Gene module reconstruction identifies cellular differentiation processes and the regulatory logic of specialized secretion in zebrafish
Description
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 factors creb3l1, creb3l2, and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program, while xbp1 partners with bhlha15 to activate a gland-like secretion program. Our study presents module identification via multi-source integration for reconstructing differentiation (MIMIR) and illustrates how transcription factors confer general and specialized cellular functions. This repository contains: 1. The microscopy images presented in the study. 2. The preprocessed scRNA-seq data from the UPR TF loss- and gain-of-function assays, in form of Scanpy objects. 3. Codes and scripts for UPR TF target gene inference using the scRNA-seq data. 4. Sequences of the plasmids used for making UPR TF mRNAs