GSE212224
Anemia Activates a Network of Cis-Regulatory Elements in Red Blood Cell Regeneration
Acute anemia elicits broad transcriptional changes in erythroid progenitors and precursors. We previously discovered a cis-regulatory transcriptional enhancer at the Samd14 locus (S14E) is required for survival in severe anemia. The S14E contains DNA binding motifs for GATA and TAL1, two transcription factors which bind to the enhancer and activate transcription during stress erythropoiesis. However, Samd14 is only one of dozens of anemia-activated genes. In a mouse model of acute anemia, we used single cell RNA sequencing to identify erythroid cell types which expanded and increased expression of genes that contain S14E-like cis-elements. Through orthogonal loss-of-function approaches (shRNA, sgRNA-guided Cas9 and Cas9-KRAB), we reveal that several S14E-like cis-elements are important for the expression of newly identified anemia induced genes, including the poorly studied Ssx-2 interacting protein (Ssx2ip). Ssx2ip expression was determined to play an important role in erythroid progenitor activity, cell cycle progression, and proliferation in anemia. Our results define a genome-wide mechanism in which S14E-like enhancers control transcriptional responses during erythroid regeneration. Furthermore, time course analysis of erythroid precursor gene activation in anemia revealed distinct transcriptional programs are established at earlier time points, distinct from S14E-like elements. These findings provide a framework to understand anemia-specific transcriptional mechanisms, ineffective erythropoiesis, anemia recovery and phenotypic variability within human populations. Overall design: Single cell suspensions of 15,000 Kit+ cells isolated from female untreated control mice and Days 1, 3, 7 post-PHZ treatment were added to arrays containing 110,000 mRNA capture beads to perform Seq-well. Two replicate mice were analyzed for control and PHZ-Day3 group.