Sequence structure of Lowary/Widom clones forming strong nucleosomes

Abstract

Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs.

Weak Signal Carried by Chromatin DNA Sequences: Zooming In and Sobering Surprises

“…Removal of intron sequences from a gene often causes discontinuity in the gene`s column (not shown). The YR tracks are often split in two in the promoter region (manuscript in preparation), which is not unusual in columns [20]. All this indicates that the study of the columns is a very promising course.…”

“…The difficulty, however, is removed by the data on reconstruction of the thermodynamically most stable nucleosomes formed by selected clones of randomly synthesized sequences [11]. Analysis of the sequences of Lowary and Widom (LW) shows that they follow the same sequence pattern as the SNs [20]. That is, the histone octamers would, indeed, prefer the SN sequences and form nucleosomes, as clones of LW do.…”

“…For this the 10-and 11-column bendability matrices have to be calculated. Such calculation is done on the sequences of the strong nucleosome clones of LW [20] and the consensuses of the matrices derived: TAGAGssCTCTA and TAGAAsssTTCTA. Here first T and last A are added to the 10-mer and to 11-mer, to fully outline the signal, from consensus (decorating) TA to consensus TA of next 10-11-mer.…”

“…Thirty some years of efforts followed by many laboratories, by various approaches in the attempts to elaborate on the structure of this "nucleosome positioning" signal, until massive sequencing in the beginning of the century provided sufficient sequence material to extract and describe in consistent details the signal. The final form of the signal, essentially, repetition of RRRRRYYYYY motif with average period 10.4 bases appeared in 2009 [7] and since then has not been challenged, except for some details characteristic of different species (of different G+C compositions) ( [16], [5]) and specific for especially strong nucleosomes ( [17], [20]). …”