Periodic Distribution of a Putative Nucleosome Positioning Motif in Human, Nonhuman Primates, and Archaea: Mutual Information Analysis

Daniela Sosa,Víctor Mireles,Juan R Bobadilla,Wentian Li,Pedro Miramontes,Marco V José

doi:10.1155/2013/963956

Abstract

Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.

Highlights

It is generally accepted that the chromatin organization of eukaryotic DNA is strongly governed by a code inherent to the DNA sequence
Since the decamer was derived from the C. elegans micrococcal nuclease (MNase) digestion data, we expect periodicities to be present in the mutual information function (MIF) profile, either due to the tandem repeats of the decamer or due to the regular spacing of the nucleosomes
The MIF profiles of the decamer on chromosomes I, III, and V, but not on chromosome II or IV, of C. elegans display a regular pattern of peaks that appear every 10, 20, 40, and 92–94 bp approximately (Figure 2), and they correspond to distance histograms

Summary

Introduction

It is generally accepted that the chromatin organization of eukaryotic DNA is strongly governed by a code inherent to the DNA sequence. Modulating the accessibility of individual DNA sequences involves many complex interactions, the most prevalent of which are the interactions between histone octamers and DNA in compacted chromosomes [1, 2]. In Eukaryotes and Archaea, DNA is packaged into chromatin in orderly repetitive protein-DNA complexes called nucleosomes. Each nucleosome consists of approximately 146-147 bp of dsDNA wound 1.7-1.8 times around a histone octamer [3,4,5] to form the basic unit of chromatin structure, the nucleosome. Stretches of DNA called linker up to 100 bp, often with an increment of 10 bp, separate adjacent nucleosomes. Multiple nuclear proteins bind to this linker region, some of which may be responsible for the ordered wrapping of strings of nucleosomes into higher-order chromatin structures [7]

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