VISUALIZATION OF NUCLEOSOMAL SUBSTRUCTURE IN NATIVE CHROMATIN BY ATOMIC-FORCE MICROSCOPY

Intact rDNA minichromosomes from Tetrahymena thermophila were isolated as native chromatin and imaged by atomic force microscopy (AFM). AFM measurements of condensed rDNA chromatin were consistent with a 30 nm fiber that frequently (87% of molecules observed) contained stretches of nucleosome cores arranged in a zig-zag conformation. Examination of rDNA chromatin in a dispersed conformation by tapping mode AFM in low humidity resulted in high resolution images of partially dissociated nucleosome cores and associated linker DNA. A majority of these nucleo some cores contained six to eight smaller particles with dimensions co nsistent with those of individual histones. Many of the nucleosome cor es showed a striking resemblance to the wedge (35%), axial (15%), and front (6%) views of the nucleosome histone octamer modeled by Arents c t al. [Arents, G., Burlingame, R. W., Wang, B.-C., Love, W. E., and Mo udrianakis, E. N. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 10148-10152 ]. This direct visualization of histone subunits and nucleosomal subst ructure in native chromatin illustrates the potential use of AFM to lo calize individual proteins in condensed cellular chromatin.