RNA-seq reveals that deletion of Rasgef1b affects gene expression under basal and LPS-induced conditions in macrophages

Ras guanine exchange factor member 1b (RasGEF1b) of the RasGEF/CDC25 domain-containing family is preferentially expressed by macrophages. However, information is lacking about its role in macrophage function. In this study, we generated mice with ubiquitous deletion of Rasgef1b and used RNA-seq-based transcriptomics to compare the global gene expression in wild-type and knockout primary bone-marrow-derived macrophages under basal conditions and after lipopolysaccharide (LPS) treatment. Transcriptional filtering identified several uniquely differentially expressed genes (DEGs) with significant differences in the mRNA levels between wild-type and knockout macrophages. In total, 49 and 37 DEGs were identified at baseline and in LPS-activated macrophages, respectively. Distinct biological processes were significantly linked to downregulated genes at the basal condition only, and largely included chemotaxis, response to cytokines, and positive regulation of GTPase activity. Importantly, validation by RT-qPCR revealed that expression of the genes Ch25h, Serpinb2, and Ptchd1, which were identified as downregulated after LPS stimulation, was also decreased under basal conditions in the knock-out cells. This study provides a small collection of genes that shows relative expression changes affected by the absence of RasGEF1b in macrophages. Thus, we present the first evidence that RasGEF1b mediates the regulation of both steady-state and signal-dependent expression of genes and indicate that this GEF plays a role in the maintenance of the basal transcriptional level in macrophages. The data establish a resource that warrants further investigation to understand the physiological role of RasGEF1b. RNA-seq with polyadenylated RNA of bone-marrow-derived macrophages, with and without LPS stimulation for 4 h, isolated from wildtype or Rasgef1b knockout mice. All samples in biological triplicate.