SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [ChIP-seq]

Despite the pleiotropic role of SUMOylation, this pathway mainly functions to repress innate immunity in myeloid cells. Inactivating SUMOylation triggers a potent basal type I interferon (IFN1) response, amplified and coupled with an inflammatory response upon stimulation. These findings transposed to pre-clinical models with the demonstration that SUMOylation inhibitors (SUMOi) activate antitumor immunity in an IFN1-dependent manner. Yet, how SUMOylation represses immune signaling remains largely unknown. We identified murine MORC3, a critical transcriptional repressor of the IFNB1 gene, as the top SUMO2/3 substrate in myeloid cells. We show that, in human monocytes, SUMO functions to repress basal IFNB1 in cis through an atypical/repeated MORC3-regulated element (MRE) concentrating/homing multiple PU.1 binding motifs. Inhibiting SUMOylation induces a 3D genome reorganization centered on the MRE, which, in turn, acquires both insulator and PU.1-driven enhancer activities, together with loss of H3.3 and H3K9me3 repressive marks and increased PU-1 binding. Paradoxically, MORC3, that binds PU.1, is massively recruited, yet unable to repress the MRE. Finally, we show that both MORC3 ATPase cycle and SUMOylation are critical for full MORC3 repressive activity. Our study identifies an unconventional mechanism in which SUMO, in concert with MORC3, orchestrates a metastable H3.3/H3K9me3 heterochromatin state on a multi-PU.1 binding platform element to shutdown unscheduled myeloid-specific IFN1 response. Overall design: Serie 1 : ChIP-seq H3.3 in RAW 264.7 macrophages upon ML-792 treatment Serie 2 : ChIP-seq Morc3 and in RAW 264.7 macrophages Serie 3 : ChIP-seq SUMO2/3 and H3K9me3 in RAW 264.7 macrophages upon ML treatment Serie 4 : ChIP-seq MORC3 in BlaER1 monocytes, WT, IFNAR-/-, IFNAR-/- MORC3-/-, upon TAK treatment and H3K9me3 in BlaER1 monocytes, WT upon TAK treatment Serie 5 : ChIP-seq MORC3 and H3K9me3 in BlaER1 lymphocytes ctrl Serie 6 : ChIP-seq MORC3 in BlaER1 lymphocytes, upon TAK treatment Serie 7 : ChIP-seq H3.3 in BlaER1 cells, WT, upon TAK treatment Serie 8 : ChIP-seq SUMO2/3 in BlaER1 cells IFNAR-/- Serie 9 : ChIP-seq CTCF, H3K27me3 and H3K4me3 in BlaER1 cells WT, upon TAK treatment Serie 10 : ChIP-seq H3K9me3 in IFNAR -/- and IFNAR -/- MORC3 -/- BlaER1 monocyte Serie 11 : ChIP-seq MORC3 in THP1 macrophages (PMA treated) upon TAK treatment