Effect of CLK2 expression in the regulation of intron retention during heat shock [RNA-seq]

Intron retention (IR) constitutes a less explored form of alternative splicing, wherein introns are retained within mature mRNA transcripts. Our investigation demonstrates that the CDC-like kinase 2 (CLK2) undergoes liquid-liquid phase separation (LLPS) within nuclear speckles in response to heat shock (HS). The formation of CLK2 condensates depends on the intrinsically disordered region (IDR) located within the N-terminal amino acids 1-148. Phosphorylation at residue T343 sustains CLK2 kinase activity and facilitates autophosphorylation, thus inhibiting the LLPS activity of the IDR. These CLK2 condensates initiate the reorganization of nuclear speckles, transforming them into larger, rounded structures. Moreover, these condensates facilitate the recruitment of splicing factors into these compartments, potentially restricting their access to mRNA for intron splicing. Consequently, the formation of CLK2 condensates promotes the IR. Overall design: We established the HeLa cells expressing the GFP (Control) , CLK2 (WT) or CLK2 knockdown (KD) and subjected them to heat shock (HS). These cells were subjected to RNA-seq for the alternative splicing. analysis. The nuclear and cytoplasmic RNAs were exrracted from CLK2 (T343A) expressing HeLa cells (T343A-C, T343-N) and subjected to RNA-seq.