Prediction and comparative analysis of CTCF binding sites based on a first principle approach

Abstract

We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence, ChIP-seq data for the K562 cell, nucleosome positions for IMR90 cell as well as the CTCF binding sites in the mouse HOXA gene. The analysis of Homo sapiens, Mus musculus, Sus scrofa, Capra hircus and Drosophila melanogaster whole genomes shows: binding sites are organized in cluster-like groups, where two consecutive sites obey a power-law with coefficient ranging from 0.3292 ± 0.0068 to 0.5409 ± 0.0064; the distance between these groups varies from 18.08 ± 0.52 kbp to 42.1 ± 2.0 kbp. The genome of Aedes aegypti does not show a power law, but 19.9% of binding sites are 144 ± 4 and 287 ± 5 bp distant of each other. We run negative tests, confirming the under-representation of CTCF binding sites in Caenorhabditis elegans, Plasmodium falciparum and Arabidopsis thaliana complete genomes.