Altered nucleosome positions in maize haplotypes and mutants of a subset of SWI/SNF-like proteins

Chromatin remodelers alter DNA–histone interactions in eukaryotic organisms and have been well characterized in yeast and Arabidopsis. While there are maize proteins with similar domains as known remodelers, the ability of the maize proteins to alter nucleosome position has not been reported. Mutant alleles of several maize proteins (RMR1, CHR101, CHR106, CHR127, and CHR156) with similar functional domains to known chromatin remodelers were identified. Altered gene expression of Chr101, Chr106, Chr127, and Chr156 was demonstrated in plants homozygous for the mutant alleles. These mutant genotypes were subjected to nucleosome position analysis to determine whether misregulation of putative maize chromatin proteins would lead to altered DNA–histone interactions. Nucleosome position changes were observed in plants homozygous for chr101, chr106, chr127, and chr156 mutant alleles, suggesting that CHR101, CHR106, CHR127, and CHR156 may affect chromatin structure. The role of RNA polymerases in altering DNA–histone interactions was also tested. Changes in nucleosome position were demonstrated in homozygous mop2-1 individuals. These changes were demonstrated at the b1 tandem repeats and at newly identified loci. Additionally, differential DNA–histone interactions and altered gene expression of putative chromatin remodelers were demonstrated between different maize haplotypes.