Gene module reconstruction identifies cellular differentiation processes and the regulatory logic of specialized secretion in zebrafish.

ABSTRACT: During differentiation, cells become structurally and functionally specialized, but comprehensive views of the underlying remodeling processes are elusive. Here, we leverage single-cell RNA sequencing (scRNA-seq) developmental trajectories to reconstruct differentiation using two secretory tissues as models-the zebrafish notochord and hatching gland. First, we integrated expression and functional similarities to identify gene modules, revealing dozens of modules representing known and newly associated differentiation processes and their dynamics. Second, we focused on the unfolded protein response (UPR) transducer module to study how general versus cell-type-specific secretory functions are regulated. Profiling loss- and gain-of-function embryos identified that the UPR transcription factor

SUBMITTER: Wang Y 

PROVIDER: S-EPMC12097649 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature