Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation

Area of Science:

• Immunology
• Molecular Biology
• Genetics

Background:

• T cell activation is a key model for studying cellular responses.
• Intron retention (IR) has been previously linked to transcript instability.

Purpose of the Study:

• To experimentally monitor nascent transcript expression dynamics during T cell activation.
• To quantify the stability of spliced and intron-retained transcripts genome-wide.
• To investigate the role of RNA-binding proteins in T cell activation-dependent mRNA stabilization.

Main Methods:

• BruChase-Seq was employed to track nascent RNA expression in resting and activated CD4+ T cells.
• Computational modeling was utilized to determine the stability of different transcript isoforms.
• Gene knockout studies (Larp4) in mice were performed to assess functional consequences.

Main Results:

• Intron-retained transcripts exhibit significantly lower stability compared to spliced transcripts.
• T cell activation globally enhances the stability of spliced mRNAs, while intron-retained transcript stability remains constant.
• La-related protein 4 (LARP4) was identified as a key factor in T cell activation-dependent mRNA stabilization.
• Larp4 knockout in mice led to destabilization of Nfκb1 mRNAs and reduced secretion of IL-2 and IFN-γ.

Conclusions:

• A novel mechanism coordinating splicing regulation and mRNA stability controls gene expression during T cell activation.
• LARP4 plays a critical role in stabilizing mRNAs essential for T cell proliferation and function.
• Understanding these regulatory mechanisms provides insights into T cell responses and immune function.