ArticleThe Journal of biological chemistry2023
Construction and validation of customized genomes for human and mouse ribosomal DNA mapping.
Article in The Journal of biological chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
- Tcf15 promotes an open nucleolar chromatin state to safeguard ribosome biogenesis and genome stability in mouse embryonic stem cells.PLoS biology · 2026Article
- Intranucleolar Invasion of Cajal Body Remnants Suppresses Ribosomal Biogenesis inbioRxiv : the preprint server for biology · 2026Article
- Germline sequence variation within the ribosomal DNA is associated with human complex traits.Cell genomics · 2026Article
- The KMT2F histone methyltransferase interacts with the RNA polymerase I machinery to promote ribosomal RNA transcription.PLoS biology · 2026Article
- In silico mapping of non-canonical DNA structures across the human ribosomal DNA locus.G3 (Bethesda, Md.) · 2026Article
- Tandem Duplications in UBTF Create XPO1-Dependent Nuclear Export Signals that Reveal a Leukemic Therapeutic Dependency.Blood cancer discovery · 2026Article
- ZAK activation at the collided ribosome.Nature · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- rDNAcaller: a fast and robust pipeline to call ribosomal DNA variants.NAR genomics and bioinformatics · 2025Article
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
- HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs.Nature communications · 2025Article
- Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness.Genes & development · 2025Article
- Ribosomal RNA transcription regulates splicing through ribosomal protein RPL22.Cell chemical biology · 2025Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Decoding the molecular script of 2'-O-ribomethylation: Implications across CNS disorders.Heliyon · 2024Review
- Article
- The role of ribosomal DNA methylation in embryonic development, aging and diseases.Epigenetics & chromatin · 2024Review
- Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair.Nature cell biology · 2024Article
- Acute myeloid leukemias with UBTF tandem duplications are sensitive to menin inhibitors.Blood · 2024Article
- TBP facilitates RNA Polymerase I transcription following mitosis.RNA biology · 2024Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
rRNAs are transcribed from ribosomal DNA (rDNA) repeats, the most intensively transcribed loci in the genome. Due to their repetitive nature, there is a lack of genome assemblies suitable for rDNA mapping, creating a vacuum in our understanding of how the most abundant RNA in the cell is regulated. Our recent work revealed binding of numerous mammalian transcription and chromatin factors to rDNA. Several of these factors were known to play critical roles in development, tissue function, and malignancy, but their potential roles in rDNA regulation remained unexplored. This demonstrated the blind spot into which rDNA has fallen in genetic and epigenetic studies and highlighted an unmet need for public rDNA-optimized genome assemblies. Here, we customized five human and mouse assemblies-hg19 (GRCh37), hg38 (GRCh38), hs1 (T2T-CHM13), mm10 (GRCm38), and mm39 (GRCm39)-to render them suitable for rDNA mapping. The standard builds of these genomes contain numerous fragmented or repetitive rDNA loci. We identified and masked all rDNA-like regions, added a single rDNA reference sequence of the appropriate species as a ∼45 kb chromosome designated "chromosome R," and created annotation files to aid visualization of rDNA features in browser tracks. We validated these customized genomes for mapping of known rDNA-binding proteins and present a simple workflow for mapping chromatin immunoprecipitation-sequencing datasets. Customized genome assemblies, annotation files, positive and negative control tracks, and Snapgene files of standard rDNA reference sequences have been deposited to GitHub. These resources make rDNA mapping and visualization more readily accessible to a broad audience.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.