SUMMARY
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 2200 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 CEBPA (C/EBP alpha), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced Pol I occupancy. Our work identifies numerous potential rRNA regulators, and provides a template for dissection of TF roles in rRNA transcription.
HIGHLIGHTS
Multiple cell-type-specific transcription factors (TFs) bind canonical motifs on rDNA.
The hematopoietic TF CEBPA binds to active rDNA alleles at a conserved site.
CEBPA promotes Polymerase I occupancy and rRNA transcription in myeloid progenitors.
We present ‘47S-FISH-Flow,’ a sensitive assay to quantify nascent rRNA.
Competing Interest Statement
The authors have declared no competing interest.
