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. 2013:2013:963956.
doi: 10.1155/2013/963956. Epub 2013 Jun 10.

Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis

Daniela Sosa  1 , Pedro Miramontes, Wentian Li, Víctor Mireles, Juan R Bobadilla, Marco V José
Affiliations

Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis

Daniela Sosa et al. Int J Genomics. 2013.

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.

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Figures

Figure 1
Figure 1
MIF profile of the decamer YYYYYRRRRR from a synthetic sequence. Note the 10-base periodicity.
Figure 2
Figure 2
The MIF profiles of the decamer YYYYYRRRRR in 5 C. elegans chromosomes.
Figure 3
Figure 3
The MIF profiles of the decamer YYYYYRRRRR in all Homo sapiens chromosomes.
Figure 4
Figure 4
(a) Histogram of the spacing of the decamer YYYYYRRRRR in chromosome 21 of Homo sapiens (b) Histogram of the intact chromosome without repetitive elements; (c) Histogram of repetitive elements only.
Figure 5
Figure 5
MIF profiles of the R/Y decamer in only Alu sequences in all Homo sapiens chromosomes.
Figure 6
Figure 6
The MIF profiles of the 12-mer SWWWWWSSSSSW in some Homo sapiens chromosomes.
Figure 7
Figure 7
MIF profiles of random decamers with 5 purines and 5 pyrimidines along Homo sapiens chromosome 21, in order to compare the meaningful signal of YYYYYRRRRR as a binder nucleosome motif.
Figure 8
Figure 8
The MIF profiles of the decamer YYYYYRRRRR in all Pan troglodytes chromosomes.
Figure 9
Figure 9
The MIF profiles of the decamer YYYYYRRRRR in all Macaca mulatta chromosomes.
Figure 10
Figure 10
The three main regions of human chromosome 19, where distances around 80, 160, and 320 between the generic decamer are more highly concentrated than in the rest of the chromosomes are highlighted. Note that the clusters correspond to the peaks observed in their respective MIF profiles.
Figure 11
Figure 11
Plot of the distances between the generic decamer (ordinate) along two regions of chromosome 19 (abscissa) of Homo sapiens. Note the inverted repeat sequence.
Figure 12
Figure 12
The MIF profiles of the decamer YYYYYRRRRR in some Archaea and Eubacterial genomes.
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