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Genetic context and proliferation determine contrasting patterns of copy number amplification and loss for 5S and 45S ribosomal DNA arrays in cancer

https://doi.org/10.1101/154120
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Nucleolar size indicates the rapidity of cell proliferation in cancer tissues
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Oncogenic activation of the human trk proto‐oncogene by recombination with the ribosomal large subunit protein L7a.
inferredcites →https://doi.org/10.1007/s11105-009-0165-5openalex-snapshot
Differential rRNA Genes Expression in Hexaploid Wheat Related to NOR Methylation
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Methylated and unmethylated ribosomal RNA genes in the mouse
inferredcites →https://doi.org/10.1016/j.biocel.2004.07.007openalex-snapshot
Preferential loss of 5S and 28S rDNA genes in human adipose tissue during ageing
inferredcites →https://doi.org/10.1016/j.jmb.2009.07.032openalex-snapshot
Global Stabilization of rRNA Structure by Ribosomal Proteins S4, S17, and S20
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Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation
inferredcites →https://doi.org/10.1016/j.molcel.2010.09.024openalex-snapshot
The Nucleolus under Stress
inferredcites →https://doi.org/10.1016/s0079-6603(08)60506-1openalex-snapshot
Regulation of Mammalian Ribosomal Gene Transcription by RNA Polymerase I
inferredcites →https://doi.org/10.1016/s0968-0004(99)01460-7openalex-snapshot
The economics of ribosome biosynthesis in yeast
inferredcites →https://doi.org/10.1038/ncomms5850openalex-snapshot
Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans
inferredcites →https://doi.org/10.1038/nrc.2016.27openalex-snapshot
New frontiers in translational control of the cancer genome
inferredcites →https://doi.org/10.1038/nrc.2017.30openalex-snapshot
Erratum: New frontiers in translational control of the cancer genome
inferredcites →https://doi.org/10.1038/nrc1015openalex-snapshot
Does the ribosome translate cancer?
inferredcites →https://doi.org/10.1038/nrm.2016.88openalex-snapshot
Transcription–replication conflicts: how they occur and how they are resolved
inferredcites →https://doi.org/10.1038/nrm1276openalex-snapshot
From polyploidy to aneuploidy, genome instability and cancer
inferredcites →https://doi.org/10.1038/nrm2858openalex-snapshot
Genomic instability — an evolving hallmark of cancer
inferredcites →https://doi.org/10.1038/onc.2010.189openalex-snapshot
Ribosome biogenesis surveillance: probing the ribosomal protein-Mdm2-p53 pathway
inferredcites →https://doi.org/10.1038/sj.onc.1203690openalex-snapshot
RNA polymerase I transcription in confluent cells: Rb downregulates rDNA transcription during confluence-induced cell cycle arrest
inferredcites →https://doi.org/10.1038/sj.onc.1203875openalex-snapshot
Rb and p130 regulate RNA polymerase I transcription: Rb disrupts the interaction between UBF and SL-1
inferredcites →https://doi.org/10.1038/srep35026openalex-snapshot
Depletion of ribosomal protein S19 causes a reduction of rRNA synthesis
inferredcites →https://doi.org/10.1053/j.gastro.2009.12.065openalex-snapshot
The Chromosomal Instability Pathway in Colon Cancer
inferredcites →https://doi.org/10.1073/pnas.0334858100openalex-snapshot
Multiple mutations and cancer
inferredcites →https://doi.org/10.1073/pnas.0502521102openalex-snapshot
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
inferredcites →https://doi.org/10.1073/pnas.082005599openalex-snapshot
Characterization of the c-MYC-regulated transcriptome by SAGE: Identification and analysis of c-MYC target genes
inferredcites →https://doi.org/10.1073/pnas.0911905107openalex-snapshot
Gene duplication and the evolution of ribosomal protein gene regulation in yeast
inferredcites →https://doi.org/10.1073/pnas.1416878112openalex-snapshot
Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes
inferredcites →https://doi.org/10.1073/pnas.200372597openalex-snapshot
Induction of ribosomal genes and hepatocyte hypertrophy by adenovirus-mediated expression of c-Myc in vivo
inferredcites →https://doi.org/10.1073/pnas.51.6.1197openalex-snapshot
THE RELATIONSHIP OF THE NUCLEOLUS TO THE SYNTHESIS OF RIBOSOMAL RNA IN HELA CELLS
inferredcites →https://doi.org/10.1073/pnas.96.11.6096openalex-snapshot
Cell cycle-dependent regulation of RNA polymerase I transcription: The nucleolar transcription factor UBF is inactive in mitosis and early G 1
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/emboj/20.6.1383openalex-snapshot
N‐myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkq1326openalex-snapshot
Integrative genomic analysis of human ribosomal DNA
inferredcites →https://doi.org/10.1093/nar/gkv1157openalex-snapshot
Ensembl 2016
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040664openalex-snapshot
Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster.
inferredcites →https://doi.org/10.1101/gr.3970105openalex-snapshot
Human ribosomal RNA gene arrays display a broad range of palindromic structures
inferredcites →https://doi.org/10.1101/gr.6858507openalex-snapshot
Genomic architecture and inheritance of human ribosomal RNA gene clusters
inferredcites →https://doi.org/10.1126/science.1087447openalex-snapshot
A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
inferredcites →https://doi.org/10.1126/science.1155390openalex-snapshot
Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites
inferredcites →https://doi.org/10.1126/science.1179044openalex-snapshot
Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity
inferredcites →https://doi.org/10.1126/scisignal.2003477openalex-snapshot
Revisiting the Nucleolus: From Marker to Dynamic Integrator of Cancer Signaling
inferredcites →https://doi.org/10.1128/mcb.00703-08openalex-snapshot
Transcription of Multiple Yeast Ribosomal DNA Genes Requires Targeting of UAF to the Promoter by Uaf30
inferredcites →https://doi.org/10.1128/mcb.1.11.1007openalex-snapshot
Coordinate control of syntheses of ribosomal ribonucleic acid and ribosomal proteins during nutritional shift-up in Saccharomyces cerevisiae.
inferredcites →https://doi.org/10.1128/mcb.11.8.3842openalex-snapshot
Ribosomal Protein Genes Are Overexpressed in Colorectal Cancer: Isolation of a cDNA Clone Encoding the Human S3 Ribosomal Protein
inferredcites →https://doi.org/10.1128/mcb.20.16.5930-5938.2000openalex-snapshot
Repression of RNA Polymerase I Transcription by the Tumor Suppressor p53
inferredcites →https://doi.org/10.1128/mmbr.00011-08openalex-snapshot
Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes
inferredcites →https://doi.org/10.1158/0008-5472.can-09-2680openalex-snapshot
Human rRNA Gene Clusters Are Recombinational Hotspots in Cancer
inferredcites →https://doi.org/10.1186/1759-8753-3-4openalex-snapshot
Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia
inferredcites →https://doi.org/10.1186/gb-2011-12-4-r41openalex-snapshot
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
inferredcites →https://doi.org/10.1186/s13059-016-1104-zopenalex-snapshot
Patterns of ribosomal protein expression specify normal and malignant human cells
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1001376openalex-snapshot
Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation
inferredcites →https://doi.org/10.1371/journal.pgen.1003806openalex-snapshot
A Genome-Wide Systematic Analysis Reveals Different and Predictive Proliferation Expression Signatures of Cancerous vs. Non-Cancerous Cells
inferredcites →https://doi.org/10.1371/journal.pone.0001854openalex-snapshot
Using Ribosomal Protein Genes as Reference: A Tale of Caution
inferredcites →https://doi.org/10.2353/ajpath.2008.070752openalex-snapshot
Nucleolus, Ribosomes, and Cancer
inferredcites →https://doi.org/10.4081/1661openalex-snapshot
Structural features of nucleoli in blood, leukemic, lymphoma and myeloma cells
inferredcites →https://doi.org/10.4161/epi.3.5.6913openalex-snapshot
Chromatin organization of active ribosomal RNA genes
inferredcites →https://doi.org/10.4161/nucl.32235openalex-snapshot
Nucleolar stress with and without p53
inferredcites →https://doi.org/10.7554/elife.02935openalex-snapshot
Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer
inferredcites →https://doi.org/10.7554/elife.10769openalex-snapshot
Mitochondrial DNA copy number variation across human cancers

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s11033-023-08630-yopenalex-snapshot
Ribosomal DNA copy number alteration in blood sample from gastric cancer patients
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007006openalex-snapshot
DNA replication stress restricts ribosomal DNA copy number
inferred← citeshttps://doi.org/10.1371/journal.pone.0186047openalex-snapshot
Expression of ribosomal proteins in normal and cancerous human prostate tissue
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