The chromatin remodeling complexes chromatin accessibility complex and ATP-utilizing chromatin assembly and remodeling factor (ACF) combine the ATPase ISWI with the signature subunit ACF1. These enzymes catalyze well-studied nucleosome sliding reactions in vitro， but how their actions affect physiological gene expression remains unclear. Here， we explored the influence of chromatin accessibility complex/ACF on transcription by using complementary gain- and loss-of-function approaches. Targeting ACF1 to multiple reporter genes inserted at many different genomic locations revealed a context-dependent inactivation of poorly transcribed reporters in repressive chromatin. Accordingly， single-embryo transcriptome analysis of an knock-out allele showed that only lowly expressed genes are derepressed in the absence of ACF1. Finally， the nucleosome arrays in -deficient chromatin show loss of physiological regularity， particularly in transcriptionally inactive domains. Taken together， our results highlight that ACF1-containing remodeling factors contribute to the establishment of an inactive ground state of the genome through chromatin organization.