Transcriptomics of cold stress and recovery reveal strongly tissue-specific responses

ABSTRACT Cellular stress responses are often characterized as conserved, cell-autonomous processes. However, it remains unclear whether stress responses are coordinated uniformly across tissues within complex organisms, particularly during ecologically relevant conditions. We investigated tissue- and stage-specific transcriptional responses to cold stress in Drosophila melanogaster . Adults and larvae were independently exposed to a gradual cooling and recovery time series, and three adult tissues (gut, ovary, brain) and one larval tissue (gut) were sampled at baseline, at two time points that spanned the critical thermal minimum (before and during chill coma), and after recovery to rearing temperature. Transcriptomic analyses revealed strongly tissue- and stage-specific responses to cold stress, with limited overlap in differentially expressed genes or functional enrichment across tissues. These results indicate that the organismal response to thermal stress at the transcriptional level is not coordinated by a unified transcriptional program, but rather by largely distinct, tissue-specific regulatory processes.