Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Abstract

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.

submitted to Physical Review E

References in corpus (2)

• Universal 1/f noise, cross-overs of scaling exponents, and chromosome specific patterns of GC content in DNA sequences of the human genome
• An Unusual 500,000 Bases Long Oscillation of Guanine and Cytosine Content in Human Chromosome 21