Subjects

• Gene regulation in immune cells

The haematopoietic cells of the immune system carry out their functions within tissue frameworks created by structural cells of the epithelium, endothelium and stroma (mainly fibroblasts). Interactions of these structural cells with immune cells have been difficult to study owing to their essential roles in organ function. Krausgruber et al. used multi-omics profiling of structural cells from 12 mouse organs to create a high-resolution atlas of immune gene activity. They hope that this will aid further study of immune functions in non-haematopoietic cells — a field they refer to as ‘structural immunity’.

Next, the authors looked at gene regulation by profiling chromatin accessibility and active H3K4me2 marks. Similar to the RNA-seq data, chromatin and histone profiles were generally more similar within an organ than within a structural cell type, although a subset of immune genes (such asIfngr1) had high levels of chromatin accessibility in almost all samples. On the basis of predicted transcription factor binding sites in open chromatin and H3K4me2 regions, they identified some transcription factors that were active in all structural cells and others with cell type-specific or organ-specific activity. So, structural cells have both a core set of immune functions and additional functions determined by cell type or tissue.

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