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Register a new userUniversal spectrum for DNA base C+G concentration variability in Human chromosome Y
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Authors
A. M. Selvam
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The spatial distribution of DNA base sequence A, C, G and T exhibit selfsimilar fractal fluctuations and the corresponding power spectra follow inverse power law form, which implies the following: (1) A scale invariant eddy continuum, namely, the amplitudes of component eddies are related to each other by a scale factor alone. In general, the scale factor is different for different scale ranges and indicates a multifractal structure for the spatial distribution of DNA base sequence. (2) Long-range spatial correlations of the eddy fluctuations. Multifractal structure to space-time fluctuations and the associated inverse power law form for power spectra is generic to spatially extended dynamical systems in nature and is a signature of self-organized criticality. The exact physical mechanism for the observed self-organized criticality is not yet identified. The author has developed a general systems theory where quantum mechanical laws emerge as self-consistent explanations for the observed long-range space-time correlations, i.e. the apparently chaotic fractal fluctuations are signatures of quantum-like chaos in dynamical systems. The model provides unique quantification for the observed inverse power law form for power spectra in terms of the statistical normal distribution. In this paper it is shown that the frequency distribution of the bases C+G in all available contiguous sequences for Human chromosome Y DNA exhibit model predicted quantum-like chaos.
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Power spectra of human DNA base C+G frequency distribution in all available contiguous sections exhibit the universal inverse power law form of the statistical normal distribution for the 24 chromosomes. Inverse power law form for power spectra of space-time fluctuations is generic to dynamical systems in nature and indicate long-range space-time correlations. A recently developed general systems theory predicts the observed non-local connections as intrinsic to quantumlike chaos governing space-time fluctuations of dynamical systems. The model predicts the following. (1) The quasiperiodic Penrose tiling pattern for the nested coiled structure of the DNA molecule in the chromosome resulting in maximum packing efficiency. (2) The DNA molecule functions as a unified whole fuzzy logic network with ordered two-way signal transmission between the coding and non-coding regions. Recent studies indicate influence of non-coding regions on functions of coding regions in the DNA molecule.
The frequency distribution of DNA bases A, C, G, T exhibit fractal fluctuations ubiquitous to dynamical systems in nature. The power spectra of fractal fluctuations exhibit inverse power law form signifying long-range correlations between local (small-scale) and global (large-scale) perturbations. The author has developed a general systems theory based on classical statistical physics for fractal fluctuations which predicts that the probability distribution of eddy amplitudes and the variance (square of eddy amplitude)spectrum of fractal fluctuations follow the universal Boltzmann inverse power law expressed as a function of the golden mean. The model predicted distribution is very close to statistical normal distribution for fluctuations within two standard deviations from the mean and exhibits a fat long tail. In this paper it is shown that DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) Genome Release 4 exhibit universal inverse power law form consistent with model prediction. The observed long-range correlations in the DNA bases implies that the non-coding junk or selfish DNA which appear to be redundant, may also contribute to the efficient functioning of the protein coding DNA, a result supported by recent studies.
All genes on the human Y-chromosome were studied using fractal dimension and Shannon entropy. Clear outlier clusters were identified. Among these were 6 sequences that have since been withdrawn as CDSs and 1 additional sequence that is not in the current assembly. A methodology for ranking the sequences based on deviation from average values of FD and SE was developed. The group of sequences scored among the 10% largest deviations had abnormally high likelihood to be from centromeric or pseudoautosomal regions and low likelihood to be from X-chromosome transposed regions. lncRNA sequences were also enriched among the outliers. In addition, the number of expressed genes previously identified for evolutionary study tended to not have large deviations from the average. Keywords: Y-chromosome; Shannon di-nucleotide entropy; fractal dimension; centromeric genes; gene degredation; lncRNA
Atmospheric flows exhibit self-similar fractal space-time fluctuations on all space-time scales in association with inverse power law distribution for power spectra of meteorological parameters such as wind, temperature, etc., and thus implies long-range correlations, identified as self-organized criticality generic to dynamical systems in nature. A general systems theory based on classical statistical physical concepts developed by the author visualizes the fractal fluctuations to result from the coexistence of eddy fluctuations in an eddy continuum, the larger scale eddies being the integrated mean of enclosed smaller scale eddies. The model satisfies the maximum entropy principle and predicts that the probability distributions of component eddy amplitudes and the corresponding variances (power spectra) are quantified by the same universal inverse power law distribution which is a function of the golden mean. Atmospheric particulates are held in suspension by the vertical velocity distribution (spectrum). The atmospheric particulate size spectrum is derived in terms of the model predicted universal inverse power law characterizing atmospheric eddy spectrum. Model predicted spectrum is in agreement with the following four experimentally determined data sets: (i) CIRPAS mission TARFOX_WALLOPS_SMPS aerosol size distributions (ii) CIRPAS mission ARM-IOP (Ponca City, OK) aerosol size distributions (iii) SAFARI 2000 CV-580 (CARG Aerosol and Cloud Data) cloud drop size distributions and (iv) TWP-ICE (Darwin, Australia) rain drop size distributions.
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are well correlated with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.
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