Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning

In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ~156-bp centromeric satellite sequence (tandem repeat) CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ~10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2) lacked a detectable AA/TT periodicity but exhibited tightly phased positioning.These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres.Centromeres are the regions of chromosomes where kinetochores form and microtubules attach to guide chromosomes to opposite poles during cell division. A wide variety of centromere forms are observed in the diverse cellular contexts of different organisms, from the small point centromeres of Saccharomyces cerevisiae to the diffuse, holocentric centromeres of Caenorhabditis elegans. Even within a single individual, centromeres must meet the distinct requirements of chromosome dynamics in both meiotic and mitotic cell division. From the outset, one would guess that centromere DNA elements would specify binding sites for structural and regulatory proteins. Indeed, specific, functionally important