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Nucleic Acids Res. 2015 Apr 30;43(8):3964-71. doi: 10.1093/nar/gkv276. Epub 2015 Mar 30.

Nucleosomes undergo slow spontaneous gaping.

Author information

1
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA.
2
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801-2902, USA tjha@illinois.edu.

Abstract

In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two copies each of the histones H2A, H2B, H3 and H4. Nucleosome structures are diverse not only by histone variants, histone modifications, histone composition but also through accommodating different conformational states such as DNA breathing and dimer splitting. Variation in nucleosome structures allows it to perform a variety of cellular functions. Here, we identified a novel spontaneous conformational switching of nucleosomes under physiological conditions using single-molecule FRET. Using FRET probes placed at various positions on the nucleosomal DNA to monitor conformation of the nucleosome over a long period of time (30-60 min) at various ionic conditions, we identified conformational changes we refer to as nucleosome gaping. Gaping transitions are distinct from nucleosome breathing, sliding or tightening. Gaping modes switch along the direction normal to the DNA plane through about 5-10 angstroms and at minutes (1-10 min) time scale. This conformational transition, which has not been observed previously, may be potentially important for enzymatic reactions/transactions on nucleosomal substrate and the formation of multiple compression forms of chromatin fibers.

PMID:
25824950
PMCID:
PMC4417179
DOI:
10.1093/nar/gkv276
[Indexed for MEDLINE]
Free PMC Article

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