FACT safeguards promoter topology by maintaining nucleosomes and restricting chromatin factor spreading

Facilitates chromatin transcription (FACT) is a histone chaperone that displaces and re-assembles histones during transcription. Recent studies have reported a minor role for FACT in chromatin architecture. We have recently shown that active gene promoters form nanoscale domains and proposed they are created by the biophysical properties of nucleosome-free regions. Here we use base-pair resolution Micro Capture-C ultra to show that, following FACT degradation, nanoscale domains are lost and subnucleosomal chromatin interactions are rearranged at active promoters. Nucleosome-free regions at these promoters expand and chromatin-binding factors invade the newly accessible chromatin, indicating FACT maintains the integrity of active promoters by opposing DNA-binding factor spreading into gene bodies. Finally, we show increased interactions between promoters across topologically associating domains, suggesting large-scale structural changes upon FACT loss. Thus, we demonstrate FACT plays a major role in chromatin organisation and provide in vivo evidence that nucleosomes drive both local and long-range chromatin architecture.