Epigenomics of macrophages

Abstract

Macrophages play essential roles in tissue homeostasis, pathogen elimination, and tissue repair. A defining characteristic of these cells is their ability to efficiently adapt to a variety of abruptly changing and complex environments. This ability is intrinsically linked to a capacity to quickly alter their transcriptome, and this is tightly associated with the epigenomic organization of these cells and, in particular, their enhancer repertoire. Indeed, enhancers are genomic sites that serve as platforms for the integration of signaling pathways with the mechanisms that regulate mRNA transcription. Notably, transcription is pervasive at active enhancers and enhancer RNAs (eRNAs) are tightly coupled to regulated transcription of protein-coding genes. Furthermore, given that each cell type possesses a defining enhancer repertoire, studies on enhancers provide a powerful method to study how specialization of functions among the diverse macrophage subtypes may arise. Here, we review recent studies providing insights into the distinct mechanisms that contribute to the establishment of enhancers and their role in the regulation of transcription in macrophages.

Keywords: PU.1; eRNA; enhancer; epigenetic; macrophage; transcription.

Fig. 1. Cell type-specific selection of enhancers

Depiction of H3K4me2 ChIP-seq data obtained from mouse macrophages, T cells, and smooth muscles cells (SMC) in the vicinity of the Fos gene genomic locus. In macrophages, H3K4me2 peaks reveal an enhancer located 5kb upstream of the Fos transcription start site (TSS). This enhancer is also established in T cells but not in SMCs. On the other hand, T cells and SMCs each display a unique enhancer at 7kb and 10kb respectively. H3K4me2 marks are also present at promoters and may extend beyond the TSS at highly transcribed genes, reflecting high levels of transcriptional activity by RNAP II. Note that spacing between H3K4me2 peaks at enhancers is indicative of absence of nucleosome and concords instead with the binding of TFs.

Fig. 2. eRNAs contribute to functional chromosomal looping between enhancers and promoters to increase mRNA transcription

Under basal conditions, low level of constitutive activity promotes RNAP II activity at both a distal enhancer downstream of a gene and at the protein-coding gene. In this context, eRNAs promote enhancer-promoter interactions through cohesin/Mediator complex activity. Strong stimulation of a target SDTF leads to its efficient binding at the enhancer and increased transcription of eRNAs, leading to increase enhancer-promoter interactions strengths and/or frequencies, resulting in more transcription of the protein-coding gene. However, recruitment of a repressor complex at the enhancers interferes with SDTF binding and/or local RNAP II activity. Lower eRNA abundance decreases enhancer-promoter interactions, which correlates with lower mRNA transcription.

Fig. 3. Collaborative model of epigenomic lineage determination in macrophages

Co-occurrences of binding sequences for PU.1 and collaborative TFs, including C/EBP factors, within a ∼147 nucleotides window are relatively prevalently encoded within larger DNA sequences that promote a more defined nucleosome placement (in green). In cells that do not express PU.1, such specific nucleosome placement may protect these cells from using genomic information not relevant to their functions. Note that neighboring nucleosomes may be more mobile relative to their interaction with DNA (arrowheads). In macrophages however, the same nucleosome is probabilistically more effectively evicted and/or displaced as a result of the collaborative binding activity of PU.1 and C/EBP factors. This then allows for more efficient binding of the NF-κB p65 subunit following TLR4 stimulation, for example.