ATP-dependent chromatin remodeling generally proceeds via three pathways: nucleosome sliding along the DNA, nucleosome conformational change, and nucleosome eviction from the DNA [ 34, 35].
Htz1 binding shows a global change on chromatin and nucleosome dynamics are coupled with Htz1 binding changes upon stress.
At least one MOP1-regulated locus also exhibits changes in chromatin structure and nucleosome positioning in association with changes in transcriptional level,, suggesting that RdDM may also influence chromatin structure.
Another possibility is that the changes in transcriptional activity and changes in nucleosome distribution in mop1 1 mutants are induced by discrete mechanisms, and not related to one another.
In vivo, the TSSs of some genes are occupied by nucleosomes, and changes to nucleosome positioning will affect the genes' expression levels.
We next wished to assess the relationship between the deltaH3K4methyls ChIP-Seq signal and changes in nucleosome occupancy.
Although many factors, such as linker histones and DNA-binding proteins, can influence characteristics such as DNA wrapping and fiber compaction, the greatest changes in nucleosome structure and stability are achieved by histone chaperones and ATP-dependent chromatin remodelers.
Changes in nucleosome position and occupancy, histone variants and modifications, and chromatin remodeling are also critical elements of dynamic transcriptional regulation, but poorly understood at enhancers.
We were also interested in cell cycle genes, but we did not observe any obvious changes in expression, Htz1 binding and nucleosome occupancy in oleate-stressed cells relative to unstressed cells.
However, the relationship between nucleosome position and gene expression is complex, and there is not always a correlation between changes in nucleosome occupancy and transcriptional activity of a gene.
