Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [scRNA-seq]

Control over the accessibility of the genomic cis-regulatory information is key for the accurate deployment of gene expression programs. Such control is exerted by the combined action of pioneer transcription factors and chromatin remodelers with different ability to alter nucleosome positioning and occupancy. Here we show that SMARCA5 ( SNF2H), a chromatin remodeler enforcing linker DNA length, controls spacing of nucleosomes adjacent to sites where the myeloid lineage determining and pioneer TF PU.1 is constitutively bound, without however affecting PU.1 binding. Loss of SMARCA5 caused a widespread increase in the accessibility of sites for stimulus-regulated TFs, causing not only macrophage hyper-activation in response to inflammatory stimulation but also the induction of stimulus-inappropriate genes. SMARCA5 deficiency also determined the extensive increase in binding of C/EBPb to cognate sites normally not accessible in macrophages but instead exposed in white or brown adipogenesis. Overall, enforcement of nucleosome phasing by ISWI controls fidelity in both lineage specification and response to stimulation. scRNA-seq was performed on mouse primary BMDMs derived from wild-type or Smarca5-deficient cells, either unstimulated or treated with LPS for 2 hours, using the 10x Genomics 3’ Gene Expression assay with CellPlex multiplexing.