The packaging of DNA into chromatin makes it largely inaccessible for the central nuclear processes of transcription, replication, recombination and repair. ATP-dependent chromatin remodeling motors play key roles in both increasing DNA access within chromatin as well in generating higher-order chromatin structures that promote transcriptional repression. However, the mechanisms by which chromatin remodeling motors function are largely unknown. The overall goal of this proposal is to use concepts learnt from well-studied motors such as kinesin and helicases to understand the how a major ATP- dependent chromatin-remodeling complex, human ACF functions. ACF generates evenly spaced nucleosomes to enable higher-order chromatin folding and gene silencing. Our work over the last grant period has shown that ACF functions as a dimeric motor in which each ATPase subunit takes turns engaging either side of a nucleosome. Here we will build on these discoveries to address the following questions: (1) How are the activities of the two ATPase subunits in ACF coordinated? (2) How does ACF recognize and use specific nucleosomal features in its reaction mechanism? (3) How is ACF activity regulated by the presence of adjacent nucleosomes?

Public Health Relevance

ACF complexes play crucial roles in mediating heritable gene silencing. Consistent with these roles, mutations in the components of ACF complexes are associated with severe developmental defects and specific cancers. A detailed understanding of ACF mechanism will provide insights into how its activity is regulated and how it malfunctions.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Preusch, Peter C
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University of California San Francisco
Schools of Medicine
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Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A et al. (2016) Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife 5:
Leonard, John D; Narlikar, Geeta J (2015) A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler. Mol Cell 57:850-9
Racki, Lisa R; Naber, Nariman; Pate, Ed et al. (2014) The histone H4 tail regulates the conformation of the ATP-binding pocket in the SNF2h chromatin remodeling enzyme. J Mol Biol 426:2034-44
Canzio, Daniele; Larson, Adam; Narlikar, Geeta J (2014) Mechanisms of functional promiscuity by HP1 proteins. Trends Cell Biol 24:377-86
Al-Sady, Bassem; Madhani, Hiten D; Narlikar, Geeta J (2013) Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol Cell 51:80-91
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Rowe, Claire E; Narlikar, Geeta J (2010) The ATP-dependent remodeler RSC transfers histone dimers and octamers through the rapid formation of an unstable encounter intermediate. Biochemistry 49:9882-90
Blosser, Timothy R; Yang, Janet G; Stone, Michael D et al. (2009) Dynamics of nucleosome remodelling by individual ACF complexes. Nature 462:1022-7
Racki, Lisa R; Yang, Janet G; Naber, Nariman et al. (2009) The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462:1016-21

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