Control of ribosomal RNA synthesis by hematopoietic transcription factors

Customized genomes for human and mouse ribosomal DNA mapping

“…Most of these factors had been extensively studied for decades, and had been subjected to ChIP-seq by dozens of investigators, but their striking rDNA occupancy had passed unnoticed due to a lack of appropriate bioinformatic tools. We further demonstrated that the myeloid factor CEBPA promotes RNA Pol I occupancy on rDNA in myeloid progenitors 1 . Our work used mammalian hematopoiesis as a model system, but there is no reason to believe that the binding of cell-type-specific transcriptional regulators to rDNA is restricted to just one tissue; this is likely a universal mechanism that is repurposed across all tissues to modulate rRNA transcription rates to meet tissue-specific needs, but whose prevalence is unknown due to a dearth of suitable mapping tools.…”

“…The study of rDNA regulation has been stunted by the lack of such tools, leading most investigators to ignore rDNA in genome wide studies, creating a significant knowledge gap in our understanding of how the most abundant RNA in the cell is regulated. Our recent work 1 revealed previously-unnoticed binding of numerous mammalian transcription factors and chromatin proteins to rDNA. Several of these factors were known to play critical roles in development, tissue function, immunity, and malignancy, and had been dissected in detail for decades, but their potential rDNA roles had remained unexplored.…”

“…In all cases, negative controls (Input and IgG) showed flat background chrR coverage of significantly lower intensity compared to specific factor pulldown. UBTF and POLR1A showed the expected broad signal throughout the transcribed region, TBP showed the expected peaks at the spacer and 47S promoters, and CTCF showed the expected sharp peak slightly upstream of the TBP peak at the spacer promoter 1,11 . (Fig 3A , 3B).…”

“…The historical lack of suitable public assemblies has led investigators at large to simply ignore rDNA when profiling the binding sites of their transcriptional regulators of interest, creating a significant vacuum in the understanding of how the most abundant RNA in the cell is regulated. Recently published work by our group illustrated the extent of this vacuum, when, through unbiased mapping of ~2200 ChIP-seq datasets for ~250 target proteins to rDNA, we identified conserved patterns of rDNA binding for numerous hematopoietic transcription factors and chromatin regulators 1 . Several of the transcription factors, including the CEBP family, IRF family, and SPI1, all of which have critical roles in hematopoiesis, immune cell development and function, and leukemogenesis, showed consistent, robust peaks at canonical motif sequences.…”

“…The repetitive nature of rDNA has placed substantial bioinformatic barriers in its study. Most standard genome assemblies do not contain intact rDNA sequences, and instead contain a scattering of rDNA fragments, inhibiting the ability of investigators to effectively map high-throughput datasets to them 1 . The new telomere-to-telomere (T2T-CHM13) human genome assembly contains multiple full NOR arrays 8 , however the presence in this assembly of 219 rDNA repeats creates non-trivial mapping and interpretive complexities.…”