Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing and Translation Events during T Cell Responses

Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time-courses of 4sU-Seq, RNA-Seq, ribosome profiling and RNA polymerase II (RNAPII) ChIP-Seq during T cell activation, we illustrate genome-wide temporal dynamics for ~10,000 genes. This approach reveals immediate-early as well as posttranscriptionally-regulated genes, but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNAPII, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNAPII carboxy-terminal domain (CTD) and activation of the positive transcription elongation factor complex (pTEFb). Thus, rapid de novo recruitment of RNAPII dictates the course of events during T cell activation, in particular transcription, splicing and consequently translation. Overall design: Analysis of temporal dynamics of transcription, splicing and translation in real-time resolution during the activation of T effector cells by RNAseq, 4sU-Seq and Ribosome Profiling