RESUMO
Class II histone deacetylases (HDACs) are important in regulation of gene transcription during T cell development. However, our understanding of their cell-specific functions is limited. In this study, we reveal that class IIa Hdac4 and Hdac7 (Hdac4/7) are selectively induced in transcription, guiding the lineage-specific differentiation of mouse T-helper 17 (Th17) cells from naive CD4+ T cells. Importantly, Hdac4/7 are functionally dispensable in other Th subtypes. Mechanistically, Hdac4 interacts with the transcription factor (TF) JunB, facilitating the transcriptional activation of Th17 signature genes such as Il17a/f. Conversely, Hdac7 collaborates with the TF Aiolos and Smrt/Ncor1-Hdac3 corepressors to repress transcription of Th17 negative regulators, including Il2, in Th17 cell differentiation. Inhibiting Hdac4/7 through pharmacological or genetic methods effectively mitigates Th17 cell-mediated intestinal inflammation in a colitis mouse model. Our study uncovers molecular mechanisms where HDAC4 and HDAC7 function distinctively yet cooperatively in regulating ordered gene transcription during Th17 cell differentiation. These findings suggest a potential therapeutic strategy of targeting HDAC4/7 for treating Th17-related inflammatory diseases, such as ulcerative colitis.
Assuntos
Diferenciação Celular , Colite , Histona Desacetilases , Correpressor 1 de Receptor Nuclear , Células Th17 , Animais , Células Th17/citologia , Células Th17/metabolismo , Células Th17/imunologia , Histona Desacetilases/metabolismo , Histona Desacetilases/genética , Camundongos , Colite/genética , Colite/metabolismo , Colite/imunologia , Transcrição Gênica , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética , Correpressor 2 de Receptor Nuclear/metabolismo , Correpressor 2 de Receptor Nuclear/genética , Interleucina-17/metabolismo , Regulação da Expressão Gênica , Camundongos Endogâmicos C57BL , Humanos , Proteínas Repressoras/metabolismo , Proteínas Repressoras/genética , Interleucina-2/metabolismoRESUMO
Although reduced representation bisulfite sequencing (RRBS) measures DNA methylation (DNAme) across CpG-rich genomic regions with high sensitivity, the assay can be time-consuming and prone to batch effects. Here, we present a high-throughput, automated RRBS protocol starting with DNA extraction from frozen rat tissues. We describe steps for RRBS library preparation, library quality control, and sequencing. We also detail an optimized pipeline for sequencing data processing. This protocol has been applied successfully to DNAme profiling across multiple rat tissues. For complete details on the use and execution of this protocol, please refer to Nair et al.1.
Assuntos
Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Sulfitos , Animais , Metilação de DNA/genética , Ratos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sulfitos/química , Análise de Sequência de DNA/métodos , DNA/genética , Ilhas de CpG/genética , Biblioteca GênicaRESUMO
Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8 weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.
Assuntos
Condicionamento Físico Animal , Transcriptoma , Animais , Condicionamento Físico Animal/fisiologia , Masculino , Ratos , Feminino , Metilação de DNA , Epigênese Genética , Epigenômica , Adaptação Fisiológica/genética , Especificidade de Órgãos , Ratos Sprague-DawleyRESUMO
Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.