Abstract
BackgroundUnique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent.ResultsIn 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.ConclusionsThese 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.
Highlights
Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions
Through analysis of the centromeric histone H3 (CENH3) nucleosome core footprints at single-molecule resolution provided by 454 sequencing and through other approaches, we found a tendency for nucleosome spacing intervals to average about 190 bp, which was maintained across the three major DNA components of maize centromeres
Derivation and validation of CENH3 nucleosome core sequences A dataset of DNA sequences associated with maize CENH3 chromatin was described previously as a resource for defining functional centromere regions [29,30]; GenBank Sequence Read Archive SRA009397)
Summary
Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. Centromeres are the regions of chromosomes where kinetochores form and microtubules attach to guide chromosomes to opposite poles during cell division. One would guess that centromere DNA elements would specify binding sites for structural and regulatory proteins. Specific, functionally important DNA sequences have been identified, such as the CENP-B (centromere protein B) box site in vertebrates [1,2,3] and the CP1 binding site in S. cerevisiae [4,5]. Multiple lines of evidence indicate that core kinetochore proteins can have a large degree of sequence independence (for recent review, see [6]). Foremost among these arguments is the unexpectedly low level of DNA conservation in centromeres. Core centromeres are often megabases in length, as are the pericentromeres
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