Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?

We explore large-scale nucleotide compositional fluctuations of the human genome using multiresolution techniques. Analysis of the GC content and of the AT and GC skews reveals the existence of rhythms with two main periods of 110+/-20 kb and 400+/-50 kb that enlighten a remarkable cooperative gene organization. We show that the observed nonlinear oscillations are likely to display all the characteristic features of chaotic strange attractors which suggests a very attractive deterministic picture: gene orientation and location, in relation with the structure and dynamics of chromatin, might be governed by a low-dimensional nonlinear dynamical system.

[1]  S Nicolay,et al.  Transcription‐coupled TA and GC strand asymmetries in the human genome , 2003, FEBS letters.

[2]  J. Marko,et al.  Probing chromosome structure with dynamic force relaxation. , 2001, Physical review letters.

[3]  U. K. Laemmli,et al.  Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. , 1992, Current opinion in genetics & development.

[4]  Isochores merit the prefix 'iso' , 2002, Comput. Biol. Chem..

[5]  W. Bickmore,et al.  Genes and genomes: chromosome bands – flavours to savour , 1993 .

[6]  G Bernardi,et al.  Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.

[7]  W. Bickmore,et al.  Putting the genome on the map. , 1998, Trends in genetics : TIG.

[8]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[9]  Gail Sudlow,et al.  Interphase Cell Cycle Dynamics of a Late-Replicating, Heterochromatic Homogeneously Staining Region: Precise Choreography of Condensation/Decondensation and Nuclear Positioning , 1998, The Journal of cell biology.

[10]  Hanspeter Herzel,et al.  10-11 bp periodicities in complete genomes reflect protein structure and DNA folding , 1999, Bioinform..

[11]  J. Ostashevsky.  A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. , 1998, Molecular biology of the cell.

[12]  S. Karlin,et al.  Strand compositional asymmetry in bacterial and large viral genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Alain Arneodo,et al.  THE DYNAMICS OF TRIPLE CONVECTION , 1985 .

[14]  S. Gasser,et al.  Visualizing Chromatin Dynamics in Interphase Nuclei , 2002, Science.

[15]  Anne E Carpenter,et al.  Large-scale chromatin structure and function. , 1999, Current opinion in cell biology.

[16]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[17]  Ana Pombo,et al.  Replicon Clusters Are Stable Units of Chromosome Structure: Evidence That Nuclear Organization Contributes to the Efficient Activation and Propagation of S Phase in Human Cells , 1998, The Journal of cell biology.

[18]  Alain Arneodo,et al.  Possible new strange attractors with spiral structure , 1981 .

[19]  Wendy A. Bickmore,et al.  Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH , 2002, The Journal of cell biology.

[20]  J. Muzy,et al.  Long-range correlations in genomic DNA: a signature of the nucleosomal structure. , 2001, Physical review letters.

[21]  P. Green,et al.  Transcription-associated mutational asymmetry in mammalian evolution , 2003, Nature Genetics.

[22]  Ronald Berezney,et al.  Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci , 2000, Chromosoma.

[23]  G van den Engh,et al.  A random-walk/giant-loop model for interphase chromosomes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Peter R. Cook,et al.  Predicting three-dimensional genome structure from transcriptional activity , 2002, Nature Genetics.

[25]  Alain Arneodo,et al.  Long-Range Correlations in Genomic DNA , 2001 .

[26]  R Eils,et al.  Compartmentalization of interphase chromosomes observed in simulation and experiment. , 1999, Journal of molecular biology.

[27]  Alain Arneodo,et al.  Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes. , 2002, Journal of molecular biology.

[28]  Y. Pomeau,et al.  Order within chaos , 1986 .

[29]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[30]  G van den Engh,et al.  Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. , 1992, Science.

[31]  U. K. Laemmli,et al.  Metaphase chromosome structure: Bands arise from a differential folding path of the highly AT-rich scaffold , 1994, Cell.