The human genome: a multifractal analysis

Moreno, Pedro; Vélez, Patricia; Martínez, Ember; Garreta, Luis; Díaz, Néstor Fabián; Amador, Siler; Tischer, Irene; Gutiérrez, José Manuel; Naik, Ashwinikumar K; Tobar, Fabián; García, Felipe Martínez

doi:10.1186/1471-2164-12-506

Cited by 40 publications

(34 citation statements)

References 43 publications

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“…FD takes on non-integer values between the classical Euclidean dimensional values of one, two and three used to define the dimensions of a line, square and a cube. Fractal geometry has been used to describe molecular folding of DNA, and the nucleotide distribution in the genome [16][17][18][19]. In such instances, FD explains the complex structural organization of natural objects.…”

Section: Introductionmentioning

confidence: 99%

On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments

Toor

Rahmani

et al. 2016

J. R. Soc. Interface.

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We dedicate this work to Mr Omair Ahmed Toor and other people with Down's Syndrome and patients with congenital neurological disorders from around the world, whose constant struggle to overcome the challenges of everyday life and better themselves are an inspiration to all.On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments School of Engineering, Virginia Commonwealth University, Richmond, VA, USAThe human T-cell repertoire is complex and is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T-cell receptor (TCR) loci. The T-cell repertoire demonstrates self-similarity in terms clonal frequencies when defined by V, D and J gene segment usage; therefore to determine whether the structural ordering of these gene segments on the TCR loci contributes to the observed clonal frequencies, the TCR loci were examined for self-similarity and periodicity in terms of gene segment organization. Logarithmic transformation of numeric sequence order demonstrated that the V and J gene segments for both T-cell receptor a (TRA) and b (TRB) loci are arranged in a self-similar manner when the spacing between the adjacent segments was considered as a function of the size of the neighbouring gene segment, with an average fractal dimension of approximately 1.5. Accounting for the gene segments occurring on helical DNA molecules with a logarithmic distribution, sine and cosine functions of the log-transformed angular coordinates of the start and stop nucleotides of successive TCR gene segments showed an ordered progression from the 5 0 to the 3 0 end of the locus, supporting a log-periodic organization. T-cell clonal frequency estimates, based on V and J segment usage, from normal stem cell donors were plotted against the V and J segment on TRB locus and demonstrated a periodic distribution. We hypothesize that this quasi-periodic variation in genesegment representation in the T-cell clonal repertoire may be influenced by the location of the gene segments on the periodic-logarithmically scaled TCR loci. Interactions between the two strands of DNA in the double helix may influence the probability of gene segment usage by means of either constructive or destructive interference resulting from the superposition of the two helices.

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Section: Introductionmentioning

confidence: 99%

On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments

Toor

Rahmani

et al. 2016

J. R. Soc. Interface.

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“…The high multifractal chromosomes have the highest densities of Alu elements and genes per Mb (Moreno, et al, 2011). Particularly chromosomes 17 and 19 are by far, the most multifractal chromosomes have the highest gene densities of the whole genome and a high and medium frequencies of lentiviral integration.…”

Section: Discussionmentioning

confidence: 99%

“…The chromosomal localization of the lentiviral provirus included in the present study was performed by using the G pattern banding of each chromosome according with the International System for Human Cytogenetic Nomenclature -ISCN- (Simonis, et al, 2006). The mean values of multifractality (AvΔDq) per each chromosome were obtained from the analysis of the multifractality that included 9,389 genomic fragments of 300 Kb each one, representing 2,816,700 Kb covering more than 98.6% of the human genome (Moreno, et al, 2011).…”

Section: Mapping Of Lentivirus Integration Sites In the Human Genomementioning

confidence: 99%

“…In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality (Moreno, et al, 2011). Furthermore, the multifractal analysis of the human genome permitted to classify the human chromosomes into three different groups according with their multifractality: The first group were chromosomes 19, 17, 22 and 16 that exhibit the highest multifractality values and also the highest Alu contents; a second group included chromosomes 15,20,1,10,12,9,7,14 and 21 which have medium multifractality; and a third group of chromosomes 2, 11, 8, 6, Y, 3, 18, 5, 13, X, and 4 with the lowest multifractality (Moreno, et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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The complexity of genome integration process in human lentivirus

García-Vallejo

2016

Rev. Acad. Colomb. Cienc. Ex. Fis. Nat.

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Introduction. The distribution of human lentiviral cDNA into the host genome has been studied using a linear structural approach, however such analysis is incomplete because do not consider the dynamics and topology of interphase chromatin and the gene expression networks in infected cells. Objective. To correlate using a non-linear approach the multifractality of human chromosomes, with the composition and disturbing of chromatin topology, as complex effect promote by the lentiviral cDNA integration. Methods. From 2,409 human genome sequences flanking the 5'LTR of human and simian lentiviruses obtained from GeneBank (NCBI) database, several human genomic variables were correlated with the multifractality values AvΔDq of chromosomes covering more than 98.6% of the human genome. Moreover Cytoscape v.2.63 was used to simulate the effects of viral cDNA integration on gene expression networks in macrophages. Results. The 54.21% of lentivirus cDNA integrations were registered in chromosomes with high and medium fractality; 18.14% of these cDNA integrations was exclusively located in chromosomes 16, 17, 19 and 22 corresponding to that with high multifractality values. High scores of Pearson's correlation for AvΔDq/ chromosome vs integrations/chromosome; percentage of Alu sequences were recorded. 2,770 interactions among 28 genes located closed to HIV-1 proviruses in human macrophages were recorded. cDNA integration alters the gene interaction networks in infected cells, the topological parameters of non-infected macrophage network gene was dramatically changed upon HIV-1 integration. Conclusion. Some topological changes in those regions with high frequency of cDNA viral integrations would synergistically configure local topological chromatin environments that alters the gene interaction networks in infected cells.

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“…En este proyecto (AMGH) se aplicaron diferentes técnicas y herramientas de Bioinformática y de Geometría Fractal para la construcción de un modelo teórico, no lineal e "integrativo" que explica cómo se estructura y funciona el genoma humano (ver principales resultados del proyecto en [6] y [7]). Este estudio se adelantó a partir de la información del genoma humano publicada en el GenBank [2,5] y la gestión de datos también se basó en archivos planos, heredando de esta forma los problemas mencionados previamente.…”

Section: Introductionunclassified