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.     

Recognition of characteristic patterns in sets of functionally equivalent DNA sequences

An algorithm has been developed for the identification of unknownpatterns which are distinctive for a set of short DNA sequencesbelieved to be functionally equivalent. A pattern is definedas being a string, containing fully or partially specified nucleotidesat each position of the string. The advantage of this ‘vague’definition of the pattern is that it imposes minimum constraintson the characterization of patterns. A new feature of the approachdeveloped here is that it allows a ‘fair’ simultaneoustesting of patterns of all degrees of degeneracy. This analysisis based on an evaluation of inhomogeneity in the empiricaloccurrence distribution of any such pattern within a set ofsequences. The use of the nonparametric kernel density estimationof Parzen allows one to assess small disturbances among thesequence alignments. The method also makes it possible to identifysequence subsets with different characteristic patterns. Thisalgorithm was implemented in the analysis of patterns characteristicof sets of promoters, terminators and splice junction sequences.The results are compared with those obtained by other methods. Received on November 17, 1986; accepted on June 15, 1987     

New analytical tool for analysis of splice site sequence determinants

A new analytical method has been used to examine the set of40 exon/intron boundaries within the rat embryonic myosin heavychain (MHC_emb) gene. It has also been applied to an additionalset of 850 splice sequences selected from GenBank. Strong evidenceis obtained for the involvement of 3' ends but not 5' ends ofexon sequences in splice site recognition. It can be determinedthat signal sequences of 5' intron ends concentrate near thesplice borders, while the distributions of the 3' intron endshave a diffuse character. The possibility of re-interpretingsome known features, in terms of the absence of certain elementsrather than the presence of elements forming sequence determinants,is discussed. The analysis undertaken enabled us to work outa more detailed set of recognition sequence requirements forthe splicing of nuclear pre-mRNA. In addition to requirementswhich have already been established we suggest the following:the ‘AG-absence’ in the immediate 3' terminal intronsequences; and a minimal match between a particular sequenceand the known exon/intron consensus sequence of 5' splice junctions. Received on March 22, 1988; accepted on November 19, 1988     

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.     

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.     

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.     

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.