GSE113730
The change of mRNA stability upon T cell activation
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. In this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells, and applied computational modeling to investigate the impact of IR on the kinetics of mRNA degradation. As expected, intron retained transcripts are considerably less stable than spliced transcripts. In addition, the decrease in the steady-state IR level in activated CD4+ T cells are in part due to increased splicing efficiency and further stabilization of spliced transcripts. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to achieve spatiotemporal control of gene expression during T cell activation. We also found the mRNA stability change is not due to the 3'UTR-isoform choice but may be regulated by the RBP for example the LARP4 is the most significant binding protein in 3' UTR of the ß1-decreased genes. Furthermore, the mRNAs of the activated CD4+ T cells in LARP4 Knock-out (KO) mice showed the decreased stability and comparable transcriptional level for some genes including the NFkB1 and PSMD7 when comparing to the wild-type (WT) mice, resulting in the down-regulation of these genes. Finally, the LARP4 KO down-regulated NFkB1 target genes such as IL2 and IFNG upon CD4+ T cell activation, which is critical for the T cell proliferation and function. Overall design: To investigate the involvement of mRNA stability in CD4+ T cell activation, we employed BruChase-Seq, a high-throughput sequencing method for monitoring RNA degradation rate by pulse-chase labelling of nascent transcripts.  Resting and activated human primary CD4+ T cells were pulse labelled with Bromouridine (BrU) for 1 h. Cells were harvested 30 min or 2 h after switching back to culture medium that contains regular uridine. Labelled transcripts were immunoprecipitated by anti-BrU antibody and then fragmented. The resulting RNA fragments were subsequently analyzed by RNA-Seq.