Intron retention resolves microgravity and non-gravitational stress programs across immune organs in spaceflight

Intron retention (IR) provides an early regulatory readout of stress, often preceding steady-state changes in mRNA expression. Here, we asked whether IR can resolve complex spaceflight stress into separable mechanistic components and map how stress information propagates across tissues. We integrated high-confidence IR profiles from mouse spaceflight experiments with datasets representing mechanical unloading (microgravity) and non-mechanical, non-gravitational (NG; radiation–oxidative) stress. IR-based analysis disentangled these stress axes and uncovered a conserved five-layer regulatory architecture—mechanical input, signaling-gate, nuclear/genome-integrity, RNA/splicing–proteostasis/trafficking, and immune–metabolic adaptive output layers—through which immune organs interpret spaceflight stress. Microgravity and NG stress entered this hierarchy through distinct routes yet converged at IR as a common mode of upstream control, preceding most downstream transcriptional changes. This IR-centered framework provides a general strategy for decomposing complex, multi-factorial stress into interpretable modules. Leveraging this resolution, we identified a subset of IRGs whose normalization tracked the recovery of interacting structural partners, revealing a network-coupled “drag” phenomenon detectable when stress programmes are partitioned at the IR level. Together, our results establish IR as a unifying regulatory code—a command tier—that organizes stress-response hierarchies and exposes emergent network behaviors across mechanical, radiative, and immune perturbations.