Nucleosomes and centromeric DNA packaging

Abstract

The eukaryotic chromosome is a conserved structure, with the DNA double-helix wrapping around octamers of histone proteins to form the chromatin, which is further packaged into chromosomes. The centromere defines the kinetochore, the region of spindle microtubule attachment that pulls the two replicated chromatids of each chromosome apart during cell division (Fig. 1), leading to fidelity in transmission of genetic information. Like the telomere, centromeres are well defined morphologically and functionally, but their DNA sequence shows no conservation between species, and their coiling into chromatin is still poorly understood. In PNAS, Zhang et al. (1) give unique insight into the centromeric CenH3-nucleosomes associated with the rice CentO satellite sequence and adjacent regions of DNA, having implications for centromere specification, activity, and evolution.Centromeres are readily observed as partial constrictions on the metaphase chromosome by light or electron microscopy ( Fig. 1). However, few sequence-related characteristics of the DNA at the centromeres are conserved. In contrast, nucleosome proteins (2) and kinetochores linking centromeres and spindle microtubules with a multiprotein complex are highly conserved across all kingdoms (3).Typically, there are tandemly repeated satellite DNA sequences at the centromeres of chromosomes of animals and plants (4-6). Detailed work on the budding yeast Schizosaccharomyces pombe and brewer's yeast Saccharomyces cerevisiae identified relatively short DNA sequences and binding protein counterparts that direct chromosome segregation (7,8). The search was then on for critical "boxes" in plants and animals but, although some motifs were found to be involved in protein-DNA interactions, no motif shared across diverse phyla was found within the centromeric tandem repeats.As sequencing technology advanced, both variants of tandem repeats and almost any other class of DNA-retrotransposons, transposons, genes, transcription factors, and microsatellites-were revealed (9) underlying the kinetochore and microtubule attachment sites. Evidence from comparisons of species, mutants that still showed centromeric function, the lack of necessity for tandemly repeated satellite sequence, and the presence of (1) with ∼100 bp of the rice CentO tandem repeat sequence (red) folding once around the nucleosome core that includes CenH3 (yellow). (I) A key method for nucleosome analysis involving micrococcal nuclease digestion of chromatin and size separation of the resultant DNA fragments; the enzyme cuts DNA in the linker regions and, over the time course shown, isolates more mononucleosomes, and trims overhanging DNA not protected from digestion by the histone proteins (12). (Scale bars for A-C, 2 μm.)

Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

“… 44 Similar rules govern the human and plant centromeres where the periodicity of centromeric nucleosomes (CenH3) is found to be in accord with the satDNA monomer length, 45 – 47 being predominantly of ∼170 bp and of its double length. 4 The phenomenon observed in this work can be thus explained by the length of DNA wrapped around 1 or 2 nucleosomes as a requirement that may facilitate regular phasing of nucleosomes, and it can be a necessary prerequisite for dramatic amplification of TRs in both, centromeric and euchromatic regions. It has also been proposed for centromeric satDNAs that the monomer length longer than two nucleosomes is rare because longer sequences are unlikely to stabilize nucleosomes.…”

“… 3 In addition to extreme diversity in nucleotide sequences between species, centromeric satDNAs are typically characterized by sequential arrangement of monomers in the form of long arrays and by preferential monomer length corresponding to the size of nucleosomal DNA. 4 …”

The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1

“…A preferential satellite-DNA monomer length between 150–180 bp has been found in many centromeric satellite DNAs. It corresponds in length to the 1.67 turns around the histone octamer core (147 bp) plus the linker DNA between the nucleosomes, typically varying 10–70 bp (reviewed in [ 56 ]). PIVE-180 has a repetitive unit of 180 bp, close to the estimated mean size in plants of 165 pb [ 57 ].…”

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

“…Presumably, this prevents chromosome breakage, chromosome loss, and disruption in pericentric sister chromatid cohesion 34 . The complex structures together with the difficulty in distinguishing centromere repeats from the flanking repeats make the identification of centromere locations a daunting task 35 , 36 . For this reason, we used a combination of genetic maps, sequence search and chromosome interaction patterns derived from the Hi-C data to identify the raspberry centromere locations.…”