Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India.
Symbiosis School of Biological Sciences, Pune, Maharashtra 412115, India.
Nucleic Acids Res. 2020 Jun 19;48(11):5873-5890. doi: 10.1093/nar/gkaa321.
The chromatin organizer SATB1 is highly enriched in thymocytes and is essential for T-cell development. Although SATB1 regulates a large number of genes important for T-cell development, the mechanism(s) regulating expression of SATB1 during this process remain elusive. Using chromatin immune precipitation-seq-based occupancy profiles of H3K4me3 and H3Kme1 at Satb1 gene locus, we predicted four different alternative promoters of Satb1 in mouse thymocytes and characterized them. The expression of Satb1 transcript variants with distinct 5' UTRs occurs in a stage-specific manner during T-cell development and is dependent on TCR signaling. The observed discrepancy between the expression levels of SATB1 mRNA and protein in developing thymocytes can be explained by the differential translatability of Satb1 transcript variants as confirmed by polysome profiling and in vitro translation assay. We show that Satb1 alternative promoters exhibit lineage-specific chromatin accessibility during T-cell development from progenitors. Furthermore, TCF1 regulates the Satb1 P2 promoter switch during CD4SP development, via direct binding to the Satb1 P2 promoter. CD4SP T cells from TCF1 KO mice exhibit downregulation of P2 transcript variant expression as well as low levels of SATB1 protein. Collectively, these results provide unequivocal evidence toward alternative promoter switch-mediated developmental stage-specific regulation of SATB1 in thymocytes.
染色质组织者 SATB1 在胸腺细胞中高度富集，对 T 细胞发育至关重要。尽管 SATB1 调节了大量对 T 细胞发育很重要的基因，但在这个过程中调节 SATB1 表达的机制仍然难以捉摸。我们使用基于染色质免疫沉淀测序的 H3K4me3 和 H3Kme1 在 Satb1 基因座上的占有率图谱，在小鼠胸腺细胞中预测了 Satb1 的四个不同的替代启动子，并对它们进行了表征。具有不同 5'UTR 的 Satb1 转录变体的表达在 T 细胞发育过程中以特定于阶段的方式发生，并且依赖于 TCR 信号。在发育中的胸腺细胞中观察到 SATB1 mRNA 和蛋白质表达水平之间的差异，可以通过差异翻译能力来解释，这一点通过多核糖体分析和体外翻译实验得到了证实。我们表明，Satb1 替代启动子在 T 细胞发育过程中从祖细胞到 CD4SP 发育阶段表现出谱系特异性的染色质可及性。此外，TCF1 通过直接结合 Satb1 P2 启动子，调节 CD4SP 发育过程中的 Satb1 P2 启动子开关。来自 TCF1 KO 小鼠的 CD4SP T 细胞表现出 P2 转录变体表达下调以及 SATB1 蛋白水平降低。总之，这些结果提供了确凿的证据，证明 SATB1 在胸腺细胞中通过替代启动子开关介导的发育阶段特异性调节。
