Nucleic Acids Research Advance Access published online on June 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp524
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Gene Regulation, Chromatin and Epigenetics |
Analysis of individual remodeled nucleosomes reveals decreased histone–DNA contacts created by hSWI/SNF
1Department of Molecular Biology & Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 and 2Department of Urology and Biochemistry & Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
*To whom correspondence should be addressed. Email: jones_p{at}ccnt.usc.edu Correspondence may also be addressed to Robert E. Kingston. Tel: 617 726 5933; Fax: 617 726 6893; Email: kingston{at}molbio.mgh.harvard.edu
Received April 28, 2009. Revised June 1, 2009. Accepted June 2, 2009.
Chromatin remodeling enzymes use the energy of ATP hydrolysis to alter histone–DNA contacts and regulate DNA-based processes in eukaryotes. Whether different subfamilies of remodeling complexes generate distinct products remains uncertain. We have developed a protocol to analyze nucleosome remodeling on individual products formed in vitro. We used a DNA methyltransferase to examine DNA accessibility throughout nucleosomes that had been remodeled by the ISWI and SWI/SNF families of enzymes. We confirmed that ISWI-family enzymes mainly created patterns of accessibility consistent with canonical nucleosomes. In contrast, SWI/SNF-family enzymes generated widespread DNA accessibility. The protection patterns created by these enzymes were usually located at the extreme ends of the DNA and showed no evidence for stable loop formation on individual molecules. Instead, SWI/SNF family proteins created extensive accessibility by generating heterogeneous products that had fewer histone–DNA contacts than a canonical nucleosome, consistent with models in which a canonical histone octamer has been ‘pushed’ off of the end of the DNA.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.