Biology subjects

Stormberg, T. D.

Publications and source records attributed to Stormberg, T. D..

2 recordsLinked to original sources

bioRxiv2022

Sequence Dependent Nanoscale Structure of CENP-A Nucleosomes

CENP-A is a histone variant found in high abundance at the centromere. The centromere chromatin similar to the bulk chromatin consist of nucleosomes, but H3 histone of the bulk chromatin nucleosomes (H3 nucleosomes) is replaced with CENP-A histone. Additionally, the centromere comprises tandem repeats of -satellite DNA which CENP-A nucleosomes assemble upon. However, the effect of the DNA sequence on the nucleosome assembly and centromere formation remains poorly understood. Here we investigated the structure of nucleosomes assembled with the CENP-A variant using Atomic Force Microscopy. We assembled both CENP-A nucleosomes and H3 nucleosomes on a DNA substrate containing an -satellite motif and characterized their positioning and wrapping efficiency. We also studied CENP-A nucleosomes on the 601-positioning motif and non-specific DNA to compare their relative positioning and stability. CENP-A nucleosomes assembled on -satellite DNA did not show any positional preference along the substrate, which is similar to H3 nucleosomes and CENP-A nucleosomes on non-specific DNA. The range of nucleosome wrapping efficiency was narrower on -satellite DNA compared with non-specific DNA, suggesting a more stable complex. These findings indicate that DNA sequence and histone composition may be two of many factors required for accurate centromere assembly.

molecular biology↗

bioRxiv2022

Sequence Dependent Internucleosomal Interactions Dominate Array Assembly

The organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here we investigated the contribution of the DNA sequence and internucleosomal interactions to the organization of the nucleosomal arrays in compact structures using Atomic Force Microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of forming constructs with the close positioning of nucleosomes with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.

biophysics↗