Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality

• Published in: Cell Vol. 165; no. 5; pp. 1120 - 1133
• Main Authors: Shih, Han-Yu, Sciumè, Giuseppe, Mikami, Yohei, Guo, Liying, Sun, Hong-Wei, Brooks, Stephen R., Urban, Joseph F., Davis, Fred P., Kanno, Yuka, O’Shea, John J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19-05-2016
• Subjects: Animals; Cell Lineage; Female; Gene Expression Regulation; Gene Regulatory Networks; Lymphocytes - cytology; Lymphocytes - immunology; Lymphocytes - metabolism; Mice; Mice, Inbred C57BL; Transcriptome
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2016.04.029

Innate lymphoid cells (ILCs) play key roles in host defense, barrier integrity, and homeostasis and mirror adaptive CD4+ T helper (Th) cell subtypes in both usage of effector molecules and transcription factors. To better understand the relationship between ILC subsets and their Th cell counterparts, we measured genome-wide chromatin accessibility. We find that chromatin in proximity to effector genes is selectively accessible in ILCs prior to high-level transcription upon activation. Accessibility of these regions is acquired in a stepwise manner during development and changes little after in vitro or in vivo activation. Conversely, dramatic chromatin remodeling occurs in naive CD4+ T cells during Th cell differentiation using a type-2-infection model. This alteration results in a substantial convergence of Th2 cells toward ILC2 regulomes. Our data indicate extensive sharing of regulatory circuitry across the innate and adaptive compartments of the immune system, in spite of their divergent developing pathways.
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•Prototypical ILC subsets show distinctive regulomes•Regulatory elements of ILC effector genes are poised prior to activation•Regulomes of ILC subsets diverge early at precursor stages•Regulomes of innate and adaptive cells converge upon infection
Innate lymphoid cells and adaptive T helper cells become specialized cytokine-producing cells by distinct, but converging, routes.