151 research outputs found
Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription
We analyzed the periodic patterns in E. coli promoters and compared the
distributions of the corresponding patterns in promoters and in the complete
genome to elucidate their function. Except the three-base periodicity,
coincident with that in the coding regions and growing stronger in the region
downstream from the transcriptions start (TS), all other salient periodicities
are peaked upstream of TS. We found that helical periodicities with the lengths
about B-helix pitch ~10.2-10.5 bp and A-helix pitch ~10.8-11.1 bp coexist in
the genomic sequences. We mapped the distributions of stretches with A-, B-,
and Z- like DNA periodicities onto E.coli genome. All three periodicities tend
to concentrate within non-coding regions when their intensity becomes stronger
and prevail in the promoter sequences. The comparison with available
experimental data indicates that promoters with the most pronounced
periodicities may be related to the supercoiling-sensitive genes.Comment: 23 pages, 6 figures, 2 table
Quantumlike Chaos in the Frequency Distributions of the Bases A, C, G, T in Drosophila DNA
Continuous periodogram power spectral analyses of fractal fluctuations of
frequency distributions of bases A, C, G, T in Drosophila DNA show that the
power spectra follow the universal inverse power-law form of the statistical
normal distribution. Inverse power-law form for power spectra of space-time
fluctuations is generic to dynamical systems in nature and is identified as
self-organized criticality. The author has developed a general systems theory,
which provides universal quantification for observed self-organized criticality
in terms of the statistical normal distribution. The long-range correlations
intrinsic to self-organized criticality in macro-scale dynamical systems are a
signature of quantumlike chaos. The fractal fluctuations self-organize to form
an overall logarithmic spiral trajectory with the quasiperiodic Penrose tiling
pattern for the internal structure. Power spectral analysis resolves such a
spiral trajectory as an eddy continuum with embedded dominant wavebands. The
dominant peak periodicities are functions of the golden mean. The observed
fractal frequency distributions of the Drosophila DNA base sequences exhibit
quasicrystalline structure with long-range spatial correlations or
self-organized criticality. Modification of the DNA base sequence structure at
any location may have significant noticeable effects on the function of the DNA
molecule as a whole. The presence of non-coding introns may not be redundant,
but serve to organize the effective functioning of the coding exons in the DNA
molecule as a complete unit.Comment: 46 pages, 9 figure
A-tract clusters may facilitate DNA packaging in bacterial nucleoid
Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816–3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed ‘quasi-regularly’ throughout the genome, including both the coding and intergenic sequences. Second, there is a 10–12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in ∼100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the ∼100 bp long clusters of the phased A-tracts constitute the ‘structural code’ for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins
Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences
The level of supercoiling in the chromosome can affect gene expression. To
clarify the basis of supercoiling sensitivity, we analyzed the structural
features of nucleotide sequences in the vicinity of promoters for the genes
with expression enhanced and decreased in response to loss of chromosomal
supercoiling in E. coli. Fourier analysis of promoter sequences for
supercoiling-sensitive genes reveals the tendency in selection of sequences
with helical periodicities close to 10 nt for relaxation-induced genes and to
11 nt for relaxation-repressed genes. The helical periodicities in the subsets
of promoters recognized by RNA polymerase with different sigma factors were
also studied. A special procedure was developed for study of correlations
between the intensities of periodicities in promoter sequences and the
expression levels of corresponding genes. Significant correlations of
expression with the AT content and with AT periodicities about 10, 11, and 50
nt indicate their role in regulation of supercoiling-sensitive genes.Comment: 38 pages, 12 figure
Sequence periodicity of Escherichia coli is concentrated in intergenic regions
BACKGROUND: Sequence periodicity with a period close to the DNA helical repeat is a very basic genomic property. This genomic feature was demonstrated for many prokaryotic genomes. The Escherichia coli sequences display the period close to 11 base pairs. RESULTS: Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions. CONCLUSIONS: The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription
Nucleosome Positioning and Its Role in Gene Regulation in Yeast
Nucleosome, composed of a 147-bp segment of DNA helix wrapped around a histone protein octamer, serves as the basic unit of chromatin. Nucleosome positioning refers to the relative position of DNA double helix with respect to the histone octamer. The positioning has an important role in transcription, DNA replication and other DNA transactions since packing DNA into nucleosomes occludes the binding site of proteins. Moreover, the nucleosomes bear histone modifications thus having a profound effect in regulation. Nucleosome positioning and its roles are extensively studied in model organism yeast. In this chapter, nucleosome organization and its roles in gene regulation are reviewed. Typically, nucleosomes are depleted around transcription start sites (TSSs), resulting in a nucleosome-free region (NFR) that is flanked by two well-positioned H2A.Z-containing nucleosomes. The nucleosomes downstream of the TSS are equally spaced in a nucleosome array. DNA sequences, especially 10–11 bp periodicities of some specific dinucleotides, partly determine the nucleosome positioning. Nucleosome occupancy can be determined with high throughput sequencing techniques. Importantly, nucleosome positions are dynamic in different cell types and different environments. Histones depletions, histones mutations, heat shock and changes in carbon source will profoundly change nucleosome organization. In the yeast cells, upon mutating the histones, the nucleosomes change drastically at promoters and the highly expressed genes, such as ribosome genes, undergo more change. The changes of nucleosomes tightly associate the transcription initiation, elongation and termination. H2A.Z is contained in the +1 and −1 nucleosomes and thus in transcription. Chaperon Chz1 and elongation factor Spt16 function in H2A.Z deposition on chromatin. The chapter covers the basic concept of nucleosomes, nucleosome determinant, the techniques of mapping nucleosomes, nucleosome alteration upon stress and mutation, and Htz1 dynamics on chromatin
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