Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.
The eukaryotic genome is organized in a highly dynamic structure called chromatin. Access to DNA in the context of chromatin is granted by enzymatic activities that use the energy of hydrolysis of ATP to slide or covalently modify nucleosomes. ISWI is an evolutionarily conserved nucleosome-sliding factor that plays essential roles in transcription, DNA replication, and chromosome organization. Despite the wealth of data on ISWI function, little is known about how its activity is regulated and integrated in different physiological contexts in vivo. Using D. melanogaster as a model system, we conducted a genetic screen for factors regulating ISWI activity. One of the genes identified in our screen, Sin3A, encodes a subunit of a histone deacetylase complex that may regulate ISWI function by modifying its nucleosome substrate. Our genetic screen revealed that ISWI interacts with a network of cellular and nuclear factors that escaped previous biochemical analyses, indicating the participation of ISWI in a variety of biological processes not linked to date with known ISWI functions.