The over-representation of binary DNA tracts in seven sequenced chromosomes

Yagil, Gad
January 2004
BMC Genomics;2004, Vol. 5, p19
Academic Journal
Background: DNA tracts composed of only two bases are possible in six combinations: A+G (purines, R), C+T (pyrimidines, Y), G+T (Keto, K), A+C (Imino, M), A+T (Weak, W) and G+C (Strong, S). It is long known that all-pyrimidine tracts, complemented by all-purines tracts ("R.Y tracts"), are excessively present in analyzed DNA. We have previously shown that R.Y tracts are in vast excess in yeast promoters, and brought evidence for their role in gene regulation. Here we report the systematic mapping of all six binary combinations on the level of complete sequenced chromosomes, as well as in their different subregions. Results: DNA tracts composed of the above binary base combinations have been mapped in seven sequenced chromosomes: Human chromosomes 21 and 22 (the major contigs); Drosophila melanogaster chr. 2R; Caenorhabditis elegans chr. I; Arabidopsis thaliana chr. II; Saccharomyces cerevisiae chr. IV and M. jannaschii. A huge over-representation, reaching million-folds, has been found for very long tracts of all binary motifs except S, in each of the seven organisms. Long R.Y tracts are the most excessive, except in D. melanogaster, where the K.M motif predominates. S (G, C rich) tracts are in excess mainly in CpG islands; the W motif predominates in bacteria. Many excessively long W tracts are nevertheless found also in the archeon and in the eukaryotes. The survey of complete chromosomes enables us, for the first time, to map systematically the intergenic regions. In human and other chromosomes we find the highest over-representation of the binary DNA tracts in the intergenic regions. These over-representations are only partly explainable by the presence of interspersed elements. Conclusions: The over-representation of long DNA tracts composed of five of the above motifs is the largest deviation from randomness so far established for DNA, and this in a wide range of eukaryotic and archeal chromosomes. A propensity for ready DNA unwinding is proposed as the functional role, explaining the evolutionary conservation of the huge excesses observed.


Related Articles

  • Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Lodato, Simona; Molyneaux, Bradley J; Zuccaro, Emanuela; Goff, Loyal A; Chen, Hsu-Hsin; Yuan, Wen; Meleski, Alyssa; Takahashi, Emi; Mahony, Shaun; Rinn, John L; Gifford, David K; Arlotta, Paola // Nature Neuroscience;Aug2014, Vol. 17 Issue 8, p1046 

    The neocortex contains an unparalleled diversity of neuronal subtypes, each defined by distinct traits that are developmentally acquired under the control of subtype-specific and pan-neuronal genes. The regulatory logic that orchestrates the expression of these unique combinations of genes is...

  • Characterization and regulation of the γ-glutamyl transpeptidase gene from the fission yeast Schizosaccharomyces pombe. Hey-Jung Park, Owen P.; Hye-Won Lim; Kanghwa Kim; Il-Han Kim; Park, Eun-Hee; Chang-Jin Lim // Canadian Journal of Microbiology;Jan2004, Vol. 50 Issue 1, p61 

    The structural gene for the putative γ-glutamyl transpeptidase (GGT) was isolated from the chromosomal DNA of the fission yeast Schizosaccharomyces pombe. The determined sequence contained 3324 bp and encoded the predicted 630 amino acid sequence of GGT, which resembles counterparts in Homo...

  • The histone acetyltransferase GCN5 modulates the retrograde response and genome stability determining yeast longevity. Sangkyu Kim; Ohkuni, Kentaro; Couplan, Elodie; Jazwinski, S. Michal // Biogerontology;Oct2004, Vol. 5 Issue 5, p305 

    Transcriptional silencing decreases at both subtelomeric and silent mating-type loci and increases at the ribosomal DNA locus during the replicative life span of the yeast Saccharomyces cerevisiae. Evidence exists that epigenetic changes in the regulatory state of chromatin may be a causal...

  • How does the histone code work? Cosgrove, Michael S.; Wolberger, Cynthia // Biochemistry & Cell Biology;Aug2005, Vol. 83 Issue 4, p468 

    Patterns of histone post-translational modifications correlate with distinct chromosomal states that regulate access to DNA, leading to the histone-code hypothesis. However, it is not clear how modification of flexible histone tails leads to changes in nucleosome dynamics and, thus, chromatin...

  • Genome-wide approaches to studying chromatin modifications. Schones, Dustin E.; Zhao, Keji // Nature Reviews Genetics;Mar2008, Vol. 9 Issue 3, p179 

    Over two metres of DNA is packaged into each nucleus in the human body in a manner that still allows for gene regulation. This remarkable feat is accomplished by the wrapping of DNA around histone proteins in repeating units of nucleosomes to form a structure known as chromatin. This chromatin...

  • DNA Packaging Protein.  // Science Teacher;Apr2009, Vol. 76 Issue 4, p18 

    The article reports on research published in the journal "Genes and Development" by scientists at Albert Einstein College of Medicine of Yeshiva University, which found that a class of chromatin proteins called linker histones is vital for maintaining the structure and function of chromosomes...

  • Functional Antagonism between Sas3 and Gcn5 Acetyltransferases and ISWI Chromatin Remodelers. Lafon, Anne; Petty, Emily; Pillus, Lorraine // PLoS Genetics;Oct2012, Vol. 8 Issue 10, Special section p1 

    Chromatin-modifying enzymes and ATP-dependent remodeling complexes have been intensely studied individually, yet how these activities are coordinated to ensure essential cell functions such as transcription, replication, and repair of damage is not well understood. In this study, we show that...

  • The Origin Recognition Complex Links Replication, Sister Chromatid Cohesion and Transcriptional Silencing in Saccharomyces cerevisiae. Suter, Bernhard; Tong, Amy; Chang, Michael; Yu, Lisa; Brown, Grant W.; Boone, Charles; Rine, Jasper // Genetics;Jun2004, Vol. 167 Issue 2, p579 

    Mutations in genes encoding the origin recognition complex (ORC) of Saccharomyces cerevisiae affect initiation of DNA replication and transcriptional repression at the silent mating-type loci. To explore the function of ORC in more detail, a screen for genetic interactions was undertaken using...

  • Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. Bandyopadhyay, Sourav; Kelley, Ryan; Krogan, Nevan J.; Ideker, Trey // PLoS Computational Biology;Apr2008, Vol. 4 Issue 4, p1 

    Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics