Biomedical subjects

G Mengeritsky

Publications and source records attributed to G Mengeritsky.

8 recordsLinked to original sources

PubMed1994

Dynamics of the nucleoprotein structure of simian virus 40 regulatory region during viral development.

The regulatory region of SV40 is composed of multiple elements, including the origin of replication (ori), the encapsidation signal (ses) and the enhancer. Here, the structure of the chromatin and nucleoprotein complexes in a region encompassing ses and part of the enhancer was investigated in detail by in situ probing with DNase I. We have used a model experimental system based on plasmids which carry parts of the SV40 regulatory region. The results demonstrate that a specific nucleoprotein structure at the region is formed early after transfection. The overall structure is maintained throughout the viral life cycle. The observed DNase digestion pattern is consistent with the presence of a mixed population of viral minichromosomes with various, but not random, nucleosomal arrangements in that region. Specific modulations, which are associated with the various stages of the viral life cycle, are superimposed on the general structure. The most dramatic changes occur at nucleotides 34 and 113, located at both ends of ses and flanking the GC-box region. Some of the changes depend on the presence of viral gene product(s), probably a late (capsid) protein. The results further suggest that the condensed minichromosome within the viral particle assumes a highly specific configuration in this region. The nucleoprotein structure is sensitive to modifications of the primary nucleotide sequence and to flanking DNA elements. There is good correlation between distortions in the nucleoprotein structure and the inability of mutant plasmids to be packaged, substantiating the requirement for proper chromatin condensation in viral packaging.

Animals↗

PubMed1993

Genetic and biochemical analysis of the integration host factor of Escherichia coli.

Integration host factor (IHF) is a small, heterodimeric DNA-binding protein of Escherichia coli composed of two subunits, alpha and beta, encoded by the himA and hip genes, respectively. IHF binds to the minor groove at a consensus sequence and bends DNA. We mutagenized the hip gene and studied the activity of the mutant IHF proteins in vivo and in vitro. Substitutions at the C-terminal alpha-helix (alpha-helix 3) reduced IHF activity and relaxed the specificity to DNA without abolishing the ability of IHF to bend DNA. These results indicate that the C-terminal region of Hip participates in determining IHF specificity. Alanine substitutions in beta-strands 2 and 3 generally had no effect on IHF activity in vivo suggesting that individually, many of these residues make only small contributions to the binding of IHF to DNA. Replacing the single amino acid of Hip that differs from HU in a highly conserved region of the arm did not affect IHF activity. This finding led us to conclude that this region of Hip does not contribute to specific DNA recognition by IHF. The binding of IHF to DNA is probably not restricted to one domain, but requires the co-operative participation of a number of regions of the protein.

Bacterial Proteins↗

PubMed1991

Genes coding for integration host factor are conserved in gram-negative bacteria.

A genetic system for the selection of clones coding for integration host factor and HU homologs is described. We demonstrate that the himA and hip genes of Serratia marcescens and Aeromonas proteolytica can substitute for the Escherichia coli genes in a variety of biological assays. We find that the sequence and genetic organization of the himA and hip genes of S. marcescens are highly conserved.

Amino Acid Sequence↗

PubMed1989

New analytical tool for analysis of splice site sequence determinants.

A new analytical method has been used to examine the set of 40 exon/intron boundaries within the rat embryonic myosin heavy chain (MHCemb) gene. It has also been applied to an additional set of 850 splice sequences selected from GenBank. Strong evidence is obtained for the involvement of 3' ends but not 5' ends of exon sequences in splice site recognition. It can be determined that signal sequences of 5' intron ends concentrate near the splice borders, while the distributions of the 3' intron ends have a diffuse character. The possibility of re-interpreting some known features, in terms of the absence of certain elements rather than the presence of elements forming sequence determinants, is discussed. The analysis undertaken enabled us to work out a more detailed set of recognition sequence requirements for the splicing of nuclear pre-mRNA. In addition to requirements which have already been established we suggest the following: the 'AG-absence' in the immediate 3' terminal intron sequences; and a minimal match between a particular sequence and the known exon/intron consensus sequence of 5' splice junctions.

Animals↗

PubMed1987

Recognition of characteristic patterns in sets of functionally equivalent DNA sequences.

An algorithm has been developed for the identification of unknown patterns which are distinctive for a set of short DNA sequences believed to be functionally equivalent. A pattern is defined as being a string, containing fully or partially specified nucleotides at each position of the string. The advantage of this 'vague' definition of the pattern is that it imposes minimum constraints on the characterization of patterns. A new feature of the approach developed here is that it allows a 'fair' simultaneous testing of patterns of all degrees of degeneracy. This analysis is based on an evaluation of inhomogeneity in the empirical occurrence distribution of any such pattern within a set of sequences. The use of the nonparametric kernel density estimation of Parzen allows one to assess small disturbances among the sequence alignments. The method also makes it possible to identify sequence subsets with different characteristic patterns. This algorithm was implemented in the analysis of patterns characteristic of sets of promoters, terminators and splice junction sequences. The results are compared with those obtained by other methods.

Algorithms↗

PubMed1984

Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin.

In our previous work we have shown by comparison of experimental and computational data that the positions of the histone octamers bound to the DNA molecule appear to be completely sequence-dependent. This provides a convenient and quick method for locating the nucleosomes along the DNA molecule, as soon as the nucleotide sequence is known. Using this computational approach, the complete nucleosomal map of the SV40 minichromosome has been constructed. The map consists of 25 nucleosomes, with their coordinates (centers) being specified with high accuracy. The map is found to be in remarkable agreement with available experimental data.

Base Sequence↗

PubMed1984

Simian virus 40 replication pause sites map with the nucleosomes.

The locations of replication pause sites in the simian virus 40 minichromosome which were determined by sizing cloned fragments of nascent DNA (Zannis-Hadjopoulos et al., J. Mol. Biol. 165:599-607, 1983) were compared with the positions of simian virus 40 nucleosomes in the genome, as obtained by sequence-directed mapping (G. Mengeritsky and E. N. Trifonov, Nucleic Acids Res. 11:3833-3851, 1983; Mengeritsky and Trifonov, Cell Biophys. 6:1-8, 1984). Clear correlation between these two maps is demonstrated, suggesting that nucleosomes hinder propagation of the replication forks.

DNA Replication↗

PubMed1983

Nucleotide sequence-directed mapping of the nucleosomes.

The concept of sequence-dependent deformational anisotropy of DNA proposed earlier is further elaborated and a computational procedure is developed for the sequence-directed mapping of the nucleosomes along chromatin DNA nucleotide sequences. The deformational anisotropy is found to be nonuniform along the molecule of the nucleosomal DNA, suggesting that the DNA superhelix in the nucleosome is slightly oval rather than circular in projection. The number of superhelical turns in the nucleosome core particle is estimated to be 2.0 +/- 0.2. Preliminary mapping of the nucleosomes in various chromatin DNA sequences yields the distribution of linker lengths which shows several minima separated by about 10 base-pairs. This is explained by sterical exclusion effects due to overlapping of the nucleosomes in space when some specific linker lengths are chosen. The mapping procedure described is tested by comparing its results with all the most accurate experimental mapping data reported so far. The comparison demonstrates that the exact positions of all the nucleosomes appear to be determined exclusively by the nucleotide sequences.

Animals↗