De novo DNA methylation at nonrandom founder sites 5' from an unmethylated minimal origin of DNA replication in latent Epstein-Barr virus genomes

Latent episomal genomes of Epstein-Barr virus, a human gammaherpesvirus, represent a suitable model system for studying replication and methylation of chromosomal DNA in mammals. We analyzed the methylation patterns of CpG dinucleotides in the latent origin of DNA replication of Epstein-Barr virus using automated fluorescent genomic sequencing of bisulfite-modified DNA samples. We observed that the minimal origin of DNA replication was unmethylated in 8 well-characterized human cell lines or clones carrying latent Epstein-Barr virus genomes as well as in a prototype virus producer marmoset cell line. This observation suggests that unmethylated DNA domains can function as initiation sites or zones of DNA replication in human cells. Furthermore, 5' from this unmethylated region we observed focal points of de novo DNA methylation in nonrandom positions in the majority of Burkitt's lymphoma cell lines and clones studied while the corresponding CpG dinucleotides in viral genomes carried by lymphoblastoid cell lines and marmoset cells were completely unmethylated. Clustering of highly methylated CpG dinucleotides suggests that de novo methylation of unmethylated double-stranded episomal viral genomes starts at discrete founder sites in vivo. This is the first comparative high-resolution methylation analysis of a latent viral origin of DNA replication in human cells.

Inhibitory effect of a long-acting somatostatin analogue on EGF-stimulated cell proliferation in Capan-2 cells

Numerous studies have reported diverse effects of gut-derived regulatory peptides on growth of the normal pancreas, pancreatic neoplasms induced experimentally in animals, and pancreatic cancer cell lines, but the results of these investigations are rather controversial. The stimulatory effect of epidermal growth factor (EGF) on cell proliferation of pancreatic cell lines is well established. Whether this action can be modulated by somatostatin is not clear. Furthermore, it is not certain whether another regulatory peptide, cholecystokinin (CCK), affects the proliferation of these cells. In the present study we investigated the presence of CCK-A and CCK-B, as well as somatostatin-2 (SSTR2) receptors by RT-PCR, and studied the actions of EGF, CCK and octreotide on DNA synthesis in the human pancreatic adenocarcinoma cell line Capan-2. Octreotide, a long-acting somatostatin analogue was used as somatostatin agonist. Cells were cultured in RPMI-1640 medium. They were incubated in serum free medium containing 0.2% BSA in the absence (control) or the presence of the peptides. [3H]-thymidine incorporation into DNA was measured after 48 h of incubation. By means of RT-PCR analysis we were able to demonstrate SSTR2 expression, but not CCK-A or CCK-B receptor mRNA in Capan-2 cells. DNA synthesis evaluated by [3H]-thymidine incorporation was found to be increased by 45.2 +/- 5.6% in response to EGF (10(-8) M) and decreased by 11.7 +/- 2.6% to octreotide (10(-8) M) compared to controls (P < 0.01). The increase in [3H]-thymidine incorporation was significantly lower when EGF treatment was combined with octreotide administration (10.1 +/- 2.5% over control). In the concentration range of 10(-11)-10(-8) M, CCK did not alter significantly the incorporation of [3H]-thymidine into DNA in Capan-2 cells. In conclusion, these data support a role for EGF as a growth factor for the human pancreatic cancer cell Capan-2. Somatostatin may play an important role in regulating cell proliferation in Capan-2 cells both under basal, and growth factor-stimulated conditions. Our results suggest, however, that CCK receptors are not expressed, and CCK does not affect cell proliferation in this transformed pancreatic cell line.

NotI linking/jumping clones of human chromosome 3: mapping of the TFRC, RAB7 and HAUSP genes to regions rearranged in leukemia and deleted in solid tumors

By applying the 'recognition mask' strategy to 300 mammalian sequences containing NotI sites we demonstrated that 5' ends of genes are highly enriched in NotI sites. A NotI linking clone NL2-252 (D3S1678) containing transferrin receptor (TFRC) gene was used as an initial point for chromosomal jumping. One of the jumping clones, J21-045 traverses 210 kbp and links NL2-252 to NL26 (D3S1632), a NotI linking clone containing highly polymorphic sequences. The TFRC gene was mapped to 3q29, close to the telomeric marker D3S2344, by linkage analysis, a panel of hybrid cell lines, GeneBridge 4 panel and FISH. Clone NLM-007 (D3S4302) was found to contain ras-homologous gene RAB7. By FISH and a panel of hybrid cell lines this gene was mapped to 3q21. This region is of particular interest due to frequent rearrangements in different types of leukemia. Clone L2-081 (D3S4283) containing new member of ubiquitin-specific proteases (HAUSP gene) was localized in 3p21 inspiring further investigation of involvement of this gene in development of lung and renal carcinomas.

The activity of Na+/K(+)-ATPase and abundance of its mRNA are regulated in rat myometrium during pregnancy

The Na+/K(+)-ATPase activity and expression of mRNAs encoding alpha and beta subunits of the enzyme were examined in rat myometrium at different stages of pregnancy. The enzyme activity appeared to increase during the pregnancy and reached the highest value at the 17th day. Northern blot analysis of total RNA isolated from the same myometrial samples shows the expressions of alpha 1, alpha 3 and beta mRNAs. A2 mRNA was not detectable. By the progression of pregnancy until the 17th day the expression of all the three kinds of mRNA increased. The change in the abundance of mRNA-beta was much more higher (12-fold) than that of mRNA-alpha 1 and -alpha 3 (4 and 2.5-fold, respectively). Furthermore, the expression of mRNA-beta sharply decreased after the 17th day, while the level of alpha subunits mRNAs barely changed. We conclude that transcriptional regulation of the Na+/K(+)-ATPase subunits could be different during this physiological process.

RNA polymerase III-transcribed EBER 1 and 2 transcription units are expressed and hypomethylated in the major Epstein-Barr virus-carrying cell types

The genome of Epstein-Barr virus (EBV) codes for two non-translated small RNA molecules, EBER 1 and 2. We found that both EBERs are expressed in the major EBV-carrying cell types, group I and III Burkitt's lymphoma (BL) cell lines, lymphoblastoid cell lines (LCLs) and in two nude mouse-passaged nasopharyngeal carcinoma (NPC) tumours. The relative amount of EBER 1 and EBER 2 varied in different host cells but did not correlate with the cellular phenotype. The EBER coding and flanking sequences were predominantly hypomethylated at HpaII sites not only in LCLs which usually carry hypomethylated EBV genomes but also in BL and NPC cell lines harbouring EBV episomes that are highly methylated in other regions. Thus, the EBER transcription units, actively transcribed by RNA polymerase III in the major EBV-carrying cell types, represent a methylation-free region in the EBV genome similarly to regulatory sequences of the latent membrane protein gene when the latter is transcribed by RNA polymerase II.

New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries

A novel procedure for construction of jumping libraries is described. The essential features of this procedure are as follows: (1) two diphasmid vectors (lambda SK17 and lambda SK22) are simultaneously used in the library construction to improve representativity, (2) a partial filling-in reaction is used to eliminate cloning of artifactual jumping clones and to obviate the need for a selectable marker. The procedure has been used to construct a representative human NotI jumping library (220,000 independent recombinant clones) from the lymphoblastoid cell line CBMI-Ral-STO, which features a low level of methylation of its resident EBV genomes. A human chromosome 3-specific NotI jumping library (500,000 independent recombinant clones) from the human chromosome 3 x mouse hybrid cell line MCH 903.1 has also been constructed. Of these recombinant clones 50-80% represent jumps to the neighboring cleavable NotI site. With our previously published method for construction of linking libraries this procedure makes a new genome mapping strategy feasible. This strategy includes the determination of tagging sequences adjacent to NotI sites in random linking and jumping clones. Special features of the lambda SK17 and lambda SK22 vectors facilitate such sequencing. The STS (sequence tagged site) information obtained can be assembled by computer into a map representing the linear order of the NotI sites for a chromosome or for the entire genome. The computerized mapping data can be used to retrieve clones near a region of interest. The corresponding clones can be obtained from the panel of original clones, or necessary probes can be made from genomic DNA by PCR.

Involvement of 3p deletions in sporadic and hereditary forms of renal cell carcinoma

Deletions of the short arm of chromosome 3 and associated allele losses have been reported in the majority of sporadic renal cell carcinomas (RCC). On the basis of the combined cytogenetic and molecular data, it is reasonable to assume that a putative RCC locus, which contributes to tumor development by its loss, is located telomerically of the D3F15S2 site. Using H3E4, a D3F15S2-specific probe, we have isolated a cDNA clone (cl.4-2), and a sequence comparison revealed that the cDNA clone corresponds to the human acyl-peptide hydrolase gene. The gene is fairly universally expressed, but in RCC biopsies its expression is severely reduced, compared to the normal kidney. Cl.4-2 was used for in situ hybridization on metaphase chromosomes prepared from an Epstein-Barr virus (EBV) transformed lymphoblastoid cell line, derived from a t(3;8) (p14.2;q24.1) carrying member of the RCC family described by Cohen et al. in 1979 (N Engl J Med: 301:592-595). Carriers of this translocation regularly develop RCC by middle age. We now report that D3F15S2 is localized on the telomeric side of the constitutional breakpoint, in 3p21. The region of 3p affected by this familial translocation is thus not identical with the region of 3p most frequently deleted in sporadic RCC.

Construction of a human chromosome 3 specific NotI linking library using a novel cloning procedure

Two new diphasmid vectors (lambda SK17 and SK22) and a novel procedure to construct linking libraries are described. A partial filling-in reaction provides counter-selection against false linking clones in the library, and obviates the need for supF selection. The diphasmid vectors, in combination with the novel selection procedure, have been used to construct a chromosome 3 specific NotI linking library from a human chromosome 3/mouse microcell hybrid cell line. The application of the new vectors and the strong biochemical and biological selections resulted in a library of 60,000 NotI linking clones. As practically all of them are real NotI linking clones (no false recombinants) the library represents approximately 3,000 human recombinants (equal to 10-15 genomic equivalents of chromosome 3). Previously published methods for construction of linking libraries are compared with the procedure described in the present paper. The advantages of the new vectors and the novel protocol are discussed.

A gene near the D3F15S2 site on 3p is expressed in normal human kidney but not or only at a severely reduced level in 11 of 15 primary renal cell carcinomas (RCC)

Renal Cell Carcinoma (RCC) has been associated with the loss of heterozygosity at several loci on the short arm of chromosome 3 (3p). We have previously found that one of these loci, D3F15S2 (pH3H2) was lost in 76% of the tumor cells derived from heterozygous donors (Kovacs, G., Erlandsson, R., Boldog, F., Ingvarrsson, S., Müller-Brechlin, R., Klein, G. & Sümegi, J. (1988), Proc. Natl. Acad. Sci., 85, 1571-5). More recently we have identified a putative CpG island in the vicinity of D3F15S2, suggesting that DNA sequences in or around this site may have coding potential (Boldog, F., Erlandsson, R., Klein, G. & Sümegi, J. (1989). Cancer Genet. Cytogenet., 42, 295-306). The screening of a human placenta cDNA library with DNA probes derived from D3F15S2 has led to the isolation of several cDNA clones. They identified a 2.9 Kb long message in human placenta and kidney. In total RNA from 11 of 15 primary RCCs the gene expression was reduced to less than 20% compared to eight normal kidneys. This low level of expression may be due to contaminating normal tissue. In the remaining 4 tumors the expression varied from 24-51% compared to normal kidney. To facilitate reference, the gene was provisionally designated as 'RIK'. It was expressed in the HEK 293, one osteosarcoma (HOS), two carcinoma (COLO320 and QDMT), and three Burkitt lymphoma lines (BL2, BL29 and BL31). It was not expressed in one Burkitt lymphoma (DG75) and two EBV transformed lymphoblastoid cell lines (LCL) (NAD-20 and Cherry).

Episodic secretion of hormones and the diagnostic value of single blood estimates. I. LH, FSH, prolactin

The episode fluctuation of serum LH, FSH and prolactin levels in peripheral blood was studied to determine the reliability of single estimates of the average blood level. Radioimmunoassay of the hormones was performed in serum withdrawn every 10 min between 8 and 12 h a.m. from 8 healthy women in various periods of the menstrual cycle. The rate of fluctuation of the hormone levels was characterized by the within-person coefficient of variation of single estimates, which averaged 30.3, 15.1 and 19.2% for LH, FSH and prolactin, respectively. Due to a pronounced fluctuation of gonadotropin levels, analysis of several serum samples is recommended to approach the actual mean hormone level.