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Biomedical subjects

E R Zabarovskiĭ

Publications and source records attributed to E R Zabarovskiĭ.

At least 19 recordsLinked to original sources
PubMed1986

[Insertion of the cos-site into DNA of phage M13 and its packing in proteins of phage lambda].

The cos-site of lambda phage from pHC79 cosmide is transferred to DNA from M13 mp18 phage. The recombinant DNA thus obtained (MC18) is efficiently packaged into lambda proteins in vitro. The BamHI-HindIII fragment of pGP588 (a pBR322 derivatives containing fragment of human DNA) is subcloned into MC18. Although this pGP588 fragment contains numerous Alu repeats, no essential rearrangements of the insert were revealed. The efficiency infection by recombinant DNA packaged with lambda proteins is about 1 X 10(5) pfu/microgram DNA, whereas in the similar conditions the efficiency of lambda EMBL3A was 1 X 10(6) pfu/microgram. It is assumed that the MC vectors might be suitable for cloning and sequencing large fragments either with cohesive or blunt ends. It opens also the way to construct genomic libraries in single-stranded phages.

Bacteriophage lambda↗
PubMed1985

[Construction of a gene library using partial filling of DNA sticky ends].

To prepare gene libraries, the incomplete filling of protruding ends has been used. DNAs from phages EMBL 3 and EMBL 3a were sequentially digested with SalI and EcoRI, followed by addition of dTTP, dCTP, and DNA polymerase I (Klenow's fragment). Separately, a genomic DNA was partially cleaved with Sau3AI, followed by addition of dATP, dGTP, and Klenow's fragment. The fragmented phage and genomic DNAs were mixed and ligated, and the recombinant DNAs packed in vitro with the phage proteins. The effectiveness of packaging per microgram of genomic DNA was 10(5) to 10(6) (for the wild phage DNA, 10(7)). The proposed procedure is very rapid and needs only microgram quantities of genomic DNA for preparing a representative gene library. It is also useful for other vectors, containing SalI sites.

Animals↗
PubMed1985

[Regions of the human genome containing homologs of the oncogenes and retrovirus genes. 3. The primary structure of the mos-related region CL-1 from the ORAgp5 locus].

The nucleotide sequence of 686 bp from the cloned human genome locus gp5 has been determined. Analysis of this sequence has revealed a statistically significant homology with both the viral and murine mos genes. The region of mos homology contains two adjacent homologous domains, whereas their counterparts in viral mos gene are separated by 471 bp. The position of mos homologous region in the close vicinity to LTR of endogenous human viral-like repeat is in accordance with the hypothesis of retroviral involvement in the process of mos gene amplification.

Base Sequence↗
PubMedDate not supplied

[Alternative approaches to genome mapping and sequencing].

The main methods used for large-scale mapping of the human and other genomes are reviewed. These methods comprise two procedures of random mapping/sequencing and an approach using linking and jumping libraries. Importantly, no method used up to now has proved efficient in comparative genome analysis. A new method is presented basing on slalom libraries. These libraries provide 10-100 times higher efficiency and may be used for mapping and sequencing whole genomes by small research groups.

Animals↗
PubMedDate not supplied

[Mapping allelic deletions on the short arm of human chromosome 3 in kidney neoplasms].

Allelic deletions along the short arm of human chromosome 3 were mapped in 57 pairs of DNA samples from tumor and normal tissue of renal carcinoma patients in order to locate potential tumor suppressor genes. Twenty highly polymorphic microsatellite markers were used for deletion mapping. Allelic deletions were found in most of the samples (91%). Extended terminal deletions (56%) prevailed over shorter internal and multiple deletions and dominated (65%) in the most aggressive histopathological kidney cancer subtype, clear-cell carcinoma. Frequency analysis of loss of heterozygosity allowed detection of the human chromosome 3 regions most essential for renal carcinomas: the region adjacent to the gene VHL (3p26-p25), the region of homozygous deletions AP20 (3p22-p21.33), and a new region between markers D3S2420 and D3S2409 (3p21.31, 2.2 Mbp).

Alleles↗
PubMedDate not supplied

[New tumor suppressor genes in hot spots of human chromosome 3: new methods of identification].

Studies of the recent decade, including sequencing of numerous human genome regions, allowed a great progress in detection of new tumor suppressor genes (TSG) and development of new means of their identification and analysis. Effective methods of genome scanning and TSG identification combine DNA array techniques and subtraction hybridization. Alternative ways take advantage of new extrachromosomal vector systems (pETE, pETR) and the functional gene inactivation test. A breakthrough was made in localizing new TSG on the human chromosome 3 short arm, which harbors tumor-suppressing regions and is often rearranged in various tumors and in early carcinogenesis. On 3p, only three putative TSG were known five years ago, and at least ten were identified by the end of 2002. The role of new TSG in carcinogenesis is commonly inferred from a decrease in their transcription in tumor cell lines or primary tumors and from their ability to suppress the growth of these. Protein products of 3p TGS play an important part, constraining cell malignization. Some are directly involved in regulating the cell cycle and inducing apoptosis (RASSFIA), others suppress angiogenesis (Sema3B) or metastasis (Hyal-1). Numerous attempts to find mutations in exons of silent genes failed, and at least half of the new candidate genes (RASSFIA, CACNA2D2, BLU, HYAL1, SEMA3B, RAR-beta) proved to be inactivated by promoter methylation.

Adenoviridae↗
PubMedDate not supplied

[From identification of genomic polymorphism to diagnostic and prognostic markers of human epithelial tumors].

The review considers the results obtained by several groups in the fields of identification of polymorphic loci in the human genome, localization and analysis of genes associated with epithelial tumors of various origins, and generation of molecular markers of socially important oncological diseases. In the first two cases, work was initiated and supported by the Russian program Human Genome. To find new polymorphic loci in the human genome, di-, tri-, and tetranucleotide repeats were searched for in an ordered cosmid library of chromosome 13, NotI and cosmid clones of chromosome 3, and in brain EST. In total, nine polymorphisms and almost 200 STS were identified. Markers of NotI clones of chromosome 3 were associated with particular genes. Polymorphic loci NL1-024, NL2-007, and EST04896 were employed in analysis of deletions from chromosome 3p in tumor DNA. Deletion mapping of 3p in epithelial tumors of five types revealed six critical regions containing potential tumor suppressor genes. Of these, two were in the distal region of chromosome 3p and four, in region 3p21.3. A significant correlation was observed for the frequency of allelic deletions and the stage and the grade of tumors (P < 0.05). On the strength of these findings, genes of region 3p were associated with both tumor development and progression, and proposed as prognostic markers. Regions LUCA and AP20 (3p21.3) showed a high (90%) frequency of aberrations, including homozygous deletions in almost 20% cases. The peak of allelic deletions from region D3S2409-D3S3667 (600 kb) was statistically valid (P = 10(-3)). Regions AP20 and D3S2409-D3S3667 (3p21.3) were for the first time associated with tumorigenesis. Clusters of tumor suppressor genes were identified in regions LUCA, AP20, and D3S2409-D3S3667. Methylation of RASSF1A and RARbeta2 (3p) was associated with early carcinogenesis, and that of SEMA3B, with tumor progression. These findings are useful for early diagnostics and post-surgery prognosis of tumors.

Biomarkers, Tumor↗
PubMedDate not supplied

[Methylation of the promoter region of the RASSF1A gene, a candidate tumor suppressor, in primary epithelial tumors].

Methylation of the promoter CpG-islands of the candidate tumor suppressor gene RASSF1A (3p21.31) was studied in primary tumors of kidney, breast and ovary (172 cases). Methylation-specific PCR (MSP) and methyl-sensitive restriction endonuclease digestion followed by PCR (MSRA) were applied. Statistically significant correlation (P << 10(-6)) was shown for the results of the MSP and MSRA, and the data of bisulfite sequencing reported earlier. The frequency of RASSF1A methylation according to MSP and MSRA was 86% (25/29) and 94% (50/53) in renal cell carcinoma (RCC) and 64% (18/28) and 78% (32/41)--in breast carcinoma (BC) samples, and 59% (17/29) and 73% (33/45) in ovarian epithelial tumors (OET), respectively. The use of several methyl-sensitive restriction enzymes (HpaII, HhaI, Bsh12361, AciI) enhanced the sensitivity of MSRA and allowed to analyze methylation status of 18 CpG-pairs in the RASSF1A CpG-island. Density of methylation of the RASSF1A CpG-island was 72% (644/900) in RCC, 63% (361/576) in BC, and 58% (346/594) in OET samples (18 CpG-pairs multiplied to the number of samples shown methylation were assumed as 100%). The RASSF1A gene methylation was also observed in samples of morphologically normal tissues adjacent to corresponding tumors (11-35%), but it was not detected in blood DNAs of healthy donors (0/15). The RASSF1A methylation frequency did not show significant correlation to tumor stage, grade and metastases (P = 0.3-1.0). The RASSF1A gene methylation was observed more frequently than other investigated aberrations--hemi- and homozygous deletions inside or around this gene. These observations are consistent with the hypothesis that the RASSF1A gene methylation is an early event in the carcinogenesis and one of the dominant ways of its inactivation.

Alleles↗
PubMedDate not supplied

[NotI-STS markers for human chromosome 3 are gene markers].

Ninety four NotI-STS markers to seventy two individual NotI clones were developed basing on DNA nucleotide sequences from NotI-"jumping" and "linking" NotI-libraries of human chromosome 3. The localization of NotI-STS markers and their ordering on chromosome was established by combined data of RH-mapping (our data), contig-mapping, cytogenetic mapping and in silico mapping. Performed comparison of NotI-STS DNAs with human genome sequences revealed two gaps in the regions, 3p21.33 (marker NLI-256) and 3p21.31 (NL3-005), and segmental duplication. Identical DNA fragments are localized in the regions 12q and 3p22-21.33 (marker NL3-007). In the region 3q28-q29 (marker NLM-084) a fragment was detected with its identical copies present also on chromosomes 1, 2, 15 and 19. For 69 NotI-STSs, significant homologies with nucleotide sequences of 70 genes and two cDNAs were detected taking in consideration homologies to NotI-STS 5'- and 3'-terminal sequences. Association of NotI-STSs with genes is confirmed by high correlation of gene density distribution with the density of NotI-STS markers on the map of human chromosome 3. Obtained data evidence possibility of NotI-STS marker application as gene markers and allow considering constructed NotI-map as gene map of human chromosome 3.

Base Sequence↗