Genomic imprinting in Dicer1-hypomorphic mice.

To address the function of RNA interference (RNAi) in transcriptional silencing in mammals, we analyzed genomic imprinting in Dicer1-hypomorphic mice, in which Dicer1 expression was significantly reduced. We did not observe any abnormality in the allelic expression of imprinted genes in these mice or their offspring, suggesting that reduced expression of Dicer1 did not significantly affect the maintenance and reprogramming of imprinting.

Genome-wide profiling of promoter methylation in human.

DNA methylation in the promoter region of a gene is associated with a loss of that gene's expression and plays an important role in gene silencing. The inactivation of tumor-suppressor genes by aberrant methylation in the promoter region is well recognized in carcinogenesis. However, there has been little study in this area when it comes to genome-wide profiling of the promoter methylation. Here, we developed a genome-wide profiling method called Microarray-based Integrated Analysis of Methylation by Isoschizomers to analyse the DNA methylation of promoter regions of 8091 human genes. With this method, resistance to both the methylation-sensitive restriction enzyme HpaII and the methylation-insensitive isoschizomer MspI was compared between samples by using a microarray with promoter regions of the 8091 genes. The reliability of the difference in HpaII resistance was judged using the difference in MspI resistance. We demonstrated the utility of this method by finding epigenetic mutations in cancer. Aberrant hypermethylation is known to inactivate tumour suppressor genes. Using this method, we found that frequency of the aberrant promoter hypermethylation in cancer is higher than previously hypothesized. Aberrant hypomethylation is known to induce activation of oncogenes in cancer. Genome-wide analysis of hypomethylated promoter sequences in cancer demonstrated low CG/GC ratio of these sequences, suggesting that CpG-poor genes are sensitive to demethylation activity in cancer.

Identification of a new imprinted gene, Rian, on mouse chromosome 12 by fluorescent differential display screening.

Systematic screening of differentially expressed genes among androgenetic, parthenogenetic, and normal embryos by means of fluorescent differential display revealed five imprinted genes. One of them, named Rian, was expressed exclusively from the maternal allele and was closely linked to an imprinted gene, Meg3(Gtl2), mapped to the distal end of chromosome 12. The Rian transcript did not have any apparent open reading frame, and its transcript was exclusively localized to the nucleus.

DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1.

The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpn is explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. The U2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5' DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5' untranslated region (5'-UTR) and 3'-UTR of U2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.

Disruption of imprinted expression of U2afbp-rs/U2af1-rs1 gene in mouse parthenogenetic fetuses.

The present study shows that the U2afbp-rs gene, a paternally expressed imprinted gene, is activated and expressed in a biallelic manner from maternal alleles in parthenogenetic mouse fetuses on day 9.5 of gestation. The mean expression was detected to be 88% (31-134%) of that in control biparental fetuses, using real-time quantitative reverse transcription and polymerase chain reaction. This disrupted expression of the gene was associated with changes in the chromatin structure but not with the methylation pattern in the regulation region. The present results show that parental specific expression of imprinted genes is not always maintained in uniparental embryos. This suggests that both parental genomes are necessary to establish parental specific expression of the U2afbp-rs gene.

Methylation-sensitive genome scanning.

Imprinted genes in mammals are expressed exclusively from one of the parental alleles (1-6). This is regulated by parental-allele-specific CpG methylation. For example, H19 is methylated exclusively on the paternal allele, which is repressed, and is expressed exclusively from the maternal allele, which is unmethylated. Therefore, one way to find imprinted genes is searching for parental-allele-specific CpG methylation. Southern analysis using methylation-sensitive restriction enzymes could be used for such a purpose. However, usually only one gene can be analyzed by one Southern analysis. Moreover, Southern analysis requires one DNA probe for each analysis. These facts indicate at least 300 Southern analyses using 300 different probes are required to find only one imprinted gene, because the population of imprinted genes is estimated to be 0.3%. Therefore, this kind of analysis is not appropriate for searching for new imprinted genes, and the development of a new method that can simultaneously analyze thousands of genes was required.

Abnormal RNA expression of 11p15 imprinted genes and kidney developmental genes in Wilms' tumor.

Wilms' tumor (WT) is caused by abnormal development of embryonal kidney cells. WT cells are frequently affected by deletions or functional inactivation of maternal alleles at chromosome 11p15, which indicates that the loss of maternally expressed genes in this region plays an important role in WT pathogenesis. Maternally expressed genes indeed exist within an imprinted region at 11p15.5. Among these, BWR1C is highly expressed in fetal but not in adult kidney, which suggests that it may fulfil an important role in kidney development. Here, we demonstrate that the lack of BWR1C expression is common in WT. Its homology with the proapoptotic gene TDAG51 suggests that the loss of BWR1C expression may be relevant in WT development. In addition, the analysis of the expression of other 11p15 imprinted genes and kidney-developmentally regulated genes indicates that IGF2 overexpression, inappropriate coexpression of RET and GDNF and, in some cases, down-regulation of CDKN1C may also play an important role in the pathogenesis of WT. Our results add new elements to the understanding of the biological basis of WT, which may have implications for WT diagnosis and therapy.

Genomic imprinting and Beckwith-Wiedemann syndrome.

Genomic imprinting is the parental-allele-specific expression of genes. Beckwith-Wiedemann syndrome (BWS), a congenital overgrowth syndrome with increased risk of childhood tumors, is one of the well-known diseases caused by imprinted genes. The imprinted genes causing BWS are discussed in this review.

Analysis of germline CDKN1C (p57KIP2) mutations in familial and sporadic Beckwith-Wiedemann syndrome (BWS) provides a novel genotype-phenotype correlation.

Beckwith-Wiedemann syndrome (BWS) is a human imprinting disorder with a variable phenotype. The major features are anterior abdominal wall defects including exomphalos (omphalocele), pre- and postnatal overgrowth, and macroglossia. Additional less frequent complications include specific developmental defects and a predisposition to embryonal tumours. BWS is genetically heterogeneous and epigenetic changes in the IGF2/H19 genes resulting in overexpression of IGF2 have been implicated in many cases. Recently germline mutations in the cyclin dependent kinase inhibitor gene CDKN1C (p57KIP2) have been reported in a variable minority of BWS patients. We have investigated a large series of familial and sporadic BWS patients for evidence of CDKN1C mutations by direct gene sequencing. A total of 70 patients with classical BWS were investigated; 54 were sporadic with no evidence of UPD and 16 were familial from seven kindreds. Novel germline CDKN1C mutations were identified in five probands, 3/7 (43%) familial cases and 2/54 (4%) sporadic cases. There was no association between germline CDKN1C mutations and IGF2 or H19 epigenotype abnormalities. The clinical phenotype of 13 BWS patients with germline CDKN1C mutations was compared to that of BWS patients with other defined types of molecular pathology. This showed a significantly higher frequency of exomphalos in the CDKN1C mutation cases (11/13) than in patients with an imprinting centre defect (associated with biallelic IGF2 expression and H19 silencing) (0/5, p<0.005) or patients with uniparental disomy (0/9, p<0.005). However, there was no association between germline CDKN1C mutations and risk of embryonal tumours. No CDKN1C mutations were identified in six non-BWS patients with overgrowth and Wilms tumour. These findings (1) show that germline CDKN1C mutations are a frequent cause of familial but not sporadic BWS, (2) suggest that CDKN1C mutations probably cause BWS independently of changes in IGF2/H19 imprinting, (3) provide evidence that aspects of the BWS phenotype may be correlated with the involvement of specific imprinted genes, and (4) link genotype-phenotype relationships in BWS and the results of murine experimental models of BWS.

Functional analysis of the p57KIP2 gene mutation in Beckwith-Wiedemann syndrome.

p57KIP2 is a potent tight-binding inhibitor of several G1 cyclin/cyclin-dependent kinase (Cdk) complexes, and is a negative regulator of cell proliferation. The gene encoding p57KIP2 is located at 11p15.5, a region implicated in both sporadic cancers and Beckwith-Wiedemann syndrome (BWS). Previously we demonstrated that p57KIP2 is imprinted and only the maternal allele is expressed in both mice and humans. We also showed mutations found in p57KIP2 in patients with BWS that were transmitted from the patients' carrier mothers, indicating that the expressed maternal allele was mutant and that the repressed paternal allele was normal. In the study reported here, we performed functional analysis of the two mutated p57KIP2 genes. We showed that the nonsense mutation found in the Cdk inhibitory domain in a BWS patient rendered the protein inactive with consequent complete loss of its role as a cell cycle inhibitor and of its nuclear localization. We also showed that the mutation in the QT domain, although completely retaining its cell cycle regulatory activity, lacked nuclear localization and was thus prevented from performing its role as an active cell cycle inhibitor. Consequently, no active p57KIP2 would have existed, which might have caused the disorders in BWS patients.

A novel gene, ITM, located between p57KIP2 and IPL, is imprinted in mice.

We searched for new imprinted genes using a positional cloning method in a region of human chromosome 11p15.5, which contains several imprinted genes including p57KIP2 and IPL, and found a novel ITM gene located between p57KIP2 and IPL. We also obtained the mouse homologue Itm in its syntenic region of mouse chromosome 7. In humans, its location is 17 kb centromeric to p57KIP2 and 3 kb telomeric to IPL, and in mice, 15 kb and 2.5 kb, respectively. They are expressed in most tissue, but especially in the kidney and liver, and moderately in the heart, lung and testis. Mice exhibit a functional imprinting resulting in higher expression of maternal alleles in fetal, newborn and most adult tissues, but it is biallelically expressed in the adult kidney and liver where expression is the highest. In addition to the discrepancy between the level of expression and the strength of the imprint, Itm has several unusual features for an imprinted gene, including large introns, moderate GC content and the absence of direct repeats. Our results will be helpful in understanding the intricate regulatory mechanism of imprinted genes.

Transcriptional map of 170-kb region at chromosome 11p15.5: identification and mutational analysis of the BWR1A gene reveals the presence of mutations in tumor samples.

Chromosome region 11p15.5 harbors unidentified genes involved in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome. The genetic analysis of a 170-kb region at 11p15.5 between loci D11S601 and D11S679 resulted in the identification of six transcriptional units. Three genes, hNAP2, CDKN1C, and KVLQT1, are well characterized, whereas three genes are novel. The three additional genes were designated BWR1A, BWR1B, and BWR1C. Full-length cDNAs for these three genes were cloned and nucleotide sequences were determined. While our work was in progress, BWR1C cDNA was described as IPL [Qian, N., Franck, D., O'Keefe, D., Dao, D. , Zhao, L., Yuan, L., Wang, Q., Keating, M., Walsh, C. & Tycko, B. (1997) Hum. Mol. Genet. 6, 2021-2029]. The cloning and mapping of these genes together with the fine mapping of the three known genes indicates that the transcriptional map of this region is likely to be complete. Because this region frequently is altered in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome, we carried out a mutational analysis in tumor cell lines and Beckwith-Wiedemann syndrome samples that resulted in the identification of genetic alterations in the BWR1A gene: an insertion that introduced a stop codon in the breast cancer cell line BT549 and a point mutation in the rhabdomyosarcoma cell line TE125-T. These results indicate that BWR1A may play a role in tumorigenesis.

Comparative reverse transcription-polymerase chain reaction and in situ hybridization analyses of human imprinted p57KIP2 and insulin-like growth factor 2 gene transcripts in fetal kidney and Wilms' tumors using archival tissue.

p57KIP2 (KIP2) is a cyclin-dependent kinase inhibitor that arrests cells in G1 and an imprinted gene mapped on chromosome 11p15.5. To investigate the role of KIP2 in Wilms' tumor (WT), DNA and RNA were extracted from archival tissue sections of WT. KIP2 expression was investigated by reverse transcription-polymerase chain reaction and in situ mRNA hybridization. Thirteen of 39 WT were informative for length polymorphism of KIP2 and subjected to reverse transcription-polymerase chain reaction. KIP2 was expressed predominantly from one allele, although a low level of expression was also detected from the other. Three WT with loss of heterozygosity at the KIP2 locus demonstrated that the remaining KIP2 allele was still active, which was also confirmed by in situ hybridization. Furthermore, among 13 KIP2-informative WT, 2 were heterozygous for insulin-like growth factor II (IGF2). Allele-specific analysis demonstrated that one showed monoallelic IGF2 expression, whereas the other showed biallelic expression. In situ hybridization of fetal kidney showed that KIP2 transcripts were detected in a variety of cell types, among which differentiated epithelial structures showed higher expression than undifferentiated mesenchyme, whereas IGF2 was expressed predominantly in undifferentiated mesenchyme and renal vesicles of an early phase. WT demonstrated KIP2 and IGF2 hybridization patterns similar to fetal kidney in that KIP2 transcripts were detected in epithelial structures and blastema, whereas IGF2 transcripts were seen in blastema and immature epithelial structures. Hybridization results indicated that KIP2 expression in WT did not appear to be significantly reduced compared with that in fetal kidney and that WT demonstrated a significant amount of KIP2 transcripts regardless of retention or loss of heterozygosity at the KIP2 locus. These data suggest that although KIP2 may play a role in differentiation of the fetal kidney, it is not likely as a tumor suppressor gene, which is implicated as the cause of the development of a majority of WT.

New p57KIP2 mutations in Beckwith-Wiedemann syndrome.

Beckwith-Wiedemann syndrome (BWS) is characterized by numerous growth abnormalities and an increased risk of childhood tumors. The gene for BWS is localized in the 11p15.5 region, as determined by linkage analysis of autosomal dominant pedigrees. The increased maternal transmission pattern seen in the autosomal dominant-type pedigrees and the findings of paternal uniparental disomy reported for a subgroup of patients indicate that the gene for BWS is imprinted. Previously, we found p57KIP2, which is a Cdk-kinase inhibitor located at 11p15, is mutated in two BWS patients. Here, we screened for the mutation of the gene in 15 BWS patients.

Aberrant methylation of an imprinted gene U2af1-rs1(SP2) caused by its own transgene.

Genomic imprinting refers to the parental allele-specific expression of genes. The precise mechanism underlying this phenomenon, which may involve DNA methylation, is not yet known. U2af1-rs1(SP2) is an imprinted gene expressed from the paternal allele and is methylated on the maternal allele. Here we report an artificial system in which expression and methylation of the endogenous imprinted gene U2af1-rs1 can be affected by interaction with its own transgene in the testis. We suggest that there is a mechanism in male gametogenesis by which the U2af1-rs1 gene is kept unmethylated to be expressed in the offspring in addition to a mechanism in female gametogenesis by which the U2af1-rs1 gene is methylated and is not expressed in the offspring.

Mouse U2af1-rs1 is a neomorphic imprinted gene.

The mouse U2af1-rs1 gene is an endogenous imprinted gene on the proximal region of chromosome 11. This gene is transcribed exclusively from the unmethylated paternal allele, while the methylated maternal allele is silent. An analysis of genome structure of this gene revealed that the whole gene is located in an intron of the Murr1 gene. Although none of the three human U2af1-related genes have been mapped to chromosome 2, the human homolog of Murr1 is assigned to chromosome 2. The mouse Murr1 gene is transcribed biallelically, and therefore it is not imprinted in neonatal mice. Allele-specific methylation is limited to a region around U2af1-rs1 in an intron of Murr1. These results suggest that in chromosomal homology and genomic imprinting, the U2af1-rs1 gene is distinct from the genome region surrounding it. We have proposed the neomorphic origin of the U2af1-rs1 gene by retrotransposition and the particular mechanism of genomic imprinting of ectopic genes.

An imprinted gene p57KIP2 is mutated in Beckwith-Wiedemann syndrome.

p57KIP2 is a potent tight-binding inhibitor of several G1 cyclin/Cdk complexes, and is a negative regulator of cell proliferation. The gene encoding p57KIP2 is located at 11p15.5 (ref. 2), a region implicated in both sporadic cancers and Beckwith-Wiedemann syndrome, a cancer-predisposing syndrome, making it a tumour-suppressor candidate. Several types of childhood tumours including Wilms' tumour, adrenocortical carcinoma and rhabdomyosarcoma exhibit a specific loss of maternal 11p15 alleles, suggesting that genomic imprinting is involved. Genetic analysis of the Beckwith-Wiedemann syndrome indicated maternal carriers, as well as suggesting a role of genomic imprinting. Previously, we and others demonstrated that p57KIP2 is imprinted and that only the maternal allele is expressed in both mice and humans. Here we describe p57KIP2 mutations in patients with Beckwith-Wiedemann syndrome. Among nine patients we examined, two were heterozygous for different mutations in this gene-a missense mutation in the Cdk inhibitory domain resulting in loss of most of the protein, and a frameshift resulting in disruption of the QT domain. The missense mutation was transmitted from the patient's carrier mother, indicating that the expressed maternal allele was mutant and that the repressed paternal allele was normal. Consequently, little or no active p57KIP2 should exist and this probably causes the overgrowth in this BWS patient.

Chromosomal assignment and imprinting tests for the mouse delta subunit of the cytosolic chaperonin containing TCP-1 (Cct4) gene to proximal chromosome 11.

The CCT (chaperonin containing TCP-1) complex functions as a molecular chaperone in the eukaryotic cytosol. This complex consists of several species of related polypeptides. The chromosomal localization of the mouse Cct4 gene encoding the delta subunit of CCT was assigned in this study to proximal chromosome 11 by genetic mapping. Restriction mapping analysis using YAC and pulse-field gel electrophoresis showed that Cct4 is located within a region about 300 kb from the imprinted gene U2af1-rs1. Expression of Cct4 was biallelic, and therefore Cct4 is not imprinted in neonatal mice. The localization of the human homologue of Cct4 on chromosome 2 corresponds well with the fact that homologues of other genes in the proximal region of mouse chromosome 11 also map to the region of conserved synteny in human chromosome 2.

Genomic imprinting of human p57KIP2 and its reduced expression in Wilms' tumors.

p57KIP2 is a potent tight-binding inhibitor of several G1 cyclin complexes, and is a negative regulator of cell proliferation. The gene encoding human p57KIP2 is located on chromosome 11p15.5, a region implicated in both sporadic cancers and Beckwith-Wiedemann syndrome (BWS), a cancer syndrome, making it a tumor suppressor candidate. Several types of childhood tumors including Wilms' tumor, adrenocortical carcinoma and rhabdomyosarcoma display a specific loss of maternal 11p15 alleles, suggesting that genomic imprinting plays an important part. Genetic analysis of the familial BWS has indicated maternal carriers and suggested a role in genomic imprinting. Previously, we demonstrated that p57KIP2 is imprinted in the mouse. Here we describe the genomic imprinting of human p57KIP2 and the reduction of its expression in Wilms' tumors. High resolution mapping locates p57KIP2 in the region responsible for both tumor suppressivity and BWS.