Abstract
NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx)) has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.
Highlights
The organization of DNA in nucleosomes has a major function in controlling accessibility of DNA to the protein complexes that process genetic information
We detect nucleosome remodeling factor (NURF) remodeling and recruitment at distal insulator sites that are required for functional organisation of the genome
We postulate that NURF function at insulators as well as promoters reflects functional interaction between distant insulators and active promoters, with functional clustering of regulatory elements providing a solution to how chromatin remodeling enzymes engage multiple targets in the genome
Summary
The organization of DNA in nucleosomes has a major function in controlling accessibility of DNA to the protein complexes that process genetic information. Post-translational modification of the histone tails (HPTMs) can change associations between histones and DNA, altering chromatin flexibility and conformation (reviewed in Tessarz and Kouzarides [1]). These modifications can act as marks that can be bound by effector complexes that include ATP-dependent chromatin remodeling factors (reviewed in Swygert and Peterson [2]). These multi-subunit protein complexes utilize the energy of ATP hydrolysis to alter nucleosome dynamics. They can be divided into broad families based on the core catalytic subunit and effects on nucleosomes—eviction, sliding or variant histone replacement
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