{"doi":"10.1101/2025.06.13.659538","title":"Detection of stress-dependent m\n                  <sup>5</sup>\n                  C rRNA dynamics in\n                  <i>Escherichia coli</i>\n                  using m\n                  <sup>5</sup>\n                  C-Rol-LAMP","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  Numerous RNA modifications are known in prokaryotes, but their dynamics and function in regulation remain largely unexplored. In\n                  <jats:italic>Escherichia coli</jats:italic>\n                  , three methyltransferases catalyze the 5-methylcytosine (m\n                  <jats:sup>5</jats:sup>\n                  C) modification in ribosomal RNA. Here, we introduce m\n                  <jats:sup>5</jats:sup>\n                  C-rolling circle loop-mediated isothermal amplification (m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP) as a novel qPCR-based method that offers high sensitivity and site- specific resolution to detect and quantify m⁵C in total RNA. When applying m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP to\n                  <jats:italic>E. coli</jats:italic>\n                  under heat stress (45 °C), we observe a site-specific increase of m⁵C at position 1407 of 16S rRNA from 77% to 89%, while m\n                  <jats:sup>5</jats:sup>\n                  C levels at positions 967 (16S) and 1962 (23S) remain unchanged. In recovered cells (at 37°C), the m\n                  <jats:sup>5</jats:sup>\n                  C abundance partially returns to the no stress level. Under oxidative stress, the level of m⁵C1407 also increases, but remains high in recovered cells. These results demonstrate for the first time a reversible, stress-dependent and site-specific change in the rRNA modification level of a bacterium. m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP is a powerful and easy-to-use tool for studying m\n                  <jats:sup>5</jats:sup>\n                  C in all RNA species, allowing the quantitative and site-specific detection of this modification.\n                </jats:p>","journal":null,"year":null,"id":650409,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":667741,"name":"Sebastián Riquelme-Barrios","orcid":"0000-0001-9995-0804","position":1,"is_corresponding":false},{"id":1169720,"name":"Kirsten Jung","orcid":"0000-0003-0779-6841","position":2,"is_corresponding":false},{"id":1695893,"name":"Leonardo Vásquez-Camus","orcid":"0009-0002-7096-350X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Detection of stress-dependent m\n                  <sup>5</sup>\n                  C rRNA dynamics in\n                  <i>Escherichia coli</i>\n                  using m\n                  <sup>5</sup>\n                  C-Rol-LAMP","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  Numerous RNA modifications are known in prokaryotes, but their dynamics and function in regulation remain largely unexplored. In\n                  <jats:italic>Escherichia coli</jats:italic>\n                  , three methyltransferases catalyze the 5-methylcytosine (m\n                  <jats:sup>5</jats:sup>\n                  C) modification in ribosomal RNA. Here, we introduce m\n                  <jats:sup>5</jats:sup>\n                  C-rolling circle loop-mediated isothermal amplification (m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP) as a novel qPCR-based method that offers high sensitivity and site- specific resolution to detect and quantify m⁵C in total RNA. When applying m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP to\n                  <jats:italic>E. coli</jats:italic>\n                  under heat stress (45 °C), we observe a site-specific increase of m⁵C at position 1407 of 16S rRNA from 77% to 89%, while m\n                  <jats:sup>5</jats:sup>\n                  C levels at positions 967 (16S) and 1962 (23S) remain unchanged. In recovered cells (at 37°C), the m\n                  <jats:sup>5</jats:sup>\n                  C abundance partially returns to the no stress level. Under oxidative stress, the level of m⁵C1407 also increases, but remains high in recovered cells. These results demonstrate for the first time a reversible, stress-dependent and site-specific change in the rRNA modification level of a bacterium. m\n                  <jats:sup>5</jats:sup>\n                  C-Rol-LAMP is a powerful and easy-to-use tool for studying m\n                  <jats:sup>5</jats:sup>\n                  C in all RNA species, allowing the quantitative and site-specific detection of this modification.\n                </jats:p>","is_dataset_classified":null,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19965766","pmcid":null,"openalex_id":"https://openalex.org/W4411346007","authors":[],"funders":[],"total_grants":0,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2025,"count":1}],"oa_status":"closed","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","oa_locations":[{"url":"https://syndication.highwire.org/content/doi/10.1101/2025.06.13.659538","host_type":"publisher"},{"url":"https://doi.org/10.1101/2025.06.13.659538","host_type":"repository"}],"fields_of_study":["RNA modifications and cancer","RNA and protein synthesis mechanisms","RNA Research and Splicing"],"mesh_terms":[],"keywords":["Escherichia coli","Dynamics (music)","Physics","Chemistry","Gene","Biochemistry"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T05:27:13.287114Z","pmid":null,"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":[]}