Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes.
ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodeling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes but with different directionalities. We find that the yeast Isw1a, Isw2, and Chd1 enzymes preferentially move nucleosomes toward more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2, and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end, whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodeling by these enzymes.
Stockdale
Chris
C
Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
Flaus
Andrew
A
Ferreira
Helder
H
Owen-Hughes
Tom
T
D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000502:physiology*; D000818:Animals; D002843:Chromatin / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000502:physiology*; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000502:physiology*; D014157:Transcription Factors / Q000737:chemistry; D014982:Xenopus laevis
C489847:CHD1 protein, S cerevisiae; D002843:Chromatin; D004268:DNA-Binding Proteins; C086468:ISWI protein; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA; D000251:Adenosine Triphosphatases; C470546:ISW1 protein, S cerevisiae