Department of Physics, George Washington University, Washington, DC 20052, USA.
Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Nucleic Acids Res. 2020 Sep 4;48(15):8724-8739. doi: 10.1093/nar/gkaa643.
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Motivated by our previous finding that intron retention (IR) could lead to transcript instability, in this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells. Computational modeling was then applied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale. Beyond substantiating that intron-retained transcripts were considerably less stable than spliced transcripts, we found a global stabilization of spliced mRNAs upon T cell activation, although the stability of intron-retained transcripts remained relatively constant. In addition, we identified that La-related protein 4 (LARP4), an RNA-binding protein (RBP) known to enhance mRNA stability, was involved in T cell activation-dependent mRNA stabilization. Knocking out Larp4 in mice destabilized Nfκb1 mRNAs and reduced secretion of interleukin-2 (IL2) and interferon-gamma (IFNγ), two factors critical for T cell proliferation and function. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to control spatiotemporal gene expression during T cell activation.
T 细胞活化是研究细胞对外源刺激反应的成熟模型。受我们先前发现的内含子保留（IR）可能导致转录本不稳定性的启发，在本研究中，我们进行了 BruChase-Seq 实验，以在静息和激活的 CD4+T 细胞中实时监测新生转录本的表达动力学。然后应用计算模型在全基因组范围内定量测定剪接和内含子保留转录本的稳定性。除了证实内含子保留转录本明显不如剪接转录本稳定之外，我们还发现 T 细胞活化后剪接 mRNA 整体稳定性增加，尽管内含子保留转录本的稳定性仍然相对稳定。此外，我们发现 La 相关蛋白 4（LARP4），一种已知能增强 mRNA 稳定性的 RNA 结合蛋白（RBP），参与 T 细胞活化依赖性 mRNA 稳定。在小鼠中敲除 Larp4 会使 Nfκb1 mRNAs 不稳定，并减少白细胞介素 2（IL2）和干扰素-γ（IFNγ）的分泌，这两种因子对于 T 细胞增殖和功能至关重要。我们提出，剪接调控和 mRNA 稳定性之间的协调可能为控制 T 细胞活化过程中的时空基因表达提供了一种新的范例。
