{"doi":"10.1093/nar/gkab229","title":"The rDNA is biomolecular condensate formed by polymer–polymer phase separation and is sequestered in the nucleolus by transcription and R-loops","abstract":"The nucleolus is the site of ribosome biosynthesis encompassing the ribosomal DNA (rDNA) locus in a phase separated state within the nucleus. In budding yeast, we find the rDNA locus and Cdc14, a protein phosphatase that co-localizes with the rDNA, behave like a condensate formed by polymer-polymer phase separation, while ribonucleoproteins behave like a condensate formed by liquid-liquid phase separation. The compaction of the rDNA and Cdc14's nucleolar distribution are dependent on the concentration of DNA cross-linkers. In contrast, ribonucleoprotein nucleolar distribution is independent of the concentration of DNA cross-linkers and resembles droplets in vivo upon replacement of the endogenous rDNA locus with high-copy plasmids. When ribosomal RNA is transcribed from the plasmids by Pol II, the rDNA-binding proteins and ribonucleoprotein signals are weakly correlated, but upon repression of transcription, ribonucleoproteins form a single, stable droplet that excludes rDNA-binding proteins from its center. Degradation of RNA-DNA hybrid structures, known as R-loops, by overexpression of RNase H1 results in the physical exclusion of the rDNA locus from the nucleolar center. Thus, the rDNA locus is a polymer-polymer phase separated condensate that relies on transcription and physical contact with RNA transcripts to remain encapsulated within the nucleolus.","journal":"Nucleic Acids Research","year":2021,"id":158077,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":47,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9457,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":666305,"name":"Daniel Kolbin","orcid":"0000-0003-1203-4956","position":1,"is_corresponding":false},{"id":666306,"name":"John Stanton","orcid":"0000-0003-4960-9215","position":2,"is_corresponding":false},{"id":667180,"name":"Muznah Khan","orcid":null,"position":3,"is_corresponding":false},{"id":667181,"name":"Solenn C. de Larminat","orcid":null,"position":4,"is_corresponding":false},{"id":666307,"name":"Colleen J. Lawrimore","orcid":"0000-0002-0135-1406","position":5,"is_corresponding":false},{"id":537958,"name":"Elaine Yeh","orcid":"0000-0001-5473-0365","position":6,"is_corresponding":false},{"id":370981,"name":"Kerry Bloom","orcid":"0000-0002-3457-004X","position":7,"is_corresponding":false},{"id":370978,"name":"Josh Lawrimore","orcid":"0000-0003-2301-9073","position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":null,"created_at":"2026-07-18T23:44:26.210708Z","pmid":"33836082","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}