Analysis and identification of imprinted genes

Technical advances contribute to the study of genomic imprinting

Genomic imprinting in mammals was discovered over 30 years ago through elegant embryological and genetic experiments in mice. Imprinted genes show a monoallelic and parent of origin-specific expression pattern; the development of techniques that can distinguish between expression from maternal and paternal chromosomes in mice, combined with high-throughput strategies, has allowed for identification of many more imprinted genes, most of which are conserved in humans. Undoubtedly, technical progress has greatly promoted progress in the field of genomic imprinting. Here, we summarize the techniques used to discover imprinted genes, identify new imprinted genes, define imprinting regulation mechanisms, and study imprinting functions.

Analysis of imprinted gene expression in normal fertilized and uniparental preimplantation porcine embryos

In the present study quantitative real-time PCR was used to determine the expression status of eight imprinted genes (GRB10, H19, IGF2R, XIST, IGF2, NNAT, PEG1 and PEG10) during preimplantation development, in normal fertilized and uniparental porcine embryos. The results demonstrated that, in all observed embryo samples, a non imprinted gene expression pattern up to the 16-cell stage of development was common for most genes. This was true for all classes of embryo, regardless of parental-origins and the direction of imprint. However, several differentially expressed genes (H19, IGF2, XIST and PEG10) were detected amongst the classes at the blastocyst stage of development. Most interestingly and despite the fact that maternally and paternally expressed genes should not be expressed in androgenones and parthenogenones, respectively, both uniparental embryos expressed these genes when tested for in this study. In order to account for this phenomenon, we compared the expression patterns of eight imprinted genes along with the methylation status of the IGF2/H19 DMR3 in haploid and diploid parthenogenetic embryos. Our findings revealed that IGF2, NNAT and PEG10 were silenced in haploid but not diploid parthenogenetic blastocysts and differential methylation of the IGF2/H19 DMR3 was consistently observed between haploid and diploid parthenogenetic blastocysts. These results appear to suggest that there exists a process to adjust the expression status of imprinted genes in diploid parthenogenetic embryos and that this phenomenon may be associated with altered methylation at an imprinting control region. In addition we believe that imprinted expression occurs in at least four genes, namely H19, IGF2, XIST and PEG10 in porcine blastocyst stage embryos.

Imprinting analysis of the porcine MEST gene in 75 and 90 day placentas and prenatal tissues

Imprinted genes play important roles in mammalian growth, development and behavior. Mouse mesoderm-specific transcript (MEST) has been identified as an imprinted gene and mapped to an imprinted region of mouse chromosome 6 (MMU6). It plays essential roles in embryonic and placental growth, and it is required for maternal behavior in adult female mouse. Here, we isolated the porcine MEST gene and detected a single nucleotide polymorphism in the 3 -untranslated region. The RsaI polymorphism was used to investigate the allele frequencies in different pig breeds and the imprinting status in prenatal porcine tissues. Allele frequencies were significantly different between the native Chinese and Landrace breeds, except that most of the native Yushan pigs (21/26) are heterozygous at this locus. The results indicate that MEST was imprinted in placentas on days 75 and 90 of gestation as well as in the 75 d fetal heart, muscle, kidney, lung and liver.

DNA methylation may restrict but does not determine differential gene expression at the Sgy/Tead2 locus during mouse development

Soggy (Sgy) and Tead2, two closely linked genes with CpG islands, were coordinately expressed in mouse preimplantation embryos and embryonic stem (ES) cells but were differentially expressed in differentiated cells. Analysis of established cell lines revealed that Sgy gene expression could be fully repressed by methylation of the Sgy promoter and that DNA methylation acted synergistically with chromatin deacetylation. Differential gene expression correlated with differential DNA methylation, resulting in sharp transitions from methylated to unmethylated DNA at the open promoter in both normal cells and tissues, as well as in established cell lines. However, neither promoter was methylated in normal cells and tissues even when its transcripts were undetectable. Moreover, the Sgy promoter remained unmethylated as Sgy expression was repressed during ES cell differentiation. Therefore, DNA methylation was not the primary determinant of Sgy/Tead2 expression. Nevertheless, Sgy expression was consistently restricted to basal levels whenever downstream regulatory sequences were methylated, suggesting that DNA methylation restricts but does not regulate differential gene expression during mouse development.

Evidence that superficial basal cell carcinoma is monoclonal from analysis of the Ptch1 gene locus

BACKGROUND

Superficial basal cell carcinoma (BCC) arises as an apparently multifocal proliferation of tumour nests attached to the epidermis, which is at odds with a monoclonal origin. Computer-assisted reconstruction shows that these nests join in three dimensions, but it remains unknown whether this tumour is monoclonal. An early event in BCC formation, loss of heterozygosity (LOH) at the Patched 1 (Ptch1) locus, can be used as a tool to address whether this tumour is monoclonal.

OBJECTIVES

To determine whether superficial BCC is monoclonal by analysing individually microdissected superficial BCC nests and looking for the same pattern of LOH in each.

METHODS

Six cases of superficial BCC were analysed for LOH at the Ptch1 gene locus using the D9S287 microsatellite marker. Identical allelic patterns were sought in each nest from a given tumour. These patterns were no allelic loss, loss of the shorter allele or loss of the longer allele, each with a respective probability of occurrence, as estimated from published findings.

RESULTS

All cases were informative. Four cases showed no LOH in each nest and two showed loss of the same allele. If these nests arose independently, then the probability of this result was between 4 x 10-11 and 2 x 10-14. The lack of LOH, seen in four cases, could be due to monoclonal expansion of a cell retaining both D9S287 alleles, or due to a polyclonal proliferation. Therefore, a separate analysis excluding these cases was done, giving a probability of between 2.2 x 10-4 and 1.0 x 10-7.

CONCLUSIONS

These probabilities were so extreme that it was unlikely that the nests arose independently, thus providing the first molecular evidence that superficial BCC is monoclonal.

Imprinted genes: identification by chromosome rearrangements and post-genomic strategies

Imprinted genes are differentially expressed from the maternally and paternally inherited alleles. Accordingly, inheritance of both copies of an imprinted chromosome or region from a single parent leads to the mis-expression of the imprinted genes present in the selected region. Strains of mice with reciprocal and Robertsonian chromosomal translocations or mice with engineered chromosomal rearrangements can be used to produce progeny where both copies of a chromosomal region are inherited from one parent. In combination with systematic differential expression and methylation-based approaches, these mice can be used to identify novel imprinted genes. Advances in genome sequencing and computer-based technologies have facilitated this approach to finding imprinted genes.

Allele-specific analysis of transcription factors binding to promoter regions

In vivo footprinting techniques are useful for the identification of regulatory elements mediating transcriptional control of a gene. However, regulation of a gene can differ between the two alleles, and further steps must be taken to distinguish between the regulatory elements occupied on one allele and those used on the second allele. Many hematologic malignancies result from chromosomal translocations, which, in some cases, relocate a gene to a transcriptionally active region leading to the deregulated expression of that gene. This situation provides an example of differential expression between two alleles. In studying the t(14; 18) and t(8; 14) translocations, which involve the bcl-2 and c-myc proto-oncogenes, respectively, we have been able to identify regulatory elements important in mediating the activation of the translocated alleles and the silencing of the normal alleles. Following in vivo methylation and isolation of genomic DNA, we were able to separate the translocated and normal alleles by electrophoresis. Using the ligation-mediated polymerase chain reaction (LMPCR) technique, we could then assess protein interactions on the two different alleles. A detailed description of this methodology with examples from our studies are provided with a discussion of how these techniques may be applied to the study of other genes.

Monotreme IGF2 expression and ancestral origin of genomic imprinting

IGF2 (insulin-like growth factor 2) and M6P/IGF2R (mannose 6-phosphate/insulin-like growth factor 2 receptor) are imprinted in marsupials and eutherians but not in birds. These results along with the absence of M6P/IGF2R imprinting in the egg-laying monotremes indicate that the parental imprinting of fetal growth-regulatory genes may be unique to viviparous mammals. In this investigation, we have cloned IGF2 from two monotreme mammals, the platypus and echidna, to further investigate the origin of imprinting. We report herein that like M6P/IGF2R, IGF2 is not imprinted in monotremes. Thus, although IGF2 encodes for a highly conserved growth factor in chordates, it is only imprinted in therian mammals. These findings support a concurrent origin of IGF2 and M6P/IGF2R imprinting in the late Jurassic/early Cretaceous period. The absence of imprinting in monotremes, despite apparent interparental conflicts over maternal-offspring exchange, argues that a fortuitous congruency of genetic and epigenetic events may have limited the phylogenetic breadth of genomic imprinting to therian mammals. J. Exp. Zool. (Mol. Dev. Evol.) 291:205-212, 2001.

Unequal expression of allelic kainate receptor GluR7 mRNAs in human brains

We describe here the first example of an exonic polymorphism that affects the primary structure of a human ionotropic glutamate receptor. The human kainate receptor GluR7 gene contains a thymine (T)/guanine (G) nucleotide variation that determines a serine or alanine at position 310 in the extracellular region of GluR7 receptor subunits. Our finding contrasts with a previous report that suggested that GluR7 transcripts were RNA-edited at this site. Whole-cell patch-clamp recordings did not detect differences in receptor activation and desensitization between the human GluR7 receptor isoforms expressed in HEK-293 cells. Analysis of 41 tissue samples obtained from 30 human brains revealed expression level differences between GluR7 alleles expressed in the same brain. The expression level of the allelic GluR7 mRNAs differed in 27 samples from 1.2- to 12.7-fold. Unequal expression level of allelic mRNAs is characteristic for genes that are affected by genomic imprinting or that contain mutations. Genomic imprinting in most cases is conserved between human and mice. However, we did not detect unequal expression of allelic GluR7 mRNAs in mice. Our results are important for future studies that explore a potential role or roles for GluR7 receptors in the brain and for neurological disorders.

Imprinting of PEG3, the human homologue of a mouse gene involved in nurturing behavior

The paternally expressed Peg3 gene in mice encodes an unusual Krüppel-type zinc finger protein implicated in critical cellular and behavioral functions including growth, apoptosis, and maternal nurturing behavior. Methylation and expression analyses were used to determine whether PEG3 on chromosome 19q13.4 is imprinted in humans. The PEG3 promoter is encompassed within a large CpG-rich region that is differentially methylated in fetal tissues. Furthermore, expression studies demonstrate that PEG3 is ubiquitously imprinted throughout development and postnatally. Multiple isoforms of the PEG3 gene, including a novel transcript, are paternally expressed. These results are the first to show that human chromosome 19q13.4 contains an imprinted region. The imprinted status of PEG3 throughout life coupled with its neural expression and putative roles in regulating cell growth suggests that PEG3 may be a susceptibility locus for cancer as well as neurobehavioral deficits.

Imprinted genes, cognition and behaviour

The idea that genes can influence behavioural predispositions and their underlying psychological determinants is becoming increasingly tractable. In this article, recent findings are reviewed on a special type of inheritance, related to the transmission of traits via what have been termed 'imprinted' genes. In imprinted genes one allele is silenced according to its parental origin. This results in the inheritance of traits down the maternal or paternal line, in contrast to the more frequent mode of inheritance that is indifferent to the parental origin of the allele. Drawing on the advances made possible by combining the approaches of cognitive neuropsychology, behavioural neuroscience and contemporary molecular genetics, the detailed evidence for imprinted effects on behavioural and cognitive phenotypes is considered, focusing on findings from mental disorders, Turner's syndrome and experimental work in animal models. As prevailing evolutionary theories stress an essential antagonistic role of imprinted effects, these data might link such apparently diverse issues as neurodevelopment and the vulnerability to mental disease with the 'battle of the sexes', as joined at the level of cognitive and behavioural functioning.

M6P/IGF2R imprinting evolution in mammals

Imprinted gene identification in animals has been limited to eutherian mammals, suggesting a significant role for intrauterine fetal development in the evolution of imprinting. We report herein that M6P/IGF2R is not imprinted in monotremes and does not encode for a receptor that binds IGF2. In contrast, M6P/IGF2R is imprinted in a didelphid marsupial, the opossum, but it strikingly lacks the differentially methylated CpG island in intron 2 postulated to be involved in imprint control. Thus, invasive placentation and gestational fetal growth are not required for imprinted genes to evolve. Unless there was convergent evolution of M6P/ IGF2R imprinting and receptor IGF2 binding in marsupials and eutherians, our results also demonstrate that these two functions evolved in a mammalian clade exclusive of monotremes.

Physical mapping of the mouse genome

This review is intended to provide an overview of techniques and a source of reagents for physical mapping of the mouse genome. It focuses on those applications, methods, or resources unique to the mouse and on the generation of comparative physical maps. The reference list is not comprehensive; rather, recent reviews on each topic and selected representative examples are given.