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Molecular and Cellular Biology
Article . 2011 . Peer-reviewed
License: ASM Journals Non-Commercial TDM
Data sources: Crossref
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Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1

Authors: Jeffrey N, McKnight; Katherine R, Jenkins; Ilana M, Nodelman; Thelma, Escobar; Gregory D, Bowman;

Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1

Abstract

Chd1- and ISWI-type chromatin remodelers can sense extranucleosomal DNA and preferentially shift nucleosomes toward longer stretches of available DNA. The DNA-binding domains of these chromatin remodelers are believed to be responsible for sensing extranucleosomal DNA and are needed for robust sliding, but it is unclear how these domains contribute to directional movement of nucleosomes. Here, we show that the DNA-binding domain of Chd1 is not essential for nucleosome sliding but is critical for centering mononucleosomes on short DNA fragments. Remarkably, nucleosome centering was achieved by replacing the native DNA-binding domain of Chd1 with foreign DNA-binding domains of Escherichia coli AraC or Drosophila melanogaster engrailed. Introducing target DNA sequences recognized by the foreign domains enabled the remodelers to rapidly shift nucleosomes toward these binding sites, demonstrating that these foreign DNA-binding domains dictated the direction of sliding. Sequence-directed sliding occluded the target DNA sequences on the nucleosome enough to promote release of the remodeler. Target DNA sequences were highly stimulatory at multiple positions flanking the nucleosome and had the strongest influence when separated from the nucleosome by 23 or fewer base pairs. These results suggest that the DNA-binding domain's affinity for extranucleosomal DNA is the key determinant for the direction that Chd1 shifts the nucleosome.

Related Organizations
Keywords

Binding Sites, Saccharomyces cerevisiae Proteins, Base Sequence, Escherichia coli Proteins, Recombinant Fusion Proteins, AraC Transcription Factor, Electrophoretic Mobility Shift Assay, Saccharomyces cerevisiae, Chromatin Assembly and Disassembly, Protein Engineering, Nucleosomes, Protein Structure, Tertiary, DNA-Binding Proteins, Adenosine Triphosphate, Fluorometry, Enzyme Assays, Protein Binding, Sequence Deletion

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
100
Top 10%
Top 10%
Top 10%
bronze