Global intron retention mediated gene regulation during CD4+ T cell activation

T Ni, W Yang, M Han, Y Zhang, T Shen… - Nucleic acids …, 2016 - academic.oup.com
T Ni, W Yang, M Han, Y Zhang, T Shen, H Nie, Z Zhou, Y Dai, Y Yang, P Liu, K Cui, Z Zeng…
Nucleic acids research, 2016academic.oup.com
T cell activation is a well-established model for studying cellular responses to exogenous
stimulation. Using strand-specific RNA-seq, we observed that intron retention is prevalent in
polyadenylated transcripts in resting CD4+ T cells and is significantly reduced upon T cell
activation. Several lines of evidence suggest that intron-retained transcripts are less stable
than fully spliced transcripts. Strikingly, the decrease in intron retention (IR) levels correlate
with the increase in steady-state mRNA levels. Further, the majority of the genes …
Abstract
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Using strand-specific RNA-seq, we observed that intron retention is prevalent in polyadenylated transcripts in resting CD4+ T cells and is significantly reduced upon T cell activation. Several lines of evidence suggest that intron-retained transcripts are less stable than fully spliced transcripts. Strikingly, the decrease in intron retention (IR) levels correlate with the increase in steady-state mRNA levels. Further, the majority of the genes upregulated in activated T cells are accompanied by a significant reduction in IR. Of these 1583 genes, 185 genes are predominantly regulated at the IR level, and highly enriched in the proteasome pathway, which is essential for proper T cell proliferation and cytokine release. These observations were corroborated in both human and mouse CD4+ T cells. Our study revealed a novel post-transcriptional regulatory mechanism that may potentially contribute to coordinated and/or quick cellular responses to extracellular stimuli such as an acute infection.
Oxford University Press