Restriction Landmark Genomic Scanning Profile Research Articles

Folate Deficiency and Supplementation Result in DNA Methylation Defects in Sperm.

Folate is a nutrient that is essential for cell proliferation and involved in the biosynthesis of nucleotides and S-adenosylmethionine (SAM). SAM is the methyl donor for numerous cellular biochemical reactions including DNA methylation, an important epigenetic modification implicated in the control of gene expression, genomic imprinting and normal fertility. Although folate supplementation is used as a treatment for human male infertility, little is known about the effects of low or high dietary folate concentrations on sperm DNA methylation patterns. Our goal was to use a mouse model to examine the effects of folic acid deficiency and supplementation on epigenetic patterns in male germ cells. Male Balb/c strain mice were fed, from weaning age (day 21) to one year of age, either a control diet containing an adequate amount of folic acid (2 mg/kg diet), a 7X low folic acid diet (0.3 mg/kg diet) or a 20X high folic acid diet (40 mg/kg diet). The mice were sacrificed at 12 months and reproductive organs (testes, epididymides and seminal vesicles) collected and weighed. Sperm were collected from the cauda epididymides and genomic DNA extracted. Restriction landmark genomic scanning (RLGS) was used to assess genome-wide levels and patterns of DNA methylation (n=4 samples/group). Although weight gain and reproductive organ weights were not affected by the folate deficiency or supplementation, for both treatment groups, RLGS demonstrated evidence of epigenetic abnormalities in sperm. Mice in the folic acid supplemented group exhibited six consistent changes in their methylation profiles, all of which were hypermethylation. Interestingly, among the 14 loci showing methylation alterations in all of the folic acid deficient mice, 10 were hypermethylated and four were hypomethylated. The loci with altered methylation are in the process of being identified using a virtual RLGS profile. Together, the results indicate that DNA methylation patterns in mouse sperm can be altered by long term exposure to both low and high dietary folate. (Supported by CIHR) (poster)

Aberrant DNA methylation status in human uterine leiomyoma

Aberrant DNA methylation has been implicated in tumorigenesis. This study was undertaken to establish the genome-wide DNA methylation profile in uterine leiomyomas and to investigate whether DNA methylation status is altered in uterine leiomyomas. For this purpose, restriction landmark genomic scanning (RLGS) was performed on a paired sample of leiomyoma and adjacent normal myometrium. The RLGS profile revealed 29 aberrant methylation spots (10 methylated and 19 demethylated) in leiomyoma in comparison with myometrium. One of the differently methylated genomic loci was newly identified as GS20656 from the human genome sequence database. In 9 of the 10 paired samples, the DNA methylation levels of the first exon of GS20656 were significantly lower in leiomyoma than in myometrium, suggesting the existence of a genomic locus under epigenetic regulation in uterine leiomyomas. Unexpectedly, DNA methyltransferase 1 (DNMT1) and DNMT3a mRNA expression levels were higher in leiomyoma than in myometrium. These facts suggest that other epigenetic factors besides DNMT are involved in local changes of DNA methylation at genome loci. The present study indicates not only aberrant genome-wide DNA methylation status in uterine leiomyomas but also the existence of a genomic locus that is differently methylated between normal myometrium and uterine leiomyoma.

Analysis of Bud Sport Cultivars of Peach (Prunus persica (L.) Batsch) by Simple Sequence Repeats (SSR) and Restriction Landmark Genomic Scanning (RLGS)

To detect genetic mutations in bud sport cultivars of peach, RLGS (restriction landmark genomic scanning) analysis was performed on 7 putative bud sport mutant cultivars after SSR (simple sequence repeats) analysis for identifying false-mutants. Three cultivars, ‘Yawata Hakuho’, ‘Odoroki’, and ‘Kanoiwa Hakuto’, postulated to be bud sport mutants, were confirmed as false-mutant cultivars. This suggests that other false-mutant strains of peach are also likely to be registered with the Plant Variety Authority as bud mutant cultivars. A stable RLGS profile of peach, obtained using NotI as a landmark enzyme, showed about 400 spots in a single experiment. Comparing the profiles between mutant and original cultivars, polymorphic spots were discovered in 2 mutatnt cultivars, ‘Gyosei’ and ‘Nagasawa Hakuho’, but were not detected by SSR analysis. RLGS was thus considered to be an effective method to detect very small genomic variations in mutant strains.

Genome‐wide and locus‐specific DNA hypomethylation in G9a deficient mouse embryonic stem cells

In the mammalian genome, numerous CpG-rich loci define tissue-dependent and differentially methylated regions (T-DMRs). Euchromatin from different cell types differs in terms of its tissue-specific DNA methylation profile as defined by these T-DMRs. G9a is a euchromatin-localized histone methyltransferase (HMT) and catalyzes methylation of histone H3 at lysines 9 and 27 (H3-K9 and -K27). To test whether HMT activity influences euchromatic cytosine methylation, we analyzed the DNA methylation status of approximately 2000 CpG-rich loci, which are predicted in silico, in G9a(-/-) embryonic stem cells by restriction landmark genomic scanning (RLGS). While the RLGS profile of wild-type cells contained about 1300 spots, 32 new spots indicating DNA demethylation were seen in the profile of G9a(-/-) cells. Virtual-image RLGS (Vi-RLGS) allowed us to identify the genomic source of ten of these spots. These were confirmed to be cytosine demethylated, not just at the Not I site detected by the RLGS but extending over several kilobase pairs in cis. Chromatin immunoprecipitation (ChIP) confirmed these loci to be targets of G9a, with decreased H3-K9 and/or -K27 dimethylation in the G9a(-/-) cells. These data indicate that G9a site-selectively contributes to DNA methylation.

DNA Methylation Profiles of Donor Nuclei Cells and Tissues of Cloned Bovine Fetuses

Methylation of DNA in CpG islands plays an important role during fetal development and differentiation because CpG islands are preferentially located in upstream regions of mammalian genomic DNA, including the transcription start site of housekeeping genes and are also associated with tissue-specific genes. Somatic nuclear transfer (NT) technology has been used to generate live clones in numerous mammalian species, but only a low percentage of nuclear transferred animals develop to term. Abnormal epigenetic changes in the CpG islands of donor nuclei after nuclear transfer could contribute to a high rate of abortion during early gestation and increase perinatal death. These changes have yet to be explored. Thus, we investigated the genome-wide DNA methylation profiles of CpG islands in nuclei donor cells and NT animals. Using Restriction Landmark Genomic Scanning (RLGS), we showed, for the first time, the epigenetic profile formation of tissues from NT bovine fetuses produced from cumulus cells. From approximately 2600 unmethylated NotI sites visualized on the RLGS profile, at least 35 NotI sites showed different methylation statuses. Moreover, we proved that fetal and placental tissues from artificially inseminated and cloned cattle have tissue-specific differences in the genome-wide methylation profiles of the CpG islands. We also found that possible abnormalities occurred in the fetal brain and placental tissues of cloned animals.

Global Assessment of Promoter Methylation in a Murine Model of Cancer Identifies ID4 as a Putative Novel Tumor Suppressor Gene in Human Leukemia.

We developed a mouse model of acute T/natural killer (NK) acute lymphoblastic leukemia (ALL) that is always preceded by polyclonal lymphocyte expansion to determine how aberrant promoter DNA methylation and consequent gene silencing might be contributing to leukemic transformation. We demonstrated the non-random nature of methylation in the transformation from benign polyclonal expansion to leukemia, and identified a novel tumor suppressor gene silenced in the majority of human leukemia but not solid tumors. To this, we utilized restriction landmark genomic scanning (RLGS) on eight IL-15 transgenic (tg) mice with T/NK ALL, and performed RLGS on an additional five spleens from IL-15tg mice without ALL, but with polyclonal T/NK expansion, and on four spleens from wild type (wt) mice. A total of 2447 RLGS fragments with good resolution on each RLGS profile were analyzed. Only 1–2 variable changes were detected in either wt or polyclonal T/NK expansion controls. In contrast, the eight spleens with clonal T/NK leukemia had 45 to 209 changes (1.8 to 8.5% of total fragments) consistent with aberrant DNA methylation. The association of RLGS fragment losses or reduced intensity with leukemic transformation versus polyclonal expansion was highly significant (P<0.001). The promoter of Inhibitor of DNA binding 4 (Id4) was found methylated in 87.5% of the mouse T/NK ALLs. ID4 was found methylated in 85.7% (72/84) of primary human acute myeloid leukemias (AML) and in 100% (61/61) of chronic lymphocytic leukemias (CLL). Id4 was silenced secondary to promoter methylation in 100% mouse T/NK ALLs (n=5) and human acute leukemias (n=6). Overexpression of Id4 induced apoptosis in mouse cell line YAC-1 and inhibited tumor growth both in vitro and in vivo. These data, and an analysis of 219 RLGS profiles from different types of human tumors demonstrate that the ID4 promoter is preferentially methylated and functions as a putative novel tumor suppressor gene in mouse and human leukemia. This study highlights the use of a novel animal model, novel mouse NotI-EcoRV arrayed library, and RLGS to examine the role of methylation in leukemic transformation and to identify new targets for prevention and therapeutic strategies.

A NotI– EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignancies

Aberrant promoter methylation and associated chromatin changes are primarily studied in human malignancies. Thus far, mouse models for human cancer have been rarely utilized to study the role of DNA methylation in tumor onset and progression. It would be advantageous to use mouse tumor models to a greater extent to study the role and mechanism of DNA methylation in cancer because mouse models allow manipulation of the genome, study of samples/populations with a homogeneous genetic background, the possibility of modulating gene expression in vivo, the statistical power of using large numbers of tumor samples, access to various tumor stages, and the possibility of preclinical trials. Therefore, it is likely that the mouse will emerge as an increasingly utilized model to study DNA methylation in cancer. To foster the use of mouse models, we developed an arrayed mouse NotI– EcoRV genomic library, with clones from three commonly used mouse strains (129SvIMJ, FVB/NJ, and C57BL/6J). A total of 23,040 clones representing an estimated three- to fourfold coverage of the mouse genome were arrayed in 60 × 384-well plates. We developed restriction landmark genomic scanning (RLGS) mixing gels with 32 plates to enable the cloning of methylated sequences from RLGS profiles run with NotI– EcoRV– HinfI. RLGS was used to study aberrant methylation in two mouse models that overexpressed IL-15 or c-Myc and developed either T/NK-cell leukemia or T-cell lymphomas, respectively. Careful analysis of 198 sequences showed that 188 (94.9%) identified CpG-island sequences, 132 sequences (66.7%) had homology to the 5′ regions of known genes or mRNAs, and all 132 NotI– EcoRV clones were located at the same CpG islands with the predicted promoter sequences. We have also developed a modified pGL3-based luciferase vector that now contains the NotI, AscI, and EcoRV restriction sites and allows the rapid cloning of NotI– EcoRV library fragments in both orientations. Luciferase assays using NotI– EcoRV clones confirmed that the library is enriched for promoter sequences. Thus, this library will support future genetic and epigenetic studies in mouse models.

Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets.

CpG island methylation is an epigenetic alteration that contributes to tumorigenesis by transcriptional inactivation of genes. Little is known about the overall levels of CpG island methylation in chronic lymphocytic leukemia (CLL). To provide a baseline estimate of global aberrant methylation and identify target sequences for additional investigation, we performed Restriction Landmark Genomic Scanning on 10 CLL samples. Two methylation-sensitive landmark enzymes were used (NotI and AscI), allowing assessment of over 3000 CpG islands in each sample. Tumor-derived Restriction Landmark Genomic Scanning profiles were compared with profiles from CD19-selected B cells from normal volunteers and matched normal neutrophils from 4 CLL patients. We found 2.5-8.1% (mean 4.8%) of the CpG islands in CLL samples were aberrantly methylated compared with controls, and the methylation events had a nonrandom distribution (P < 0.0001). Furthermore, we identified 193 aberrantly methylated sequences, of which 93% have CpG island characteristics and 90% have homology to genes or expressed sequences. One such gene, the G protein-coupled metabotropic glutamate receptor 7 (GRM7), possibly inhibits cyclic AMP signaling in the induction of apoptosis. Bisulfite sequencing of GRM7 confirmed extensive CpG island methylation, and treatment with 5-aza-2'-deoxycytidine (decitabine) resulted in up-regulated expression of several genes in vitro with concurrent cellular depletion of DNMT1 protein. Our dual-enzyme global methylation study shows that CLL is characterized by widespread nonrandom CpG island methylation similar to other tumors and provides a panel of novel methylation targets that can be used in larger studies designed to assess impact on disease progression and survival.

Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice.

DNA methylation is involved in many gene functions such as gene-silencing, X-inactivation, imprinting and stability of the gene. We recently found that some CpG islands had a tissue-dependent and differentially methylated region (T-DMR) in normal tissues, raising the possibility that there may be more CpG islands capable of differential methylation. We investigated the genome-wide DNA methylation pattern of CpG islands by restriction landmark genomic scanning (RLGS) in mouse stem cells (ES, EG and trophoblast stem) before and after differentiation, and sperm as well as somatic tissues. A total of 247 spots out of 1500 (16%) showed differences in the appearance of their RLGS profiles, indicating that CpG islands having T-DMR were numerous and widespread. The methylation pattern was specific, and varied in a precise manner according to cell lineage, tissue type and during cell differentiation. Genomic loci with altered methylation status seem to be more common than has hitherto been realized. The formation of DNA methylation patterns at CpG islands is one of the epigenetic events which underlies the production of various cell types in the body. These findings should have implications for the use of embryonic stem cells and cells derived from them therapeutically, and also for the cloning of animals by the transfer of somatic cell nuclei.

Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications

The field of molecular biology was revolutionized by the advent of gel electrophoresis. Restriction landmark genomic scanning (RLGS) is a type of two-dimensional electrophoresis employed in the genome-wide assessment of genomic alterations. RLGS has been used to study genetic and epigenetic changes in normal tissues, primary tumors, cancer cell lines, and various organisms such as mice, rats, hamsters, bacteria, and plants. An RLGS profile displays over 2000 radiolabeled restriction landmark sites in a single assay. When conducted with methylation-sensitive restriction enzymes whose sites are preferentially located in CpG island regulatory regions, RLGS becomes a very versatile tool for the investigation of both normal and aberrant methylation patterns. Early studies performed on tumor DNA were mainly descriptive in nature, essentially a catalogue of loci that were changed to varying degrees in different tumor types. Over time, as investigators have become more proficient with RLGS and have undertaken high-throughput studies, the need for efficient cloning, imaging, and analysis systems has become paramount. Current studies focus on identifying specific genes and pathways involved in deregulated methylation in cancer. As such, RLGS analysis of tumor samples has made tremendous contributions to our understanding of the role of DNA methylation in cancer. Future directions will take advantage of the abundant genomic sequence data available to link all of the RLGS loci to genes and create biologically relevant methylation profiles of cancer. This review discusses practical considerations of using RLGS as a genome scanning tool and the past, present, and future applications in cancer biology.

Correlation of postoperative recurrence in hepatocellular carcinoma with demethylation of repetitive sequences.

Restriction landmark genomic scanning (RLGS) was utilized to identify novel genomic alterations in hepatocellular carcinoma (HCC). Thirty-one HCC samples were examined by RLGS. Two high intensity spots were common to several RLGS profiles of different HCCs. Nucleotide sequencing and homology search analysis showed that these spots represented repetitive sequences, Human tandem repeat sequence (Genbank, L09552) and centromeric NotI cluster (Genbank, Y10752). These intensified signals were attributable to the occurrence of demethylated areas in the recognition sequence of the NotI site of the corresponding fragments. The intensity of these spots in the RLGS profile reflects their degree of demethylation, which was significantly correlated with postoperative recurrence, even in patients regarded as belonging to the good prognosis group by conventional prognostic factors. Multivariate analysis showed that the intensities of the two spots retained independent prognostic value. This is a new type of predictive factor for HCC based on epigenetic changes in hepatocarcinogenesis, and in the future it is expected to be of great value in making preoperative diagnosis and selecting postoperative therapy.

Chlorophyll-deficient mutants of rice demonstrated the deletion of a DNA fragment by heavy-ion irradiation.

Heavy-ion irradiation is a new method of mutation breeding to produce new cultivars. We established the application of this method in rice plants to obtain mutants. Rice seeds were irradiated by C or Ne ions (135MeV/u) with a LET (linear energy transfer) of 22.7 or 64.2 keV/microm, respectively. Chlorophyll-deficient mutants (CDM) segregated in M2 progeny were albino, pale-green, yellow or striped-leave phenotypes. The highest rate of CDM with C-ion irradiation, 7.31%, was obtained at 40 Gy among the doses examined. Ne-ion irradiation gave the highest rate, 11.6%, at 20 Gy. We used the RLGS (Restriction Landmark Genomic Scanning) method to analyze DNA deletion in an albino mutant genome. Not I-landmark RLGS profiles detected about 2000 spots in rice. We found that one of the polymorphic spots was strongly linked to the albino phenotypic mutant derived from deleting of a DNA fragment, and demonstrated the high ability to detect of polymorphic regions by the RLGS method.

Hypermethylation as a potential prognostic factor and a clue to a better understanding of the molecular pathogenesis of medulloblastoma--results of a genomewide methylation scan

The molecular mechanisms controlling initiation and progression of medulloblastomas are largely unclear. Changes in DNA methylation of promoter regions have been shown to disturb the expression of growth regulatory genes. We evaluated DNA methylation patterns in 17 medulloblastomas, 5 stPNETs and 5 medulloblastoma cell lines using Restriction Landmark Genomic Scanning (RLGS), a method displaying up to 2.000 potential gene loci in a single gene. To test whether previously characterized tumor suppressor genes are affected by hypermethylation we performed MS-PCR for p15INK4B, p16INK4A, VHL, TP53 and E-cadherin. The analysis of RLGS profiles from tumors revealed an abundance of hypermethylation in primary tumors and cell lines. Extrapolated to the human genome with its approximately 36,000 genes a total of 420 loci become hypermethylated in the tumor genomes. The previously characterized medulloblastoma breakpoint cluster in 17p11.2 appears to be a hotspot for aberrant methylation. Cox regression analysis of survival data identified seven CpG islands for which hypermethylation is suggestive of a poor prognosis. MS-PCR analysis of known genes demonstrated hypermethylation of p16INK4A in a limited number of tumors. The pattern of DNA hypermethylation was similar in medulloblastomas and stPNETs. However, some CpG islands were shown to be specific for a tumor type, while others were shared targets. Hypermethylation is a common abnormality in primary medulloblastomas and supratentorial PNETs. Several hundreds of CpG islands are potential targets for methylation in medulloblastomas including the breakpoint cluster in 17p11.2. The methylation status of certain gene sequences appears to be associated with the clinical outcome. Promoter hypermethylation has an outstanding potential as a marker for the identification of novel tumor suppressors as well as diagnostic and therapeutic targets in medulloblastomas.

DNAinsight: a web based image processing system for large scale RLGS analysis.

DNA methylation occurring within the context of CpG site in the promoter element generally correlates with transcriptional silencing, delayed replication, condensed chromatin and mammalian genome imprinting (Nature Genet 24:101-2, 2000). We have been focusing attention on Restriction Landmark Genomic Scanning (RLGS) method as the powerful experimental procedure which can used to determine DNA methylation status change occurring on a genome simultaneously. To support systematic analysis with RLGS method, we have developed the automated processing algorithms for two-dimensional electrophoretograms of genomic DNA based on RLGS method (RLGS profile). Our powerful processing algorithms realize the automated spot recognition from RLGS profiles and the automated comparison of a huge number of such profiles. To make systematic RLGS analysis more easy and objective, we equipped our automated RLGS image processing algorithms with a WWW interface and relational database which stores the RLGS profile images together with their accompanying information, such as DNA sample specification, two-dimensional electrophoresis conditions and so forth. The web based RLGS image processing system "DNAinsight" can be accessed via URL http://www.methylome.jp/DNAinsight/.

Adaptation of Restriction Landmark Genomic Scanning (RLGS) to plant genome analysis

Restriction Landmark Genomic Scanning (RLGS) profiles, which are based on the concept of using restriction enzyme sites as landmarks and are generated by two-dimensional gel electrophoresis, were applied to the analysis of plant genomes. This study identified landmark enzymes in RLGS profiles of rice, tobacco, and arabidopsis, because the success of RLGS analysis depends on finding useful landmarks and these are the most frequently studied higher plants. As the results demonstrate, in each plant RLGS analysis various landmark enzymes were identified as useful landmark enzymes. However, the number of spots in a single profile was smaller than in mouse RLGS profiles and differed remarkably in the various plants. In addition, we demonstrate the optimal electrophoresis conditions and a convenient spot-cloning method.

Intratumoral genomic heterogeneity in human hepatocellular carcinoma detected by restriction landmark genomic scanning

Background/Aims: One of the unique features of advanced hepatocellular carcinoma (HCC) is the morphological heterogeneity in a single tumor nodule. In order to investigate the intratumoral genomic heterogeneity of HCC, we performed Restriction Landmark Genomic Scanning (RLGS), which allows genomic DNAs to be surveyed at approximately 2000 landmark sites in a single 2-dimensional gel electrophoresis. Methods: RLGS profiles of two regions from a single HCC nodule in six patients were compared with nontumorous liver tissue. Four HCCs consisting of moderately-differentiated cells were separated into several small parts by thin fibrous septa, but not encapsulated. DNA samples were obtained from both parts of these so-called “nodule-in-nodule” HCC. Two HCCs consisting of well-differentiated cells which did not have a definite partition appeared pathologically homogeneous, and two independent regions of the HCC were used for the analysis. Results: All six HCCs demonstrated different RLGS profiles (in total about 160 different spots) from the corresponding non-tumorous liver, and the number of different spots was greater in the 4 moderately-differentiated nodule-in-nodule HCCs (39–68 spots) than in the 2 well-differentiated homogeneous HCCs (6 and 3 spots). RLGS profiles of the two parts were different to each other in all 4 nodule-in-nodule HCCs. On the other hand, two other homogeneous HCCs showed the same RLGS profiles in the two regions. Conclusion: Thus, intratumoral genomic heterogeneity was demonstrated in the advanced HCC samples, and the genomic alterations may relate to the progression of HCC.

A genetic linkage map of the MSM Japanese wild mouse strain with restriction landmark genomic scanning (RLGS).

A high-resolution genetic map of the Mus musculus molossinus (MSM) Japanese wild mouse strain was constructed with restriction landmark genomic scanning (RLGS) and compared with that of the laboratory strain C3H. MSM is phylogenetically 1 million years apart from common laboratory mouse strains and is distinctly resistant to chemical carcinogenesis. Since it exhibits frequent genetic polymorphisms with laboratory mice but can still be easily crossed with laboratory strains, hybrids between MSM and carcinogen-sensitive laboratory mouse strains provide excellent materials for analysis of modifier genes and genetic changes during carcinogenesis. We have generated MSM backcross progeny with the C3H strain, which is extremely sensitive to hepatocarcinogenesis, to construct the present map. RLGS profiles with two combinations of restriction enzymes (NotI-PvuII-PstI, NotI-PstI-PvuII) yielded more than 2000 spots each. The polymorphism rate was about 39.2%, and of a total of 1732 polymorphic spot loci identified, 1371 could be assigned to specific chromosomes by comparison with 79 microsatellite marker loci. Thus, 1450 loci, on all chromosomes except for Y, effectively mapped 90% of the genome (1431.7 cM length). Although some spots might be derived from the same NotI site, each NotI site potentially generating two fragments, the presence of at least 515 loci groups with different progeny distribution patterns dispersed through the genome with an average spacing of 3 cM, means that this genetic map should be useful for analysis of various biological phenomena, including carcinogenesis and ontogenesis, at the gene level.

Genomic DNA analyses of spontaneous hepatocellular carcinomas in LEC rat liver using a new technique.

An inbred rat strain, LEC (long evans cinnamon) has been used as a model of human Wilson's disease. This animal suffers from a severe type of hepatitis, the clinical manifestations of which are similar to human fulminant hepatitis for 4-5 months which is caused by accumulation of copper in the liver. The surviving rats develop chronic hepatitis, followed by the development of spontaneous hepatoma. In contrast to studies with hepatocellular carcinomas (HCCs), the studies have great advantages in that the animals have identical genetic background, can be raised under a fixed condition, and the development of HCC is reproducible. We took two HCC samples and analysed their genomic DNA using RLGS (restriction landmark genomic scanning), which involves two-dimensional electrophoresis of genomic DNA allowing the survey of some 1,000 NotI sites throughout the genome. Using this technique, we discovered landmark spots that were either decreased or increased in intensity in HCC and compared them with the RLGS profile obtained from the DNA of control normal LEC rat liver. Approximately 1,300 spots were compared, and the intensity of two spots was found to be decreased about half and one was increased 1.3-1.7 folds. Although the mechanism of these changes and the properties of the changed DNA are yet to be studied, recurrent genomic changes in the LEC rat HCC could prove to be a good model system for elucidating the essential genetic events in association with hepatocarcinogenesis.

A Web Based System for Computation and Management of Massive Number of 2-D Gel Electrophoretograms of Genomic DNA

DNAmethylation occurring within the context of CpG site in the promoter element generally correlates with transcriptional silencing, delayed replication and condensed chromatin [1]. Recently, it was reported that CpG-islands of several tumor-suppressor gene promoters were hypermethylated in tumor and there were tumor-type-specific hypermethylation patterns [3]. It is also strongly suggested that DNA methylation correlates to mammalian genome imprinting. Restriction landmark genomic scanning (RLGS) method [2] is one of the most powerful strategies which profiles methylation status of several thousands of CpG-islands across the genome. In RLGS method, NotI endnuclease recognition sites are imaged as several thousands of landmark spots on RLGS electrophoretogram (RLGS profile). The DNA methylation or gene amplification changes can be emerged by comparing several related RLGS profiles. It is difficult, however, by visual inspection to detect the locations and intensities of the RLGS landmark spots from the RLGS profile and to compare them rapidly and objectively. Thus, the computer-assisted analysis of the RLGS profile is necessary. Besides, RLGS profiles should be processed by computer without any human interaction, in order to manage large amount of RLGS profiles and to retrieve DNA methylation status of the CpG islands. In this poster, a web based system “WebDNAinsight”, in which the fully-automated RLGS image processing algorithms [4] are integrated with the powerful image database, is presented. With the web interface, one can register, search, process and analyze massive number of RLGS profiles easily, using networked computer with web browser.

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)