[Effect of DNA hypermethylation on NOR1 promoter activity and expression].

OBJECTIVE: To analyze the effect of DNA hypermethylation on NOR1 promoter activity and expression. METHODS: NOR1 promoter plasmids were treated with SssI methyltransferase. The plasmids were modified by sodium bisulfite and purified. Sodium bisulfite-modified plasmids were subjected to PCR with primers designed to analyze the methylation status of 26 CpG sites in a 311-bp region of the NOR1 promoter. Cells were transfected by methylated or mock-methylated promoter plasmids. The promoter activities were assessed by the luciferase levels of cell lysates or by directly observing GFP expression under fluorescence microscope. HL60 cells were treated with different concentrations of 5-aza-dC. Total RNA was isolated from harvested cells. Real-time RT-PCR was used to measure the expression level of NOR1 mRNA. RESULTS: Bisulfite sequencing confirmed that SssI methyltransferase treatment successfully resulted in intensive hypermethylation of the NOR1 promoter plasmids. The promoter activity of NOR1 promoter plasmids was totally blocked by SssI methyltransferase treatment. NOR1 expression levels in HL60 cells were restored by 5-aza-dC treatment. CONCLUSION: NOR1 promoter plasmids are intensively hypermethylated by SssI methyltransferase treatment. The promoter activity of NOR1 promoter plasmids are totally blocked by SssI methyltransferase treatment. The 5-aza-dC treatment may restore the endogenous NOR1 mRNA level in HL60 cells.

The effect of CpG sequences on the B cell response to a viral glycoprotein encoded by a plasmid vector.

The effect of palindromic CpG sequences on the B cell response to plasmid vectors expressing a highly immunogenic viral glycoprotein was investigated. Methylation of the CpG sequences of bacterial expression vectors abolished their ability to induce an antibody response to the transgene product in mice. The antibody response could be rescued by concomitant injection of oligonucleotides carrying immunostimulatory sequences. The B cell response to two plasmid vectors, both expressing the same viral glycoprotein but containing a different content of the highly stimulatory AACGTT motif, was compared. Comparable B cell responses were induced to the two constructs given at an optimal vaccine dose while the vector containing additional palindromic sequences resulted in higher antibody titers at a suboptimal dose. These data indicate that deletion of CpG motifs or methylation of such sequences in plasmid DNA can abrogate the immune response to the vector encoded antigen and might thus enhance their usefulness as gene therapy vehicles.

Sequencing and functional analysis of the SNRPN promoter: in vitro methylation abolishes promoter activity.

The gene encoding the small nuclear ribonucleoprotein-associated polypeptide N (SNRPN) maps to the Prader-Willi syndrome critical region on chromosome 15 and is expressed preferentially from the paternal allele. A CpG island encompassing the first exon of SNRPN is methylated on the inactive maternal allele. DNA sequence was determined for a cosmid containing the first three exons of SNRPN and extending 20 kb upstream and 15 kb downstream from the CpG island. This region is extremely rich in Alu elements and other repetitive sequences and contains a single CpG island, which includes numerous short direct repeat sequences. Functional analysis of the first exon revealed strong promoter activity for a 260-bp fragment extending 207 bp upstream from the exon. In vitro methylation of this 260-bp fragment abolished promoter activity completely, suggesting that the silencing of the maternal SNRPN allele may be a direct consequence of methylation of the promoter region.

Analysis of Epstein-Barr virus BamHI F DNA fragment in nude mouse-passaged nasopharyngeal carcinoma tissues.

Two nude mouse-passaged nasopharyngeal carcinoma (NPC) tissues, NPC-295 and NPC-306, were different in ability to transform cord blood lymphocytes and contained Epstein-Barr virus (EBV) genomes with difference in BamHI F DNA fragment. Four clones containing DNA sequences of the BamHI F fragment (54,853-62,249) were obtained from genomic libraries of NPC-295 and NPC-306 and their partial restriction enzyme maps and sequences were determined. The restriction enzyme maps of EBV DNA at the BamHI F fragment in NPC-295 and NPC-306 appeared to be similar to that of EBV B95-8 strain. However, 8 nucleotide differences were revealed between NPC-295 and the B95-8 strain when 566 nucleotides (55,405-55,970) were compared, and 15 out of 677 nucleotides analyzed (55,410-56,086) were different between NPC-306 and B95-8.

Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus.

The use of partial restriction digests for mapping complex genomes by pulsed-field gel electrophoresis has been limited by the difficulty of consistently obtaining these digests in agarose, which is a necessary matrix for high-molecular-weight DNA. Enzyme cleavage in agarose is faster then diffusion for most of the enzymes which cleave infrequently. We have developed a method for the production of partial digests in agarose for the endonuclease NotI (5' . . . GC/GGCCGC . . . 3') which circumvents the diffusion problem by using the blocking methylase M. BspRI (5' . . . GGmCC . . . 3'), which competes for the same sites. Using various ratios of the methylase and endonuclease results in partial digests in any size range desired. We report the successful application of this technique to the production of NotI partial digests of human genomic DNA for the mapping of the ABL locus of human chromosome 9.

Induction of chromosomal aberrations by restriction endonucleases encapsulated in liposomes.

We used liposomes to deliver the restriction endonucleases BamHI and SmaI into human heteroploid HEp-2 cells. With this method very low concentrations of enzymes (2 units/ml) were active in the production of chromosomal aberrations. SmaI, which produces blunt-ended double-strand breaks in the DNA molecule, induces chromosomal aberrations more effectively than BamHI, which produces cohesive ends. Our results indicate that liposomes are suitable vectors for introducing restriction endonucleases into cultured human cells.

In situ nick translation of human chromosomes using Alu I: unmasking of recognition sites by proteinase K pretreatment.

Human chromosomes prepared according to routine methods were treated with the restriction endonuclease Alu I followed by staining with Giemsa solution or fluorescent dyes. This procedure results in a C-band-like appearance of the chromosomes due to removal of DNA from euchromatic chromosomal regions. The resistance of heterochromatic regions against cleavage by the enzyme has mainly been interpreted by the absence or rareness of recognition sites for this particular enzyme in these regions. Proteinase K pretreatment followed by a nick translation procedure with Alu I was combined to check this hypothesis. The results show that heterochromatic chromosomal regions can also be labelled. Thus, they are not characterized by a lack of recognition sites. Gradual deproteinisation of chromosomes changes the labelling pattern from a reverse C-banding pattern to a C-band-like appearance. The resistance of heterochromatic chromosomal parts revealed by the technique is mainly due to local chromatin configuration rather than to the underlying DNA sequence itself.