SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophages

Transcription factors and coregulators coordinate inflammatory and metabolic pathways in macrophages through epigenetic and transcriptional mechanisms. The histone deacetylase 3 (HDAC3) corepressor complex plays fundamental roles in these mechanisms, with the homologous subunits SMRT (silencing mediator of retinoic acid and thyroid hormone receptors) and NCOR (nuclear receptor corepressor) being critical for complex assembly and interactions with transcription factors and chromatin. However, the relative contribution of SMRT and NCOR in controlling complex-dependent macrophage pathways remains poorly understood. Here, we assessed their genome-wide roles in mouse macrophage RAW264.7 cells and in bone marrow-derived macrophages. Transcriptome analysis upon corepressor depletion identified six differentially expressed gene clusters. SMRT depletion primarily upregulated inflammation-related pathways, whereas NCOR depletion primarily upregulated metabolism-related pathways. Epigenome analysis revealed that corepressor depletion differentially altered chromatin accessibility and H3K27 acetylation, consistent with transcriptome changes. Cistrome analysis revealed that both corepressors differentially influence each other at chromatin. SMRT uniquely controls the chromatin binding and nuclear localization of NCOR, GPS2 (G protein pathway suppressor 2), and HDAC3, thus acting as the chromatin anchor for the corepressor complex. Finally, corepressor depletion differentially modulated macrophage reprogramming in response to TLR4, IL4, and LXR signaling. Overall, our study reveals a hitherto underappreciated non-redundant role of SMRT and NCOR in coordinating chromatin accessibility, H3K27 acetylation, enhancer activity, and transcription to differentially regulate inflammatory and metabolic macrophage pathways.