Single-base Resolution Nucleosome Mapping on DNA Sequences

Abstract

Nucleosome DNA bendability pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendability matrix. The matrix can be used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted, separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is +/-1 base. The procedure is placed on publicly accessible server and can be applied to any DNA sequence of interest.

High resolution positioning of intron ends on the nucleosomes

“…New perspectives for the chromatin studies have been recently opened by introduction of a single-base resolution nucleosome mapping technique, based on the chromatin sequence code (Gabdank et al, 2009(Gabdank et al, , 2010aTrifonov, 2010a,b), and on deformational properties of DNA base pair stacks (Cui and Zhurkin, 2010;Tolstorukov et al, 2008;Trifonov, 2010a;Wang et al, 2010). In the high resolution maps the nucleosomes appear as series of several peaks indicating locations of local dyads in the nucleosome DNA.…”

“…Already simple numerology is suggestive of the structural relation between chromatin and gene splicing (Beckmann and Trifonov, 1991). Typical sizes of both exons and introns (major modes of the respective size distributions) are 80-120 bases (Hong et al, 2006;Zhang, 1998), while the size of DNA in contact with histones in the nucleosomes is about 115 bases (Gabdank et al, 2010a;Harp et al, 2000).…”

“Anticipated” nucleosome positioning pattern in prokaryotes

“…This is especially clear in case of eukaryotes where the protein coding sequences comprise only few percents of the genome. One of the first additional codes that drew attention of the sequence research community was, indeed, eukaryotic chromatin code (Trifonov, 1980;Trifonov and Sussman, 1980), the most recent version of which is described in Gabdank et al (2009Gabdank et al ( , 2010 and Trifonov (2010Trifonov ( , 2011. The latest work boils down to a conclusion that all other nucleosome positioning patterns suggested during three decades by various authors match to the universal pattern YRRRRRYYYYYR, of which GAAAATTTTC and AAAAATTTTT are the most representative of generally A + T rich eukaryotic sequences.…”

Universal full-length nucleosome mapping sequence probe

“…A consensus sequence of the nucleosome DNA (R 5-6 Y 5-6 ) 11 , where 11 stands for the number of DNA periods in contact with the histone octamer (Trifonov, 2011), should consist, therefore, of intermingled periods of lengths 10 and 11 bases, making together the average period 10.4 bases. The same holds for the matrix of nucleosome DNA bendability (Gabdank, Barash, & Trifonov, 2010a, 2010bMengeritsky & Trifonov, 1983) where the occurrences of all 16 dinucleotides are taken into account, each preferentially located at their respective positions within the 10.4 base period. In the study of Gabdank et al (2010aGabdank et al ( , 2010b a full-length matrix is derived from nucleosome DNA sequences of C. elegans, the first of the kind.…”

“…The same holds for the matrix of nucleosome DNA bendability (Gabdank, Barash, & Trifonov, 2010a, 2010bMengeritsky & Trifonov, 1983) where the occurrences of all 16 dinucleotides are taken into account, each preferentially located at their respective positions within the 10.4 base period. In the study of Gabdank et al (2010aGabdank et al ( , 2010b a full-length matrix is derived from nucleosome DNA sequences of C. elegans, the first of the kind. It was preceded, though, by an incomplete AA/TT only matrix (Ioshikhes, Bolshoy, Derenshteyn, Borodovsky, & Trifonov, 1996).…”