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Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state [Iso-Seq]

ABSTRACT: 3’ untranslated regions (3’UTRs) are critical elements of most messenger RNAs: they contain binding sites for RNA-binding proteins (RBP) and microRNAs that affect various aspects of the RNA life cycle including transcript stability. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3’UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3’UTR dynamics in T helper cells we investigated division-dependent alternative polyadenylation (APA). We generated 3’ end UTR sequencing in naïve, 48h activated (anti-CD3/CD28 cultured), memory and regulatory CD4+ Tcells. 48h activated Tcells were CTV-separated into three populations: cells not yet divided, divided once and twice. 3’UTR length changes were estimated using non-negative matrix factorization approach and partially compared with long-read PacBio sequencing. We found that, in T helper cells, APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNAseq dataset, we found that APA genes were not significantly associated with either post-transcriptional or transcriptional regulation, differential gene expression or transcript usage, demonstrating a marginal effect of APA on transcript abundance. 3’UTR sequence analysis revealed conserved binding sites for important microRNAs and RBPs co-evolving with APA events. These results highlight the important role of polyA site usage in the control of cell fate decisions and homeostasis.

ORGANISM(S): Mus musculus

PROVIDER: GSE209603 | GEO | 2023/11/06

REPOSITORIES: GEO

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Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state [A-Seq]

Project description:3’ untranslated regions (3’UTRs) are critical elements of most messenger RNA species and can contain binding sites for RNA-binding proteins (RBP) and microRNAs that affect various aspects of RNA life cycles including transcript stability. Cells of the adaptive immune system undergo massive expansion during the effector phase of the immune response and dynamically modify their 3’UTRs in a response to T cell receptor activation. Whether this phenomenon is a secondary effect of proliferation or a mechanism to directly regulate the abundance of specific mRNAs remains unclear. To study 3’UTR dynamics in T helper cells we investigated division-dependent alternative polyadenylation and observed a transient character of global 3’UTR shortening/lengthening in T helper cells that return to a naïve-like polyadenylation state after effector phase expansion. We also showed that 3’UTR lengthening is associated with higher transcript abundance and post-transcriptional regulation than 3’UTR shortening. Sequence analysis of conserved microRNA and RBP binding sites located within varying 3’ UTR regions highlighted the putative involvement of several microRNAs during this process. Our study emphasizes the value of polyadenylation isoforms analysis for understanding cell behaviors, revealing new aspects of the highly complex interplay of transcriptional and post-transcriptional layers in triggering transcript abundance.

2023-11-06 | GSE183424 | GEO

Alternative cleavage and polyadenylation in spermatogenesis coordinates chromatin regulation and post-transcriptional control

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Alternative cleavage and polyadenylation in spermatogenesis coordinates chromatin regulation and post-transcriptional control

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2020-05-15 | GSE138759 | GEO

SRSF7 and SRSF3 affectSRSF7 and SRSF3 affect 3’UTR length in opposite directions by controlling proximal poly(A)-site usage and CFIm levels 3’UTR length in opposite directions by controlling proximal poly(A)-site usage and CFIm levels

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