Control of ribosomal RNA synthesis by hematopoietic transcription factors.

Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA quantification, we demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Our work identifies numerous potential rRNA regulators and provides a template for dissection of TF roles in rRNA transcription. [Display omitted] • Multiple cell-type-specific TFs bind canonical motifs on rDNA • The hematopoietic TF CEBPA binds to active rDNA alleles at a conserved site • CEBPA promotes RNA Pol I occupancy and rRNA transcription in myeloid progenitors • We present "47S-FISH-Flow," a sensitive assay to quantify nascent rRNA Antony et al. mapped existing ChIP-seq datasets to human and mouse rDNA and identified binding profiles of cell-type-specific transcription factors (TFs). The myeloid TF CEBPA bound rDNA at a conserved motif, and its degradation reduced rDNA occupancy of the RNA Pol I-RRN3 complex and nascent 47S rRNA transcription. [ABSTRACT FROM AUTHOR]