution of imprinting across genomes will be crucial for understanding the roles played by imprinting in normal mammalian growth and development. Using mice carrying uniparental disomies or duplications, microarray screening and stringent bioinformatics, we have developed the first large-scale tissue-specific screen for imprinted gene detection. We quantify the stringency of our methodology and relate it to previous non-tissue-specific large-scale studies. We report the identification in mouse of four brain-specific novel paternally expressed transcripts and an additional three genes that show maternal expression in the placenta. The regions of conserved linkage in the human genome are associated with the Prader-Willi Syndrome (PWS) and Beckwith-Wiedemann Syndrome (BWS) where imprinting is known to be a contributing factor. We conclude that large-scale systematic analyses of this genre are necessary for the full impact of genomic imprinting on mammalian gene expression and phenotype to be elucidated.

Chromatin remodeling and neuronal function: exciting links

Regulation of gene expression occurs at different levels, from DNA to protein, and through various mechanisms. One of them is modification of the chromatin structure, which is involved in the definition of transcriptional active and inactive regions of the chromosomes. These phenomena are associated with reversible chemical modifications of the genetic material rather than with variability within the DNA sequences inherited by the individual and are therefore called 'epigenetic' modifications. Ablation of the molecular players responsible for epigenetic modifications often gives rise to neurological and behavioral phenotypes in humans and in mouse models, suggesting a relevant function for chromatin remodeling in central nervous system function, particularly in the adaptive response of the brain to stimuli. We will discuss several human disorders that are due to altered epigenetic mechanisms, with special focus on Rett syndrome.

Tissue-specific reactivation of gene expression at an imprinted locus

Genomic imprinting is the phenomenon where the expression pattern of an allele at a locus differs depending on the allele's parent of origin. In most cases, one of the two alleles is transcriptionally silent. Recent empirical work has shown some genes to be imprinted in a tissue-specific manner, where the silenced allele becomes reactivated in particular cell lineages during development. Here I describe an evolutionary model of tissue-specific transcriptional reactivation. The model describes the relationships among various inclusive fitness functions and phenotypic effects necessary for natural selection to favor the epigenetic reprogramming required for this sort of reactivation, and makes predictions regarding the nature and magnitude of phenotypic and fitness consequences of mutations in particular somatic tissues. In particular, if an imprinted gene is reactivated in one of two tissues that interact in producing a particular phenotype, expression of the gene in those two tissues is expected to have opposite phenotypic effects. The model predicts that in some cases, mutations affecting the silenced allele at an imprinted locus may be phenotypically more severe than those affecting the expressed allele. These predictions are contrasted with those of an alternative explanation for reactivation: protection against deleterious recessive somatic mutations. The inclusive-fitness model of reactivation indicates that the intragenomic conflicts present in the parental germ lines and developing embryo persist though adult life, and can have complex effects on phenotypes and patterns of gene expression in somatic tissues.

Characterization of three novel imprinted snoRNAs from mouse Irm gene

Most, if not all, of snoRNAs in mammals are intron-encoded, implying the expressional and functional relativeness between the snoRNA and their hosts. By computational analysis of an intron database extracted from 65 known mouse imprinted genes, three novel orphan box C/D snoRNAs were identified from Irm gene which is maternally expressed and related to human disorders. The snoRNAs were positively detected and found to express in all the mouse tissues except kidney. The imprinted snoRNAs exhibit stringent structures, but quite variable in locations at their host introns, suggesting their maturation probably through a splicing independent manner. We characterized Irm as a new kind of snoRNA host gene which has no protein-coding capacity and no 5'TOP structure in its mRNA. The newly identified snoRNAs appear mouse-specific, however, their function remains to be elucidated.

Epigenetic deregulation of genomic imprinting in human disorders and following assisted reproduction

Imprinted genes play important roles in the regulation of growth and development, and several have been shown to influence behavior. Their allele-specific expression depends on inheritance from either the mother or the father, and is regulated by "imprinting control regions" (ICRs). ICRs are controlled by DNA methylation, which is present on one of the two parental alleles only. These allelic methylation marks are established in either the female or the male germline, following the erasure of preexisting DNA methylation in the primordial germ cells. After fertilization, the allelic DNA methylation at ICRs is maintained in all somatic cells of the developing embryo. This epigenetic "life cycle" of imprinting (germline erasure, germline establishment, and somatic maintenance) can be disrupted in several human diseases, including Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS), Angelman syndrome and Hydatidiform mole. In the neurodevelopmental Rett syndrome, the way the ICR mediates imprinted expression is perturbed. Recent studies indicate that assisted reproduction technologies (ART) can sometimes affect the epigenetic cycle of imprinting as well, and that this gives rise to imprinting disease syndromes. This finding warrants careful monitoring of the epigenetic effects, and absolute risks, of currently used and novel reproduction technologies.

Imprinted gene expression in the brain

In normal mammals, autosomal genes are present in duplicate (i.e. two alleles), one inherited from the father, and one from the mother. For the majority of genes both alleles are transcribed (or expressed) equally. However, for a small subset of genes, known as imprinted genes, only one allele is expressed in a parent-of-origin dependent manner (note that the 'imprint' here refers to the epigenetic mechanism through which one allele is silenced, and is completely unrelated to classical 'filial imprinting' manifest at the behavioural level). Thus, for some imprinted genes expression is only (or predominantly) seen from the paternally inherited allele, whilst for the remainder, expression is only observed from the maternally inherited allele. Early work on this class of genes highlighted their importance in gross developmental and growth phenotypes. Recent studies in mouse models and humans have emphasised their contribution to brain function and behaviour. In this article, we review the literature concerning the expression of imprinted genes in the brain. In particular, we attempt to define emerging organisation themes, especially in terms of the direction of imprinting (i.e. maternal or paternal expression). We also emphasise the likely role of imprinted genes in neurodevelopment. We end by pointing out that, so far as discerning the precise functions of imprinted genes in the brain is concerned, there are currently more questions than answers; ranging from the extent to which imprinted genes might contribute to common mental disorders, to wider issues related to how easily the new data on brain may be accommodated within the dominant theory regarding the origins and maintenance of imprinting, which pits the maternal and paternal genomes against each other in an evolutionary battle of the sexes.