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Ribosomal DNA Accessibility in Hematopoiesis

ABSTRACT: 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.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE307498 | GEO | 2025/09/13

REPOSITORIES: GEO

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Source:

			Action	DRS
		Other
	GSE307498_BFU_E.bw	Other
	GSE307498_CD34Pos_scATAC_GEO_Thongon_SRX10499712.rds	Other
	GSE307498_CLP.bw	Other
	GSE307498_Combined_K562_scATAC_ENCODE_ENCLB417HJU_ENCLB227NCE_ENCLB662FMI.rds	Other

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Project description:Transcription of the several hundred of mouse and human Ribosomal RNA (rRNA) genes accounts for the majority of RNA synthesis in the cell nucleus and is the determinant of cytoplasmic ribosome abundance, a key factor in regulating gene expression. The rRNA genes, referred to globally as the rDNA, are clustered as direct repeats at the Nucleolar Organiser Regions, NORs, of several chromosomes, and in many cells the active repeats are transcribed at near saturation levels. The rDNA is also a hotspot of recombination and chromosome breakage, and hence understanding its control has broad importance. Despite the need for a high level of rDNA transcription, typically only a fraction of the rDNA is transcriptionally active, and some NORs are permanently silenced by CpG methylation. Various chromatin-remodelling complexes have been implicated in counteracting silencing to maintain rDNA activity. However, the chromatin structure of the active rDNA fraction is still far from clear. Here we have combined a high-resolution ChIP-Seq protocol with conditional inactivation of key basal factors to better understand what determines active rDNA chromatin. The data resolve questions concerning the interdependence of the basal transcription factors, show that preinitiation complex formation is driven by the architectural factor UBF (UBTF) independently of transcription, and exclude a significant role for termination by a torpedomechanism. They further reveal the existence of an asymmetric Boundary Complex formed by CTCF, Cohesin and three phased nucleosomes lying adjacent to the rDNA Enhancer and an arrested RNA Polymerase I complex. We find that this complex is the only site of active histone modification in the whole 45kbp rDNA repeat. Strikingly, the Enhancer Boundary Complex not only delimits each functional rRNA gene, but also is stably maintained after gene inactivation and the re-establishment of surrounding repressive chromatin. Our data define the poised state of rDNA chromatin and place the Enhancer Boundary Complex as the likely entry point for the chromatin remodelling complexes.

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Ribosomal DNA Accessibility in Hematopoiesis

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