Respiratory pauses highlight sleep architecture in mice

Brain activity and breathing rate influence each other but it remains unclear how fine respiratory features vary across vigilance states. Using simultaneous nasal pressure and hippocampal local field potential recordings in freely-moving mice, we show that the position of respiratory pauses within breathing cycles distinguish Wake, Rapid Eye Movement (REM) and non-REM (NREM) sleep states. Model-based predictions of vigilance states based on respiratory features perform well even on animals outside of the training set, suggesting the rules are generalized. Respiratory features underwent specific changes at state transitions, such as progressive elimination of pauses after inhalation foreshadowing REM. During NREM, respiratory changes predicted moment-to moment sigma power variations beyond movement-defined packets delineated by micro-arousals, as pauses after inhalation fragmented NREM sleep into ∼30s windows of high sigma power. Overall, our findings reveal that respiratory features structure the macro- and micro-architecture of sleep, opening new windows into brain states through respiration.