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Antony, Charles; George, Subin S.; Blum, Justin; Somers, Patrick; Thorsheim, Chelsea L.; Wu-Corts, Dexter J.; Ai, Yuxi; Gao, Long; Lv, Kaosheng; Tremblay, Michel G.; Moss, Tom; Tan, Kai; Wilusz, Jeremy E.; Ganley, Austen R.D.; Pimkin, Maxim; Paralkar, Vikram R.
Molecular cell, 10/2022, Letnik: 82, Številka: 20Journal Article
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.
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in: SICRIS
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