Ribosomal DNA Accessibility in Hematopoiesis

Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping process, its cell-type-specific regulation is widely neglected. We profiled rRNA transcription rate and mature rRNA (ribosome subunit) levels in detail across mouse hematopoiesis, and observed that rRNA abundance is cell-type-specific and largely uncoupled from cell cycling and protein synthesis rates. We tested the longstanding assumption that rRNA levels are elevated in acute myeloid leukemia (AML) and found that leukemic progenitors showed notably higher nascent and mature rRNA levels than matched normal counterparts. Across contexts of hematopoiesis, trends in rRNA transcription paralleled changes in chromatin accessibility of rDNA repeats. Absolute quantification of rRNA molecules unexpectedly revealed that large ribosome subunits are in excess to small subunits in all cell types, most prominently in the normal myeloid lineage. Collectively, our work provides a detailed profile of the complex dynamics of rRNAs within and between normal and leukemic hematopoiesis. Reanalysis of published scATAC-Seq datasets from GEO (GSM5222812/GSE171220; GSM5567440/GSE183675) and ENCODE (ENCSR217VXJ/ENCBS249EEJ; ENCSR332SXG/ENCBS991GWL; ENCSR308ZGJ/ENCBS337EJK). Raw FASTQ files were downloaded from GEO or ENCODE as applicable. Raw Reads were mapped using cellranger-atac. Peakcalling and motif analysis were done using ArchR. Cell type barcodes were assigned using ArchR and used to split the BAM files into subfiles per celltype. BigWig tracks were generated using bamCoverage from deepTools. custom genomes: https://github.com/vikramparalkar/rDNA-Mapping-Genomes/blob/main/Human_hg38-rDNA_genome_v1.0.tar.gz; https://github.com/vikramparalkar/rDNA-Mapping-Genomes/blob/main/Mouse_mm39-rDNA_genome_v1.0.tar.gz. Reanalysis processed data includes: rds files from ArchR and BigWig tracks. *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. The reanalysis_samples.xlsx file also lists accessions reused/reanalyzed for this study. ***************************************************************