Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method

Screening for imprinted genes by allelic message display: identification of a paternally expressed gene impact on mouse chromosome 18

A systematic screen termed the allelic message display (AMD) was developed for the hunting of imprinted genes. In AMD, differential display PCR is adopted to image allelic expression status of multiple polymorphic transcripts in two parental mouse strains, reciprocal F1 hybrids and pooled backcross progenies. From the displayed patterns, paternally and maternally expressed transcripts can be unequivocally identified. The effectiveness of AMD screening was clearly demonstrated by the identification of a paternally expressed gene Impact on mouse chromosome 18, the predicted product of which belongs to the YCR59c/yigZ hypothetical protein family composed of yeast and bacterial proteins with currently unknown function. In contrast with previous screening methods necessitating positional cloning efforts or generation of parthenogenetic embryos, this approach requires nothing particular but appropriately crossed mice and can be readily applied to any tissues at various developmental stages. Hence, AMD would considerably accelerate the identification of imprinted genes playing pivotal roles in mammalian development and the pathogenesis of various diseases.

Parental chromosome-specific chromatin conformation in the imprinted U2af1-rs1 gene in the mouse

The imprinted U2af1-rs1 gene on mouse chromosome 11 is expressed exclusively from the paternal allele. We found that U2af1-rs1 resides in a chromosomal domain that displays marked differences in chromatin conformation and DNA methylation between the parental chromosomes. Chromatin conformation was assayed in brain and liver, in fetuses, and in embryonic stem cells by sensitivity to nucleases in nuclei. In all these tissues, the unmethylated paternal chromosome is sensitive to DNase-I and MspI and has two DNase-I hypersensitive sites in the 5'-untranslated region. In brain and in differentiated stem cells, which display high levels of U2af1-rs1 expression, a paternal DNase-I hypersensitive site is also readily apparent in the promoter region. On the maternal chromosome, in contrast, the entire U2af1-rs1 gene and its promoter are highly resistant to DNase-I and MspI in all tissues analyzed and are fully methylated. No differential MNase sensitivity was detected in this imprinted domain. The parental chromosome-specific DNA methylation and chromatin conformation were also present in parthenogenetic and androgenetic cells and in tissues from animals maternally or paternally disomic for chromosome 11. This demonstrates that these parental chromosome-specific epigenotypes are independently established and maintained and provides no evidence for interallelic trans-sensing and counting mechanisms in U2af1-rs1.

Genomic imprinting in the brain

Human genetic studies have directed attention to genetic imprinting in a number of syndromes involving brain dysfunction, such as Prader-Willi syndrome, Angelman syndrome, Turner's syndrome, bipolar depression and schizophrenia. Molecular genetics is providing insights into the complexity of these imprinting mechanisms, while experimental studies are revealing the differential roles that maternal and paternal genomes may play in brain development and growth.

A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA

Recognition of a functional 3' splice site in pre-mRNA splicing requires a heterodimer of the proteins U2AF65/U2AF35. U2AF65 binds to RNA at the polypyrimidine tract, whereas U2AF35 is thought to interact through its arginine/serine-rich (RS) domain with other RS-domain-containing factors bound at the 5' splice site, assembled in splicing enhancer complexes, or associated with the U4/U6.U5 small nuclear ribonucleoprotein complex. It is unclear, however, how such network interactions can all be established through the small RS domain in U2AF. Here we describe the function of a U2AF35-related protein (Urp), which is the human homologue of a mouse imprinted gene. Nuclear extracts depleted of Urp are defective in splicing, but activity can be restored by addition of recombinant Urp. U2AF35 could not replace Urp in complementation, indicating that their functions do not overlap. Co-immunodepletion showed that Urp is associated with the U2AF65/U2AF35 heterodimer. Binding studies revealed that Urp specifically interacts with U2AF65 through a U2AF35-homologous region and with SR proteins (a large family of RS-domain-containing proteins) through its RS domain. Therefore, Urp and U2AF35 may independently position RS-domain-containing factors within spliceosomes.

Requirement for protein synthesis during embryonic genome activation in mice

Embryonic genome activation (EGA) occurs by the 2-cell stage in mouse embryos. To understand the molecular basis of EGA, it is important to determine whether EGA can be supported by maternally inherited factors or if it requires the synthesis of additional transcription factors. We used a quantitative reverse transcription-polymerase chain reaction (RT-PCR) method to test whether protein synthesis is required for the transcriptional activation of six housekeeping genes (U2afbp-rs, Hprt, Pdha1, Prps1, Odc, and Cox7c). Cycloheximide treatment reduced the expression of these mRNAs in 2-cell embryos to the same degree as alpha-amanitin treatment. Cycloheximide treatment did not reduce the expression of maternally inherited mRNAs, indicating that its effect is specific for transcription-dependent gene expression. These results contrast with earlier results reported for the Hsp70 gene. This difference may reflect differences in promoter requirements. We conclude that protein synthesis is required for the activation of most, if not all, housekeeping genes in the mouse embryo, and that the time of EGA may be controlled, in part, by the regulated recruitment of maternal mRNAs encoding key transcription factors.

Molecular evolution of imprinted genes: no evidence for antagonistic coevolution

Genomically imprinted genes are those for which expression is dependent on the sex of the parent from which they are derived. Numerous theories have been proposed for the evolution of genomic imprinting: one theory is that it is an intra-individual manifestation of classical parent -offspring conflict. This theory is unique in predicting that an arms race may develop between maternally and paternally derived genes for the control of foetal growth demands. Such antagonistic coevolution may be mediated through changes in the structure of the proteins concerned. Comparable coevolution is the most likely explanation for the rapid changes seen in antigenic components of parasites and antigen recognition components of immune systems. We have examined the evolution of insulin-like growth factor Igf2, and its antagonistic receptor Igf2r) and find that in contrast to immune genes, at the sites of mutual binding they are highly conserved. In addition, we have analysed the rate of molecular evolution of seven imprinted genes including Igf2 and Igf2r), sequenced in both mouse and rat, and had that this is the same as that of nonimprinted receptors and significantly lower than that of immune genes controlling for differences in mutation rates. Contrary to the expectations of the conflict hypothesis, we hence find no evidence for antagonistic coevolution of imprinted genes mediated by changes in sequence.

DNA methylation in genomic imprinting

As a reversible epigenetic modification which can affect gene expression, DNA methylation has been an attractive candidate for the biochemical mechanism of genomic imprinting. Many correlations in mice and humans link allele-specific DNA methylation to the allele-restricted RNA expression which is the hallmark of imprinted genes. Moreover, abnormal DNA methylation accompanies the pathological functional imprinting of certain human genes on chromosome 11p15.5 in Wilms' tumors and in the Beckwith-Weidemann syndrome and on chromosome 15q11-13 in the Prader-Willi and Angelman syndromes. A role for DNA methylation in maintaining the transcriptional silence of imprinted alleles at some loci has been supported by pharmacological manipulation with 5-aza-2'-deoxycytidine and by experiments with methyltransferase deletion mice. Gametic differences in DNA methylation could also account for the initiation of imprints, but this remains unproven. Comprehensive physical models for the role of DNA methylation in imprinting must account not only for local allele-restricted gene expression but also for the existence of large chromosomal domains containing multiple coordinately imprinted genes.

Loss of imprinting of human insulin-like growth factor II gene, IGF2, in acute myeloid leukemia

Genomic imprinting is a non-Mendelian form of gene regulation resulting in differential allelic expression of a gene and plays an important role in the development of certain types of cancer and genetic diseases. Imprinting of IGF2 was demonstrated in normal placenta and fetal kidney by showing monoallelic paternal expression. In contrast, several kinds of tumor showed biallelic expression of IGF2, suggesting that relaxation of the normal imprinting of this growth cytokine may be a feature of some tumors. In this study we wished to determine whether relaxation of IGF2 imprinting was also common in human leukemias. An intragenic Apa I polymorphism within the 3' untranslated region of the gene was used to examine allele-specific transcription in leukemic blasts derived from 24 primary patients with acute myeloid leukemia by RT-PCR. Leukemic samples from 12 of the 24 leukemia patients were identified as heterozygous for IGF2 and potentially informative for the RT-PCR assay. RNA-PCR from these informative leukemia samples studied showed biallelic expression of IGF2, indicating loss of normal imprinting of this gene to be very frequent. In conclusion, constitutional loss of monoallelic expression in 50% of the leukemia samples tested suggests that abnormal imprinting of IGF2 could play an important role in either leukemogenesis or cytokine dysregulation for leukemic cells.

A unique downregulation of h2-calponin gene expression in Down syndrome: a possible attenuation mechanism for fetal survival by methylation at the CpG island in the trisomic chromosome 21

To understand the effect of trisomic chromosome 21 on the cause of Down syndrome (DS), DNA methylation in the CpG island, which regulates the expression of adjacent genes, was investigated with the DNAs of chromosome 21 isolated from DS patients and their parents. A methylation-sensitive enzyme, BssHII, was used to digest DNAs of chromosome 21, and the resulting DNA fragments were subjected to RLGS (restriction landmark genomic scanning). Surprisingly, the CpG island of the h2-calponin gene was shown to be specifically methylated by comparative studies with RLGS and Southern blot analysis. In association with this methylation, h2-calponin gene expression was attenuated to the normal level, although other genes in the DS region of chromosome 21 were expressed dose dependently at 1.5 times the normal level. These results and the high miscarriage rate associated with trisomy 21 embryos imply that the altered in vivo methylation that attenuates downstream gene expression, which is otherwise lethal, permits the generation of DS neonates. The h2-calponin gene detected by the RLGS procedure may be one such gene that is attenuated.

Association of IGF2 and H19 imprinting with choriocarcinoma development

We studied IGF2 and H19 expression, and methylation status of H19 gene in androgenetic moles and choriocarcinomas. The human placentae were examined similarly as a control. The CpG sites analyzed for methylation covered the 5' portion and the entire coding regions of H19. Although the paternal IGF2 and the maternal H19 allele were exclusively transcribed in full-term placentae, both H19 alleles were active in early placentate of 6-8 weeks gestation. The level of H19 expression in the mole was similar to that in normal placentae, which is compatible with the finding that half of the H19 gene was methylated and the remaining one was hypomethylated en masse in the complete mole. These imply the importance of regulating the level of H19 transcription not only for normal embryogenesis but also for the development of androgenetic moles. Choriocarcinomas were characterized by a low expression of IGF2 and a high expression of H19 with the transcripts being apparently intact in size. Biallelic expression of IGF2 or H19 was found frequently but not consistently in choriocarcinomas. Contrary to expectation, enhanced H19 expression was accompanied by hypermethylation of CpG sites over the entire gene region, apparently being at variance with the finding in normal placentae and androgenetic moles. The hypermethylation of CpG sites was also recognized in choriocarcinoma specimens surgically removed. The active H19 allele was unmethylated in placentae and probably so in androgenetic moles, but it was heavily methylated in choriocarcinomas. These findings provide the possibility that the mutated promoter is responsible for overcoming transcriptional suppression by CpG methylation in the H19 gene.

Genomic imprinting and its relevance to genetic diseases

Genomic imprinting is a biological phenomenon determined by an evolutionally acquired, underlying system that may control harmonious development and growth in mammals. It is also relevant to some genetic disorders in man. In this article, lines of biological evidence of imprinting, characteristics of the mouse and human imprinted genes, and findings and mechanisms on the occurrence of several human imprinting disorders are reviewed.

A novel serine/threonine kinase gene, Gek1, is expressed in meiotic testicular germ cells and primordial germ cells

We have isolated a novel serine/ threonine kinase gene designated Gek1 from mouse primordial germ cell-derived embryonic germ cell. Gek1 is preferentially expressed in meiotic testicular germ cells and primordial germ cells. Gek1 mRNA is also detected in several other tissues, including hematopoietic organs in adult mice and central nervous system in embryos. The Gek1 cDNA encodes a protein with the consensus sequence of the catalytic domain of protein kinases in its N-terminal region. The deduced amino acid sequence of Gek1 in the kinase domain is related to those encoded by the Saccharomyces cerevisiae STE20, CDC15, and Drosophila melanogaster ninaC. The patterns of expression and the structural features of Gek1 suggest that the gene product is involved in signal transduction or nuclear division of germ cells and other proliferating cells. We also show that Gek1 locates on chromosome 11, near the wr locus, showing neuronal and reproductive defects.

DNA methylation: biology and significance

The modification of DNA by cytosine methylation is crucial for normal development. DNA methylation patterns are distinctive between tissues and are maintained with high fidelity during cell division. DNA methylation probably exerts its effects through alterations in chromatin structure, with a resultant effect on genetic transcription. 5-methylcytosine is also prone to spontaneous hydrolytic deamination to thymine. Whilst most G:T mismatches so produced are repaired, failure of mismatch repair leads to established mutation. Indeed, mutations that are the result of 5-methylcytosine transitions account for a disproportionate number of genetic mutations described in malignant and non-malignant disease. There is also evidence for substantial deregulation of DNA methylation in malignancy. Whether this deregulation is crucial for the transformation process, or simply an epiphenomenon associated with it, is still not established.

Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M

Normal mammalian development requires a diploid combination of both haploid parental genomes. Uniparental disomy for certain segments of specific chromosomes results in aberrant development or prenatal lethality, indicating that the parental genomes have undergone modifications during gametogenesis. These modifications result in parent-of-origin specific expression for some genes, a phenomenon called genomic imprinting. Recent work with DNA methyltransferase deficient mice showed that differential methylation is the probable basis of the imprinted character of several genes. Screening for endogenous imprinted loci using restriction landmark genomic scanning with methylation sensitive enzymes (RLGS-M) identified eight imprinted RLGS (Irigs) candidate loci. Molecular analysis of the genomic region of one of the loci (Irigs2) resulted in the discovery of the paternally imprinted U2afbp-rs gene within a previously identified imprinted region on mouse chromosome 11 (refs 5, 7). This paper describes the characterisation of a novel imprinted RLGS-M locus, Irigs3, on mouse chromosome 9 (ref. 6). Within this locus we identified the Grf1 (also called Cdc25Mm) gene, which is homologous to the RAS-specific guanine nucleotide exchange factor gene, CDC25, in Saccharomyces cerevisiae. Grf1 is located about 30 kb downstream of the methylation imprinted site, identified by RLGS-M, and shows paternal allele specific expression in mouse brain, stomach and heart. Our results indicate that imprinting may have a role in regulating mitogenic signal transduction pathways during growth and development.

Time of initiation and site of action of the mouse chromosome 11 imprinting effects

Previous studies have shown that mice with paternal disomy for chromosome 11 are consistently larger at birth than their normal sibs, whereas mice with the maternal disomy are consistently smaller. An imprinting effect with monoallelic expression of some gene/s affecting growth was indicated. Here we show that the size differences become established prior to birth and are only maintained subsequently, indicating that the gene repression is limited to prenatal development. Fetal analysis was limited to 12.5-17.5 days post coitum. However by extrapolating the data backwards it could be calculated that both the maternal and paternal size effects might commence as early as 7 days post coitum, although possibly slightly later. It may be deduced that initiation of expression of the gene/s responsible may occur at about this time in development. The two disomy growth rates were mirror-images of each other, suggesting that expressed gene dosage is the underlying cause. Differential growth of the placentas of the two disomies was also found, and extrapolation of these data backwards suggested that the placental size differences were initiated later in development than those for the fetuses. The differential placental growth of the maternal and paternal disomies may therefore have developed independently or emerged as a consequence of the differential fetal growth. In either event it would seem that the expression of the responsible gene occurs in the fetus itself to cause the anomalies of growth. The data therefore provide information on the temporal and tissue specificity of the gene/s responsible for the chromosome 11 imprinting effects. Possible candidate genes are discussed.

Genomic imprinting in unstable DNA diseases

Evidence for recombination suppression has been identified in linkage studies of several unstable DNA diseases. Also sex-specific changes in recombination frequency have been detected at the loci of Huntington's disease and myotonic dystrophy. It can be hypothesized that meiotic recombination is regulated by genome-wide genomic imprinting and that changes in meiotic recombination imply the presence of the genomic imprinting defect. If aberrant recombination at the locus of trinucleotide repeat expansion is verified, new theoretical and experimental opportunities will arise in studies on the role of genomic imprinting in the unstable DNA disease.

Imprinted genes and regulation of gene expression by epigenetic inheritance

Six new imprinted genes have recently been identified by association with established imprinted regions, in systematic screens or by serendipity. This brings the total to seventeen imprinted genes, which display a wide variety of functions. Some imprinted genes have been shown to be both physically and mechanistically linked within domains that are under the control of an imprinting centre. Others may apparently undergo imprinting independently. Methylation is clearly required for maintenance of mono-allelic expression while chromatin structure and non-coding RNAs may also play a role.

Expression of H19 and Igf2 genes in uniparental mouse ES cells during in vitro and in vivo differentiation

Genomic imprinting is a process that results in the differential expression of genes according to their parental inheritance. Two imprinted genes, insulin-like growth factor 2 (Igf2) and H19 are closely linked on mouse chromosome 7, and are expressed from the paternal and maternal alleles, respectively. The genes show striking similarity in their tissue-specific expression patterns, which led to the proposal that their transcription is controlled by a common regulatory domain that enables only one gene to be active from each chromosome. Evidence is accumulating, however, that the expression of H19 and Igf2 genes is not always from their respective maternal and paternal alleles. This suggests that their expression is regulated independently of imprinting in some tissues and teratomas. We have analysed the extent of non-imprinted expression of H19 and Igf2 in uniparental mouse embryonic stem (ES) cells during in vitro differentiation, and differentiation in teratomas using Northern blot and in situ hybridisation analysis. The expression patterns observed indicate that both imprinting and non-imprinting mechanisms regulate transcription of these genes. Expression of one or the other gene was observed in certain cell types in differentiated cultures and in teratomas, suggesting that imprinting regulates the expression of H19 and Igf2 genes in some differentiating cell lineages. At the same time, in other subpopulations of cells, co-expression of both genes was observed, demonstrating that the expression of these genes is not always regulated by genomic imprinting.

Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes

Embryonic stem (ES) cells homozygous for a disruption of the DNA (cytosine-5)-methyltransferase gene (Dnmt) proliferate normally with their DNA highly demethylated but die upon differentiation. Expression of the wild-type Dnmt cDNA in mutant male ES cells caused an increase in methylation of bulk DNA and of the Xist and Igf2 genes to normal levels, but did not restore the methylation of the imprinted genes H19 and Igf2r. These cells differentiated normally in vitro and contributed substantially to adult chimeras. While the Xist gene was not expressed in the remethylated male ES cells, no restoration of the normal expression profile was seen for H19, Igf2r, or Igf2. This indicates that ES cells can faithfully reestablish normal methylation and expression patterns of nonimprinted genes but lack the ability to restore those of imprinted genes. Full restoration of monoallelic methylation and expression was imposed on H19, Igf2, and Igf2r upon germ-line transmission. These results are consistent with the presence of distinct de novo DNA methyltransferase activities during oogenesis and spermatogenesis, which specifically recognize imprinted genes but are absent in the postimplantation embryo and in ES cells.

Multiple roles for DNA methylation in gametic imprinting

Allele-specific DNA methylation has been observed for all tested imprinted genes and has a clear role in the imprinting mechanism. It remains to be resolved whether this role is to act as the gametic imprinting signal or to cause or maintain allele-specific expression.

Restriction landmark cDNA scanning (RLCS): a novel cDNA display system using two-dimensional gel electrophoresis

We have developed a new method, designated restriction landmark cDNA scanning (RLCS), which displays many cDNA species quantitatively and simultaneously as two-dimensional gel spots. In this method cDNA species of uniform length were prepared for each mRNA species using restriction enzymes. After the restriction enzyme sites were radiolabeled as landmarks, the labeled fragments were subjected to high resolution two-dimensional gel electrophoresis. In analyses of cDNA samples from adult mouse liver and brain (cerebral cortex, cerebellum and brain stem) we detected approximately 500 and >1000 discrete gel spots respectively of various intensities at a time. The spot patterns of the three brain regions were very similar, although not identical, but were quite different from the pattern for the liver. RNA blot hybridization analysis using several cloned spot DNAs as probes showed that differences in intensity of the spots among RLCS profiles correlated well with expression levels of the corresponding mRNA species in the brain regions. Because the spots and their intensities reflect distinct mRNA species and their expression level respectively, the RLCS is a novel cDNA display system which provides a great deal of information and should be useful for systematic documentation of differentially expressed genes.

Initiation binding repressor, a factor that binds to the transcription initiation site of the histone h5 gene, is a glycosylated member of a family of cell growth regulators [corrected]

Initiation binding repressor [corrected] (IBR) is a chicken erythrocyte factor (apparent molecular mass, 70 to 73 kDa) that binds to the sequences spanning the transcription initiation site of the histone h5 gene, repressing its transcription. A variety of other cells, including transformed erythroid precursors, do not have IBR but a factor referred to as IBF (68 to 70 kDa) that recognizes the same IBR sites. We have cloned the IBR cDNA and studied the relationship of IBR and IBF. IBR is a 503-amino-acid-long acidic protein which is 99.0% identical to the recently reported human NRF-1/alpha-Pal factor and highly related to the invertebrate transcription factors P3A2 and erected wing gene product (EWG). We present evidence that IBR and IBF are most likely identical proteins, differing in their degree of glycosylation. We have analyzed several molecular aspects of IBR/F and shown that the factor associates as stable homodimers and that the dimer is the relevant DNA-binding species. The evolutionarily conserved N-terminal half of IBR/F harbors the DNA-binding/dimerization domain (outer limits, 127 to 283), one or several casein kinase II sites (37 to 67), and a bipartite nuclear localization signal (89 to 106) which appears to be necessary for nuclear targeting. Binding site selection revealed that the alternating RCGCRYGCGY consensus constitutes high-affinity IBR/F binding sites and that the direct-repeat palindrome TGCGCATGCGCA is the optimal site. A survey of genes potentially regulated by this family of factors primarily revealed genes involved in growth-related metabolism.

Stage-specific and cell type-specific aspects of genomic imprinting effects in mammals

Recent studies have revealed that maternal and paternal alleles of some imprinted genes are differentially expressed from the earliest time of expression, with virtually no expression from one of the two alleles, while for other imprinted genes the normally silent allele can be transcribed during early development. In addition, a number of imprinted genes manifest their imprints only in select tissues. These observations indicate that the marks that denote parental chromosome origin need not directly determine allele expression, but rather bias later epigenetic modifications toward a particular allele. Thus, factors expressed at specific stages or in specific cell types are required to silence one parental allele or another. Stage-dependent and tissue-specific epigenetic modifications include the progressive establishment of the mature adult parental allele-specific DNA methylation patterns. These changes resemble and may share a common mechanistic basis with other epigenetic modifications that occur during development. Understanding the mechanisms by which these post-fertilization epigenetic modifications are mediated and regulated will be essential for understanding how genomic imprinting leads to differences in parental allele expression.

Indirect gene diagnoses for complex (multifactorial) diseases--a review

The analysis of multifactorial diseases requires the efficient investigation of large numbers of (gene) loci and patient (family) samples. Since simple repetitive DNA markers are dispersed all over the chromosomes, molecular techniques employing these tools render most conventional screening procedures obsolete. Examples of tumors, autoimmune diseases and infections are presented to validate concepts of indirect gene diagnoses via simple, tandemly arranged, repetitive DNA sequences. The salient advantages of microsatellite technologies vs. those of multilocus DNA fingerprinting are weighed.

CpG islands and genes

Of the estimated 45,000 CpG islands in the human genome, the overwhelming majority are found at the 5' ends of genes and their identification and cloning are proving very useful for finding and isolating genes. Recent work has shed light on the chromosomal distribution and origin of CpG islands. It has been shown unequivocally that CpG islands are concentrated in the R band chromosomal regions and that intact transcription factor binding sites and required for their maintenance. Cases of methylation of CpG islands and inactivation of the associated genes have been reported which may be important in ageing, tumorigenesis and imprinting.

Deregulation of both imprinted and expressed alleles of the insulin-like growth factor 2 gene during beta-cell tumorigenesis

In a mouse model of multistage carcinogenesis elicited by the SV40 large T-antigen (Tag) oncogene in pancreatic beta cells, the gene for insulin-like growth factor IGF2 is focally up-regulated and functionally implicated in tumour development. The IGF2 gene is differentially regulated in normal tissues: the paternal allele is transiently expressed during embryogenesis, whereas the maternal allele is genomically imprinted and inactive. Crossbred mice carrying the Tag oncogene and a disruption of either the paternal or maternal allele of IGF2 reveal that both alleles are co-activated early during tumour development, and that each contributes to malignant hyperproliferation and consequent tumour volume.

Regulation of genomic imprinting by gametic and embryonic processes

Parental genomic imprinting refers to the phenomenon by which alleles behave differently depending on the sex of the parent from which they are inherited. In the case of the murine transgene RSVIgmyc, imprinting is manifest in two ways: differential DNA methylation and differential expression. In inbred FVB/N mice, a transgene inherited from a male parent is undermethylated and expressed; a transgene inherited from the female parent is overmethylated and silent. Using a series of RSVIgmyc constructs and transgenic mice, we show that the imprinting of this transgene requires a cis-acting signal that is principally derived from the repeat sequences that make up the 3' portion of the murine immunoglobulin alpha heavy-chain switch region. Such imprinting is relatively independent of the site of transgene insertion but is influenced by the structure of the transgene itself. Imprinting is also modulated by genetic background. Detailed studies indicate that the paternal allele is undermethylated and expressed in inbred FVB/N mice and in heterozygous F1 FVB/N/C57Bl/6J mice but is overmethylated and silent in inbred C57Bl/6J mice. Consequently, the FVB/N genome appears to carry alleles of modulating genes that dominantly block methylation and permit expression of the paternally imprinted transgene. Furthermore, our results suggest that overmethylation is the default status of both parental alleles and that the paternal allele can be marked in trans by polymorphic factors that act in postblastocyst embryos.

A novel strategy to identify maternal and paternal inheritance in the mouse

A novel strategy for identifying proteins which reveal maternal or paternal inheritance in the mouse is presented. Using two-dimensional electrophoresis we investigated protein expression patterns of adult liver and different embryonic and extraembryonic tissue in C57BL/6Crl and in DBA/2Crl mice, as well as in their reciprocal hybrids. We found three groups of protein spots which showed maternal or paternal inheritance of quantitative variations. These proteins were characterized by N-terminal or internal amino acid sequencing, by determination of the amino acid composition, by glycoprotein staining and RNA expression analysis. The three proteins identified were: alpha-enolase, cyclophilin and beta-group hemoglobins. The parental effects observed for alpha-enolase and cyclophilin were found to be due to parent-specific post-translational modifications of these proteins. For the beta-group hemoglobins our results suggested parental effects on the transcriptional level.

A paternal-specific methylation imprint marks the alleles of the mouse H19 gene

Imprinting, the differential expression of the two alleles of a gene based on their parental origin, requires that the alleles be distinguished or marked. A candidate for the differentiating mark is DNA methylation. The maternally expressed H19 gene is hypermethylated on the inactive paternal allele in somatic tissues and sperm, but to serve as the mark that designates the imprint, differential methylation must also be present in the gametes and the pre-implantation embryo. We now show that the pattern of differential methylation in the 5' portion of H19 is established in the gametes and a subset is maintained in the pre-implantation embryo. That subset is sufficient to confer monoallelic expression to the gene in blastocysts. We propose that paternal-specific methylation of the far 5' region is the mark that distinguishes the two alleles of H19.

Accessibility to tissue-specific genes from methylation profiles of mouse brain genomic DNA

The DNA methylation status of a large number of genomic loci is visualized simultaneously and quantitatively as two-dimensional gel spots in the newly developed restriction landmark genomic scanning with a methylation-sensitive restriction enzyme (RLGS-M). Here, we demonstrate that RLGS-M using NorI as a methylation-sensitive enzyme could also scan gene loci of mammalian genomes, since almost all of the NotI loci corresponding to randomly chosen RLGS-M spots were located near or in transcriptional units (6 out of 7 NotI-linking clones) when mouse brain genomic DNA was used. This supports the previous prediction that most NotI sites are located in CpG islands (Lindsay and Bird, Nature 1987, 327, 336-338). Furthermore, beginning with RLGS-M spots we examined how to approach their corresponding RNA messages, whose expression may be associated with methylation. We compared RLGS-M patterns among various developmental stages of the mouse brain from embryonic day 9.5 to postnatal 8 weeks or among in vitro cell lines, and detected alterations of RLGS-M spots which were due to methylation of NotI sites. Two experiments using NotI-linking clones or polymerase chain reaction (PCR) were carried out to approach to their corresponding RNA messages. Consequently, we isolated two PCR-amplified clones (# 15 and # 91) which corresponded to methylatable loci and gave positive signals to mRNA from the adult brain. Furthermore, we identified two NotI-linking clones (C211 and C198) whose corresponding NotI loci localized near or at transcriptional units and were methylated in cell lines.(ABSTRACT TRUNCATED AT 250 WORDS)

A spot cloning method for restriction landmark genomic scanning

We introduce two new methods for target cloning of DNA fragments corresponding to spots on the two-dimensional profile of restriction landmark genomic scanning (RLGS). One is a restriction trapper-based method and the other is a polymerase chain reaction (PCR) mediated method. Both are designed to select the target DNA fragments from a large amount of unlabeled background DNA fragments in the RLGS gel which produce background clones. The restriction trapper method is simple, with a cloning efficiency that is not biased by the length of the target DNA nor by its GC content. On the other hand, the PCR-mediated method is efficient for cloning DNA fragments from a small amount of starting materials. These methods provide us with powerful tools for isolating DNA clones identified by the RLGS system as interesting spots. This paper reports the precise protocols of these methods and discusses their application and usefulness.

The use of restriction landmark genomic scanning to scan the mouse genome for endogenous loci with imprinted patterns of methylation

Restriction landmark genomic scanning (RLGS) has been used to screen endogenous loci for imprinted patterns of methylation. The screening method is based upon the identification of genetic variation in RLGS profiles between different strains and determining whether specific variant landmarks are transmitted equally to the progeny of reciprocal F1 matings. The RLGS profiles of C57BL/6 (B6) and DBA/2 (D2) and their reciprocal hybrids were produced with two enzyme combinations that used NotI as the landmark enzyme and two combinations that used BssHII. An estimated 13% of the spots are either B5- or D2-specific in these tests, giving a total of nearly 1000 variant loci that were examined for imprinted methylation. Three candidate loci for imprinted regulation were identified in these analyses. We also used crosses of more genetically diverse parents to increase the number of variant loci screened. Interspecific crosses of B6 with the M. musculus strain PWK and intrasubspecific crosses between B6 and the M. molossinus strain MSM expanded the levels of variation between the parental strains in the cross to an estimated 31% and 26%, respectively. The RLGS patterns for one NotI combination and one BssHII profile were examined for each of these crosses, giving approximately 2000 additional loci that were screened for imprinted patterns of methylation. Eight loci with imprinted patterns of transmission were observed out of 3040 loci tested. The chromosomal locations for the three B6 and D2 specific loci, Irlgs 1-3, were identified using BXD recombinant inbred strain analysis. Irlgs 1 and 3 are B6- and D2-specific loci that had the same strain distribution pattern which mapped to the central region of chromosome 9.(ABSTRACT TRUNCATED AT 250 WORDS)

Quantitative and qualitative genetic variation in two-dimensional DNA gels of human lymphocytoid cell lines

There is a continuing need for more efficient methods to examine human (and other) populations for altered germinal and somatic cell mutation rates. To this end, we have explored the potential usefulness of two-dimensional (2-D) electrophoresis of human DNA fragments obtained from restriction-enzyme-digested genomic DNA, using samples from father/mother/child trios. On a single 2-D DNA preparation, approximately 2000 DNA fragments varying in size from 1.0 to 5.0 kbp in the first dimension and 0.3 to 2.0 kbp in the second dimension are visualized. To enter into a genetic analysis of quantitative variation, these fragments must exhibit positional and quantitative stability. With respect to the latter, if spots that are the product of two homologous DNA fragments are to be distinguished with the requisite accuracy from spots that are the product of only one fragment, the coefficient of variation of spot intensity should be approximately < or = 0.12. At present, 482 of the spots in our preparations meet these standards. In an examination of preparations based on three Japanese mother/father/child trios, 43 of these 482 spots were found to exhibit variations that segregated within families according to Mendelian principles. Additionally, of the 2000 spots, 1114 (of which the aforementioned 482 are a subset) were deemed appropriate for the study of qualitative variation. A total of 142 variable spots were identified; the heterozygosity index for these DNA fragments was 4.4%. The genetic nature of the additional variants was again established by their segregation according to Mendelian principles. We have established the feasibility of cloning fragments from such gels and determining their nucleotide sequence. This technology should be highly efficient in monitoring for mutation resulting in loss/gain/rearrangement events in DNA fragments distributed throughout the genome.

An expanded system of restriction landmark genomic scanning (RLGS Ver. 1.8)

The restriction landmark genomic scanning (RLGS) method is a high-speed genome scanning system which is based on the concept that restriction enzyme sites can be used as landmarks throughout the genome. It employs direct end-labeling of the genomic DNA digested with a rare-cutting restriction enzyme, followed by high-resolutional two-dimensional electrophoresis. Recently, this system was further developed to lower cost and to simplify the procedure. This paper reviews the RLGS principle and the breakthroughs enabling its further development. Also presented is the precise protocol of the newest version (RLGS Ver. 1.8) that offers cost effectiveness and an expanded production system. Finally, the advantages of this new RLGS method and prospects for its widespread application are discussed.

Genetic mapping of restriction landmark genomic scanning loci in the mouse

Restriction landmark genomic scanning (RLGS) was originally proposed as a high-speed method for surveying a large number of restriction landmarks in genomic DNA. The effort to apply this method to genetic analysis has been made, resulting in developing the new approach for the rapid construction of the genetic map of complex mammalian genomes (RLGS spot mapping). Especially, the use of NotI as the restriction landmark for genetic studies suggests that there is a high probability that a significant number of these RLGS loci will be associated with CpG islands of functional genes. Moreover, it is possible to use the RLGS spot mapping to analyze genetic map-poor species very rapidly for linkage of recessive mutations or segregating traits, because it does not rely upon cloned probes or sequences. In this paper, we summarize the progress that has been made in the practical application of the RLGS method to genetic analysis using congenic strains, recombinant inbred (RI) strains, and in interspecific backcrosses of mice.

Genomic imprinting proposed as a surveillance mechanism for chromosome loss

One consequence of genomic imprinting is that loss of the transcriptionally active chromosomal homologue causes a change in gene expression that might permit surveillance of chromosome-loss events. Possible selective advantages of such surveillance include protection against cancer and early elimination of monosomic and trisomic fetuses. Potential mechanisms for such surveillance are discussed.

Identification of genes showing altered expression in preimplantation and early postimplantation parthenogenetic embryos

Uniparental embryos have been instrumental in studying imprinting because contributions from the parental genomes can be determined unambiguously. In this study, we set out to identify imprinted genes showing differential expression between parthenogenetic and fertilized embryos during preimplantation and early postimplantation stages of development. We identified three genes--apolipoprotein E, pyruvate kinase-3, and protein phosphatase 1 gamma--that represent excellent candidates for imprinted genes, based on the results of the differential screen, their function in differentiation and the cell cycle, and their location within imprinted chromosomal regions. In addition, two novel genes expressed in trophoblast were identified, 1661 and RA81. These genes, together with four known imprinted genes, H19, Igf2r, Igf2, and Snrpn, showed evidence of expression from both parental alleles in early stage embryos, indicating a role for postfertilization processes in regulating imprinted gene function.

Chromatin structure and imprinting: developmental control of DNase-I sensitivity in the mouse insulin-like growth factor 2 gene

The insulin-like growth factor 2 (Igf2) gene on distal mouse chromosome 7 is expressed predominantly from the paternal allele. In previous studies we identified two regions of paternal allele-specific methylation; one at approximately 3 kb upstream of promoter 1, and a second in the 3', coding portion of the gene. The 3' region is methylated in an expressing tissue (fetal liver), whereas in a non-expressing tissue (fetal brain), it is not methylated. By contrast, in the 5' region, the paternal allele is highly methylated in all tissues. Here, we have studied another characteristic of chromatin, namely, sensitivity to DNase-I and have focused our developmental analysis on the two differentially methylated regions of Igf2. In the upstream region, four clustered DNase-I hypersensitive sites (HSS) were detected in embryonic stem (ES) cells and in midgestation embryos, but not in neonatal liver or brain. In promoter 1 (P1), at approximately 0.3 kb upstream of exon 1, we detected a tissue-specific HSS that was present in neonatal liver, in which P1 is active, but was absent in ES cells, the embryo, and in neonatal brain. No DNase-I HSS were detected in the 3' differentially methylated region of Igf2. In all these regions, we did not detect differences in DNase-I sensitivity between the parental chromosomes. These results establish major developmental and tissue-specific control of chromatin in the Igf2 locus. The presence of the HSS upstream of Igf2 precedes transcriptional activation of the Igf2 gene and may be indicative of a promoter for another transcript that is transcribed in the opposite direction. The HSS in P1 is largely liver-specific; this promoter therefore is differently regulated than the more general fetal promoters P2 and P3. Whereas methylation can be allele-specific, presumably reflecting the gene imprint, the nuclease sensitivity, as detected by our assay, is not. These results, taken together with previous observations, reveal developmental and tissue-specific complexity in the expression of the parental imprint at the level of chromatin and transcription. We propose that epigenetic features of tissue-specific control and of the control of allelic expression are intricately linked.

Mechanistic and developmental aspects of genetic imprinting in mammals

Genetic imprinting in mammals allows the recognition and differential expression of maternal and paternal alleles of certain genes. Recent results from a number of laboratories indicate that, at least for some genes, gametic imprints, which must exist in order to mark chromosomes or genes as having been transmitted via sperm or ovum, are not by themselves sufficient to determine allele expression. Other postfertilization events are required, and these events are subject to both tissue-specific and developmental stage-specific regulation. Changes in imprinted gene methylation during preimplantation and fetal life indicate that the establishment of additional allele-specific modifications is likely to contribute to imprinted regulation. Disruptions in imprinting processes, loss of imprints, and loss of nonimprinted alleles through uniparental disomy are likely to contribute to a variety of developmental abnormalities and pathological conditions in both mice and humans.

Expression of X-linked genes in androgenetic, gynogenetic, and normal mouse preimplantation embryos

A quantitative RT-PCR approach has been used to examine the expression of a number of X-linked genes during preimplantation development of normal mouse embryos and in androgenetic and gynogenetic mouse embryos. The data reveal moderately reduced expression of the Prps1, Hprt, and Pdha1 mRNAs in androgenetic eight-cell and morula stage embryos, but not in androgenetic blastocysts. Pgk1 mRNA abundance was severely reduced in androgenones at the eight-cell and morula stages and remained reduced, but to a lesser degree, in androgenetic blastocysts. These data indicate that paternally inherited X chromosomes are at least partially repressed in androgenones, as they are in normal XX embryos, and that the degree of this repression is chromosome position-dependent or gene-dependent. Gynogenetic embryos expressed elevated amounts of some mRNAs at the morula and blastocyst stages, indicative of a delay in dosage compensation that may be chromosome position-dependent. The Xist RNA was expressed at a greater abundance in androgenones than in gynogenones at the eight-cell and morula stages, consistent with previous studies. Xist expression was observed in both androgenones and gynogenones at the blastocyst stage. We conclude that the developmental arrest in early androgenones may be, in part, due to reduced expression of essential X-linked genes, particularly those near the X inactivation center, whereas the developmental defects of gynogenones and parthenogenones, by contrast, may be partially due to overexpression of X-linked genes in extraembryonic tissues, possibly those farthest away from the X inactivation center.

Loss of the imprinted IGF2/cation-independent mannose 6-phosphate receptor results in fetal overgrowth and perinatal lethality

Murine embryos that inherit a nonfunctional insulin-like growth factor-II/cation-independent mannose 6-phosphate receptor (Igf2r) gene from their fathers are viable and develop normally into adults. However, the majority of mice inheriting the same mutated allele from their mothers die around birth, as a consequence of major cardiac abnormalities. These mice do not express IGF2R in their tissues, are 25-30% larger than their normal siblings, have elevated levels of circulating IGF2 and IGF-binding proteins, and exhibit a slight kink in their tails. These results show that Igf2r is paternally imprinted and reveal that the receptor is crucial for regulating normal fetal growth, circulating levels of IGF2, and heart development.

Methylation imprinting was observed of mouse mo-2 macrosatellite on the pseudoautosomal region but not on chromosome 9

Mouse mo-2 macrosatellites consisting of 31-bp tandem repeat units are mainly located at two loci in the C57BL/6 genome, one being at the centromere-distal telomeric region of chromosome 9 and the other at the pseudoautosomal (PA) region of chromosomes X and Y. The two clusters constitute approximately 300 kb and 150 kb, respectively. Southern analysis of a methylation-sensitive enzyme, HpaII-digested DNA showed that the mo-2 macrosatellites are detected as more than 30 polymorphic bands. Comparison of those bands between reciprocally crossed F1 mice revealed that approximately 20% of the allele-specific fragments exhibit different band intensities depending on the sex of the parent of origin. The differential methylation is observed in the mo-2 macrosatellite on the PA region but not in that on chromosome 9. Several fragments including the 3.4-kb fragment without internal HpaII site are more clearly detected when paternally derived, suggesting that the male-derived macrosatellite is undermethylated. Interestingly, the difference is much more remarkable in inter-subspecific F1 mice between C57BL/6 and MSM than F1 between C57BL/6 and C3H/He. This suggests the presence of a modifier(s) that affect(s) the methylation of mo-2 in the MSM genome.

Strain-specific differences in mouse oocytes and their contributions to epigenetic inheritance

Previous experiments revealed a strain-dependent effect of egg cytoplasm on the developmental potential of androgenetic (two paternal genomes) mouse embryos. Eggs obtained from C57BL/6 mice supported androgenone development to the blastocyst stage at a much higher frequency than eggs from DBA/2 mice. Transient exposure of paternal pronuclei to DBA/2 egg cytoplasm also compromised development, indicating that the DBA/2 egg cytoplasm negatively affected the ability of paternal pronuclei to support blastocyst formation. An essential first step toward understanding the molecular mechanism by which egg modifier factors influence gene expression is to determine the number of loci that are responsible for the strain difference. To do this, (B6D2)F1 hybrid females were backcrossed to DBA/2 males and the eggs from individual female progeny assayed for their ability to support androgenetic development. Approximately one fourth of the backcross females produced eggs that failed to support androgenone development, indicating that two independently segregating genetic loci are most likely responsible for the difference between DBA/2 and C57BL/6 egg phenotypes. Comparison of DBA/2 and C57BL/6 oocytes by two-dimensional protein gel electrophoresis revealed at least 17 proteins that exhibited significant, reproducible, quantitative differences in rates of synthesis. All of these proteins were synthesized in (B6D2)F1 oocytes. These data, combined with the previous observation that the C57BL/6 egg phenotype is dominant, are consistent with a model in which a C57BL/6 allele at either locus provides a protective function, either by antagonizing the actions of the DBA/2 alleles or by providing, through partial or complete redundancy, a function not provided by the DBA/2 alleles.

Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning

Restriction landmark genomic scanning (RLGS) is a novel method which enables us to simultaneously visualize a large number of loci as two-dimensional gel spots. By this method, the status of DNA methylation can efficiently be determined by monitoring the appearance or disappearance of spots by using a methylation-sensitive restriction enzyme. In the present study, using RLGS with NotI, we examined, in comparison with a brain RLGS profile, the status of DNA methylation of more than 900 loci among three types of mouse cell lines: the embryonal carcinoma cell line P19, the stable mesenchymal cell line 10T1/2, and our established neuroepithelial (EM) cell lines. We found that the relative numbers of RLGS spots which appeared were less than 3.3% of those surveyed in all cell lines examined. However, 5 to 14% of spots disappeared, the numbers increasing with an increase in the length of the culture period, and many spots were commonly lost in 10T1/2 and in three EM cell lines. Thus, for these cell lines, many more spots disappeared than appeared. However, the numbers of spots disappearing and appearing were well balanced, and the ratio in P19 cells was almost equal to that in liver cells in vivo. These RLGS experimental observations suggested that permanent cell lines such as 10T1/2 are hypermethylated and that our newly established EM cell lines are also becoming heavily methylated at common loci. On the other hand, methylation and demethylation seem to be balanced in P19 cells in a manner similar to that in in vivo liver tissue.

Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning

Restriction landmark genomic scanning (RLGS) is a novel method which enables us to simultaneously visualize a large number of loci as two-dimensional gel spots. By this method, the status of DNA methylation can efficiently be determined by monitoring the appearance or disappearance of spots by using a methylation-sensitive restriction enzyme. In the present study, using RLGS with NotI, we examined, in comparison with a brain RLGS profile, the status of DNA methylation of more than 900 loci among three types of mouse cell lines: the embryonal carcinoma cell line P19, the stable mesenchymal cell line 10T1/2, and our established neuroepithelial (EM) cell lines. We found that the relative numbers of RLGS spots which appeared were less than 3.3% of those surveyed in all cell lines examined. However, 5 to 14% of spots disappeared, the numbers increasing with an increase in the length of the culture period, and many spots were commonly lost in 10T1/2 and in three EM cell lines. Thus, for these cell lines, many more spots disappeared than appeared. However, the numbers of spots disappearing and appearing were well balanced, and the ratio in P19 cells was almost equal to that in liver cells in vivo. These RLGS experimental observations suggested that permanent cell lines such as 10T1/2 are hypermethylated and that our newly established EM cell lines are also becoming heavily methylated at common loci. On the other hand, methylation and demethylation seem to be balanced in P19 cells in a manner similar to that in in vivo liver tissue.