The intestine, which is constantly exposed to an extensive range of antigens and immune stimuli, harbours a large number of highly diverse CD4+ T helper (Th) cells. Maintaining a balance between pro-inflammatory and tolerogenic intestinal Th cell subsets is crucial for the homeostasis and functionality of the gastrointestinal tract. Recent evidence suggests that epigenetic mechanisms play a vital role for Th cell differentiation and specialization, and dysregulation of these epigenetic regulations can result in an imbalance of Th cell subsets, causing the onset and progression of intestinal inflammatory diseases. Furthermore, epigenetic alterations might be orchestrated through microbiota-derived metabolites, which can function as epigenetic modifiers by catalyzing major enzymes involved in epigenetic modifications. In this review, we focus on the epigenetic control of Th cell differentiation and functional specialization in intestinal tissues in health and disease, and also discuss the role of microbiota in shaping intestinal Th cell epigenomes.
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