Trinucleosome Compaction Studied by Fluorescence Energy Transfer and Scanning Force Microscopy

Malte Bussiek, Katalin Tóth, Nathalie Schwarz, Jörg Langowski
2006 Biochemistry  
The effect of salt concentration, linker histone H1 and histone acetylation on the structure of trinucleosomes reconstituted on a 608 bp DNA containing one centered nucleosome positioning signal was studied. Fluorescence resonance energy transfer (FRET) in solution and scanning force microscopy (SFM) measurements in liquid were done on the same samples. The distance between the DNA ends decreases under the effect of increasing salt concentration and also by the incorporation of H1 linker
more » ... . A decrease of internucleosomal center-to-center distances by H1 was observed that was limited to a minimal value of about 20 nm. The distribution of the angle formed between consecutive nucleosomes was narrowed by H1. The effect of acetylation of all histones leads to decompaction, measured as increased distance between the DNA ends, and also increased the internucleosomal distances. Selective acetylation of histone H4, however, compacts the structure as measured by FRET. While the structure of the mono-and tetranucleosome has been determined crystallographically to atomic resolution (1-4), the arrangement of nucleosomes into a higher order chromatin fiber in solution is still a controversial question. Nucleosomes are arranged in a regular 'beads-on-a-string' structure on the DNA and are separated by variable length segments of free 'linker DNA'. Typical nucleosome repeats range between 170 and 210 bp (5, 6). The common view is that this chain then condenses into a "30 nm-fiber" (7, 8) , whose conformation can be modulated by factors such as buffer conditions, associated proteins and histone modifications. The compaction state of chromatin is known to depend on the ambient salt concentration, reflecting the electrostatic component of histone-DNA interaction (9, 10). Linker histones (11-13) associate to the linker DNA outside the nucleosome core, forming a so-called 'nucleosome stem' (13). They participate in the stabilization of the condensed state of chromatin and can be associated with the deactivation of DNA-dependent metabolic processes (14) . The covalent modification of histones plays a central role in the regulation of the active and inactive state of chromatin. In particular, histone acetylation has been associated with actively transcribed chromatin and deacetylation with inactivation or silencing (15). The mechanisms of chromatin activation or deactivation are closely related to the -still debatedmorphology of the condensed chromatin fiber. According to the solenoid model, consecutive nucleosomes are closely packed and are helically arranged along the fiber (7, 16). In the 'zig-zag'model derived from cryo-electron microscopy imaging, linker DNAs are straight (12), and nucleosomes form a two-start helix (4, 17). This structure is stabilized by lateral interactions between nucleosomes i and i+2 and a linker histone-induced reduction of the angle between the DNA entering and exiting the nucleosomes (12, 13,(18)(19)(20) (21) (22) . Recent work, including the crystallographic structure of a cross-linked tetranucleosome seems to favor a straight-linker zig-zag structure (4), but the controversy is not fully resolved (23).. One approach to study oligonucleosome structure in solution and determine possible changes in compaction state is to determine distances between characteristic features within or between nucleosomes, varying external conditions including buffer composition, presence of linker histone,
doi:10.1021/bi060807p pmid:16953569 fatcat:x4mjn5o7jrarfn7ijkfzstbs24