Meta-unstable mRNAs in activated CD8+ T cells are defined by interlinked AU-rich elements and m6A mRNA methylation

ABSTRACT: CD8 ⁺ T cells can rapidly produce effector molecules following activation. This activation triggers fast changes in gene expression that rely on control of mRNA levels via multiple transcriptional and post-transcriptional mechanisms, including RNA modifications. N ⁶ -methyladenosine (m ⁶ A) is an abundant post-transcriptional modification that promotes the decay of messenger RNAs in the cytosol. How recognition of m ⁶ A sites is integrated with other regulatory mechanisms that alter the fate of immunoregulatory mRNAs in CD8 ⁺ T cells remains unexplored. Here, we applied the m ⁶ A-iCLIP (miCLIP) method and identified m ⁶ A antibody binding in RRACH and in AU-rich (ARE) motifs within 3’UTRs of CD8 ⁺ T cell mRNAs. The combined miCLIP signal in both motifs defined and predicted meta-unstable mRNAs that rapidly decayed upon CD8 ⁺ T cell activation. We demonstrate that mutations in the identified AREs are epistatic with RRACH mutations in their effects on TNF mRNA stability. Notably, the AREs in these mRNAs show enriched iCLIP crosslinking of YTHDF proteins, which were also identified by proteomic analyses of methylated ARE sequences along with additional novel RNA-binding proteins. Our study thus reveals a hitherto unexplored regulatory layer that interlinks m ⁶ A and ARE biology in CD8 ⁺ T cells, providing new approaches for modulating mRNA decay through m ⁶ A and ARE sites.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Peripheral Blood Mononuclear Cell

SUBMITTER: Aniek Martens  

LAB HEAD: Jernej Ule

PROVIDER: PXD059083 | Pride | 2025-11-24

REPOSITORIES: Pride