Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation

Dalal, Yamini; Fleury, Tomara J.; Cioffi, Alfred; Stein, Arnold

doi:10.1093/nar/gki224

Cited by 20 publications

(25 citation statements)

References 23 publications

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“…Following standard salt dialysis of histones purified from human cells 22 combined with plasmid DNA containing α-satellite arrays, we observed that bulk histones form chromatin arrays packaged with nucleosomes whose sizes were consistent with those of canonical octamers (Fig. 1 and Table 1).…”

Section: Single Molecule Microscopy Can Distinguish Between Cenp-a Ocmentioning

confidence: 89%

The CENP-A nucleosome

Bui

Walkiewicz

Dimitriadis

et al. 2013

Nucleus

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The structure of the centromere-specific histone centromeric protein A (CENP-A) nucleosome has been a hot topic of debate for the past five years. Structures proposed include octamers, hexamers, homotypic and heterotypic tetramers. This controversy has led to the proposal that CENP-A nucleosomes undergo cell-cycle dependent transitions between the multiple states previously documented to exist in vivo and in vitro. In recent work from our laboratory, we sought to test this hypothesis. We discovered that CENP-A nucleosomes undergo unique oscillations in human cells, a finding mirrored in a parallel study performed in budding yeast. This review provides additional insights into the potential mechanisms for the interconversion of CENP-A nucleosomal species, and speculates on a biological role for oscillations in vivo.

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Section: Single Molecule Microscopy Can Distinguish Between Cenp-a Ocmentioning

confidence: 89%

The CENP-A nucleosome

Bui

Walkiewicz

Dimitriadis

et al. 2013

Nucleus

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“…The HAP-chromatin matrix was then incubated with 1 × PBS supplemented with 2 M NaCl to release histones from the DNA-bound HAP matrix overnight. Under these conditions, histone H3/H4 dimers and H2A/H2B dimers are released from DNA (Dalal et al, 2005). The 2 M NaCl/PBS eluted histone preparation was concentrated ~10 fold by using Amicon centrifugation, dialyzed down to 0.35 M NaCl/PBS.…”

Section: Methodsmentioning

confidence: 99%

Cell-Cycle-Dependent Structural Transitions in the Human CENP-A Nucleosome In Vivo

Bui

Dimitriadis

Hoischen

et al. 2012

Cell

128

183

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SUMMARY In eukaryotes, DNA is packaged into chromatin by canonical histone proteins. The specialized histone H3 variant CENP-A provides an epigenetic and structural basis for chromosome segregation by replacing H3 at centromeres. Unlike exclusively octameric canonical H3 nucleosomes, CENP-A nucleosomes have been shown to exist as octamers, hexamers, and tetramers. An intriguing possibility reconciling these observations is that CENP-A nucleosomes cycle between octamers and tetramers in vivo. We tested this hypothesis by tracking CENP-A nucleosomal components, structure, chromatin folding, and covalent modifications across the human cell cycle. We report that CENP-A nucleosomes alter from tetramers to octamers before replication and revert to tetramers after replication. These structural transitions are accompanied by reversible chaperone binding, chromatin fiber folding changes, and previously undescribed modifications within the histone fold domains of CENP-A and H4. Our results reveal a cyclical nature to CENP-A nucleosome structure and have implications for the maintenance of epigenetic memory after centromere replication.

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“…DNA was cross-linked to the membrane by using a Gene Linker (program C3, 150 mJ) from Bio-Rad (Hercules, CA). Cross-linked membranes were then incubated in hybridization solution for a minimum of 1 h before addition of probe, which was generated by random priming in the presence of either [ 32 P]dATP or [ 32 P]dCTP (53). Blots were incubated with probe overnight at 60°C and then washed three times (2ϫ SSC, 2ϫ SSC/1% SDS, 0.1ϫ SSC) to remove nonspecific signal.…”

Section: Mnase Treatment Of Yeast Nucleimentioning

confidence: 99%

Centromere identity is specified by a single centromeric nucleosome in budding yeast

Furuyama

Biggins

2007

Proc. Natl. Acad. Sci. U.S.A.

240

216

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Chromosome segregation ensures that DNA is equally divided between daughter cells during each round of cell division. The centromere (CEN) is the specific locus on each chromosome that directs formation of the kinetochore, the multiprotein complex that interacts with the spindle microtubules to promote proper chromosomal alignment and segregation during mitosis. CENs are organized into a specialized chromatin structure due to the incorporation of an essential CEN-specific histone H3 variant ( CenH3 ͉ chromatin ͉ kinetochore C hromosome segregation is directed by the multiprotein kinetochore (KT) complex that assembles on centromeres (CENs) and interacts with the spindle apparatus to control chromosome movement during cell division (for reviews, see refs. 1 and 2). Although KT function is conserved, phylogenetic analysis of centromeric DNA reveals no common sequence element that would identify a CEN across species. Like all other parts of the genome, the DNA of CENs is organized into chromatin, a higher order structure in which DNA is wrapped around histones to generate nucleosomes. Typical octameric nucleosomes contain two molecules of each of four histones, H2A, H2B, H3, and H4, whereas centromeric nucleosomes are structurally distinct, containing an evolutionarily conserved CEN-specific histone H3 variant (CenH3) in place of canonical H3 (for review, see ref.3). The conservation of CenH3 across eukaryotes and its strict CEN localization in all species suggest that it is the epigenetic CEN identifier. Consistent with this finding, overexpression of the Drosophila CenH3 leads to its localization in euchromatin and the formation of ectopic KTs, resulting in subsequent defects in genomic stability (4).Despite the requirement for CenH3 in CEN specification, it is unclear how CenH3 nucleosomes structurally organize centromeric DNA to promote KT formation. In humans, CenH3 associates with centromeric ␣ satellite repeats (5), resulting in megabase expanses of centromeric nucleosomes. These centromeric nucleosomes drive the assembly of the KT structure that interacts with multiple microtubules. However, the number of CenH3 nucleosomes far exceeds the number of microtubules associated with a CEN, making the minimal number and arrangement of CenH3 nucleosomes necessary to assemble a single functional KT unclear. In flies and humans, blocks of CenH3 nucleosomes are interspersed with blocks of H3 nucleosomes (6), suggesting that higher order folding of the centromeric

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Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation

Cited by 20 publications

References 23 publications

The CENP-A nucleosome

The CENP-A nucleosome

Cell-Cycle-Dependent Structural Transitions in the Human CENP-A Nucleosome In Vivo

Centromere identity is specified by a single centromeric nucleosome in budding yeast

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