Macrophage plasticity in response to inflammatory signals relies on rapid and reversible chromatin remodeling, tightly coupled to transcriptional changes. While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure is now well established, that of corepressors remains largely unknown. It is precisely this gap that the present study addresses, using inflammatory activation of macrophages as a model.
The authors analyzed a corepressor complex containing GPS2 and SMRT, both at the genome-wide scale and at the Ccl2 locus, which encodes the chemokine CCL2 (also known as MCP-1). Corepressor recruitment emerges as a general feature of inflammatory enhancers. Unexpectedly, these corepressors occupy candidate enhancers jointly with the coactivators CBP, an acetyltransferase of histone H3 at lysine 27 (H3K27), and MED1, a subunit of the Mediator complex. However, they exert an antagonistic action there, repressing enhancer RNA (eRNA) transcription coupled to H3K27 acetylation. By combining genome editing, transcriptional interference, and cistrome analysis, the team showed that apparently related enhancer and silencer elements control Ccl2 transcription in opposite ways.
To understand the three-dimensional organization of this locus, the researchers used chromosome conformation capture coupled with sequencing (4C-seq), which enabled the characterization of the loops connecting enhancers, silencer, and promoter within the topological domain of the Ccl2 gene. These analyses indicate that corepressor depletion and inflammatory signaling operate through similar mechanisms to trigger enhancer activation. Notably, eRNA repression was achieved in RAW macrophages using a dCas9-KRAB (CRISPRi) system targeting the Ccl2 enhancer regions.
The physiological relevance of this pathway was tested in vivo in ob/ob mice, a model of obesity. Selective depletion, in adipose tissue macrophages, of the eRNA transcribed by the Ccl2 enhancer reduces metaflammation, that is, the chronic low-grade inflammation associated with metabolic dysregulation. Together, these findings reveal a pathway linking corepressors, eRNA, and chemokine that is functional in the organism. Beyond describing a novel epigenetic mechanism—in which corepressors govern the coordinated remodeling of enhancers and silencers via eRNA transcription—this work suggests that targeting eRNAs could represent a therapeutic avenue in immunometabolic diseases.