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

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.

Flow of Information during an Evolutionary Process: The Case of Influenza A Viruses

“…The use of information theory in biology is not new. For example, the use of entropy and mutual information has been used for detecting gene-gene associations [47], multivariate entropy distance method has been developed for prokaryotic gene identification [48], the construction of phylogenetic trees using relative information between DNA sequences based on Lempel-Ziv complexity (particularly useful when multiple alignment based strategies fail) [49]; for detecting heart arrhythmias [50] and for determining nucleosome positioning motifs [51]. We use as an example 39 viral genomes comprising 312 sequences of influenza A that span over almost a century.…”

WEB-server for search of a periodicity in amino acid and nucleotide sequences

“…This period could not be identified using the entire previously developed software programs, such as TRF [12], T-REKS [9], Mreps [13], ATR hunter [14], TRStalker [3], Repfind [15], as well as the other developed methods and algorithms. This also applies to the spectral approaches developed in certain woks [16][17][18].…”

Search for Latent Periodicity in Amino Acid Sequences with Insertions and Deletions

“…Spectral approaches enable the discovery of enough "fuzzy" periodicity in protein sequences without insertion(s) or deletion(s) of amino acids. Fourier transform, wavelet transform, information decomposition and some other methods can be attributed to a number of spectral methods (Tiwari et al, 1997;Lobzin and Chechetkin, 2000;Kravatskaya et al, 2011;Korotkov et al, 2003a;de Sousa Vieira, 1999;Meng et al, 2013;Suvorova et al, 2014;Sosa et al, 2013;Kumar et al, 2006). However, these approaches have a significant limitation, such as the fact that they do not allow the detection of periodicity with insertions and deletions.…”