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Flexibility profiling of gene transcription start and end sites on human and fruit fly DNA

Flexibility of a DNA molecule plays a significant role in some important biological processes such as transcription and chromosome packaging. Curvature and bendability are sequence-dependent intrinsic properties of the DNA double helix where curvature is a measure of torsional flexibility, and bendability is a measure of anisotropic bending flexibility of a DNA molecule. We wanted to see if such a structure-encoded signal exists near transcription start (TSS) and end sites (TES) of fruit fly (D. melanogaster) and human transcripts. Using a program with an implemented BEND algorithm (1), developed inside our Bioinfo group, we managed to make profiles of DNA sequences by appending a curvature and bendability value to each nucleotide. We created curvature and bendability profiles for human and fruit fly transcripts. Fruit fly transcripts were grouped by promoter modules (2) and by a k-means algorithm. Our preliminary results show that curvature and bendability are significantly altered in close proximity to TSSs and TESs in both human and fruit fly, suggesting that the curving and bending of the sequence may have a specific function in regulation of initiationand termination of transcription. (1) Goodsell, D. S., Dickerson, R. E. 1994. Bending and curvature calculations in B-DNA. Nucleic Acids Research 22 (24), 5497-5503. (2) Ohler, U., Liao, G., Niemann, H., Rubin, G. M. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biology 3 (12), research0087.1-0087.12.

DNA; curvature; bendability; transcription

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