DNA STRUCTURAL PATTERNS AND NUCLEOSOME POSITIONING

There is no clear picture to date of the mechanisms determining nucleo some positioning. Generally, local DNA sequence signals (sequence-depe ndent positioning) or non-local signals (e.g. boundary effects) are po ssible. We have analyzed the DNA sequences of a series of positioned a nd mapped nucleosome cores in a systematic search for local sequence s ignals. The data set consists of 113 mapped nucleosome cores, mapped i n vivo, in situ, or in reconstituted chromatin. The analysis focuses o n the periodic distribution of sequence elements implied by each of si x different published DNA structural models. We have also investigated the periodic distribution of all mono-, di-, and trinucleotides. An i dentical analysis was performed on a set of isolated chicken nucleosom e cores (nucleosome data from the literature) that are presumably posi tioned due to local sequence signals. The results show that the sequen ces of the isolated nucleosome cores have a number of characteristic f eatures that distinguish them clearly from randomly chosen reference D NA. This confirms that the positioning of these nucleosomes is mainly sequence-dependent (i.e., dependent on local octamer-DNA interactions) and that our algorithms are able to detect these patterns. Using the same algorithms, the sequences of the mapped nucleosome cores, however , are on average very similar to randomly chosen reference DNA. This s uggests that the position of the majority of these nucleosomes can not be attributed to the sequence patterns implemented in our algorithms. The arrangement of positioned nucleosomes seems to be the result of a dynamic interplay of octamer-DNA interactions, nucleosome-nucleosome interactions and other positioning signals with varying relative contr ibutions along the DNA.