Differentiation-coupled intron retention reveals a candidate NKG2D-TR-like isoform at the murine Klrk1 locus

NKG2D, a receptor found in cytotoxic lymphocytes, is activated in humans by post-transcriptional regulation. In mice, the connection between NKG2D regulation and intron retention remains unclear. In a study involving four RNA-seq datasets of 50 murine samples, researchers investigated the retained-intron isoform Klrk1-203. This transcript maintains its initial start codon, but its stop codon is within the final exon, potentially allowing it to bypass the genetic error-correction mechanism known as nonsense-mediated decay.

If expressed, Klrk1-203 would produce a truncated protein retaining essential cytoplasmic and transmembrane domains, but lacking most of the ligand-binding region. Unlike its human counterpart, the mouse protein contains a short C-terminal sequence from the retained intron. While Klrk1-203 was undetectable in unstimulated naive and early-effector T cells, it was induced in differentiated effector and memory populations, making up around one-fifth of total Klrk1 transcripts in one such sample.

Read-level analysis supported increased intron 4 retention during differentiation, but short-read sequencing could not conclusively separate Klrk1-203 from its co-retained counterpart Klrk1-204, necessitating model-based quantification. An independent coding-potential algorithm classified Klrk1-203 as non-coding, providing a contrasting perspective to the structural predictions.

The findings reveal Klrk1-203 as a potential NMD-resistant, differentiation-associated regulator of murine NKG2D and a possible counterpart of human NKG2D-TR that requires experimental validation.