{"entity": "journal", "iuid": "73ebb18300e545fdbd0ff35ecadb97cc", "timestamp": "2026-06-10T15:35:16.254Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/RNA.json"}, "display": {"href": "https://publications.scilifelab.se/journal/RNA"}}, "title": "RNA", "issn": "1469-9001", "issn-l": "1355-8382", "publications_count": 5, "publications": [{"entity": "publication", "iuid": "fd4b4d71ebb544eba77fab8cedca6a01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd4b4d71ebb544eba77fab8cedca6a01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd4b4d71ebb544eba77fab8cedca6a01"}}, "title": "Suppression of the Escherichia coli rnpA49 conditionally lethal phenotype by different compensatory mutations.", "authors": [{"family": "Babina", "given": "Arianne M", "initials": "AM", "orcid": "0000-0002-4635-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe7f6d7d7a64bc3b829bea72dc1ca63.json"}}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}, {"family": "Andersson", "given": "Dan I", "initials": "DI", "orcid": "0000-0001-6640-2174", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb042b3dfa21450e862a29951ea0c1eb.json"}}], "type": "journal article", "published": "2024-07-16", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "30", "issue": "8", "pages": "977-991", "issn-l": "1355-8382"}, "abstract": "RNase P is an essential enzyme found across all domains of life that is responsible for the 5'-end maturation of precursor tRNAs. For decades, numerous studies have sought to elucidate the mechanisms and biochemistry governing RNase P function. However, much remains unknown about the regulation of RNase P expression, the turnover and degradation of the enzyme, and the mechanisms underlying the phenotypes and complementation of specific RNase P mutations, especially in the model bacterium, Escherichia coli In E. coli, the temperature-sensitive (ts) rnpA49 mutation in the protein subunit of RNase P has arguably been one of the most well-studied mutations for examining the enzyme's activity in vivo. Here, we report for the first time naturally occurring temperature-resistant suppressor mutations of E. coli strains carrying the rnpA49 allele. We find that rnpA49 strains can partially compensate the ts defect via gene amplifications of either RNase P subunit (rnpA49 or rnpB) or by the acquisition of loss-of-function mutations in Lon protease or RNase R. Our results agree with previous plasmid overexpression and gene deletion complementation studies, and importantly suggest the involvement of Lon protease in the degradation and/or regulatory pathway(s) of the mutant protein subunit of RNase P. This work offers novel insights into the behavior and complementation of the rnpA49 allele in vivo and provides direction for follow-up studies regarding RNase P regulation and turnover in E. coli.", "doi": "10.1261/rna.079909.123", "pmid": "38688559", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251521"}, {"db": "pii", "key": "rna.079909.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2024-11-27T15:36:05.495Z", "modified": "2024-11-27T15:36:59.692Z"}, {"entity": "publication", "iuid": "11f33634ab3146e69138a533798e7438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11f33634ab3146e69138a533798e7438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11f33634ab3146e69138a533798e7438"}}, "title": "Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.", "authors": [{"family": "Ramos", "given": "Jillian", "initials": "J", "orcid": "0000-0001-8139-5793", "researcher": {"href": "https://publications.scilifelab.se/researcher/d56276e8c1ca41c7afe82887f174caf4.json"}}, {"family": "Proven", "given": "Melissa", "initials": "M"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Hagelskamp", "given": "Felix", "initials": "F"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Phelan", "given": "Benjamin", "initials": "B"}, {"family": "Bell", "given": "Ryan", "initials": "R"}, {"family": "Kellner", "given": "Stefanie M", "initials": "SM"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Fu", "given": "Dragony", "initials": "D", "orcid": "0000-0002-8725-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/77103dd473a54326a9af7151af9d2ef7.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "RNA", "issn": "1469-9001", "issn-l": "1355-8382", "volume": "26", "issue": "11", "pages": "1654-1666"}, "abstract": "The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.", "doi": "10.1261/rna.076380.120", "pmid": "32763916", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "rna.076380.120"}, {"db": "pmc", "key": "PMC7566568"}], "notes": [], "created": "2020-09-15T07:06:13.955Z", "modified": "2024-01-16T13:48:41.471Z"}, {"entity": "publication", "iuid": "648b4af06fe24d8a9f646def6e1e9115", "links": {"self": {"href": "https://publications.scilifelab.se/publication/648b4af06fe24d8a9f646def6e1e9115.json"}, "display": {"href": "https://publications.scilifelab.se/publication/648b4af06fe24d8a9f646def6e1e9115"}}, "title": "A robust and versatile method for production and purification of large-scale RNA samples for structural biology.", "authors": [{"family": "Karlsson", "given": "Hampus", "initials": "H"}, {"family": "Baronti", "given": "Lorenzo", "initials": "L"}, {"family": "Petzold", "given": "Katja", "initials": "K"}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "26", "issue": "8", "pages": "1023-1037", "issn-l": "1355-8382"}, "abstract": "Recent findings in genome-wide transcriptomics revealed that RNAs are involved in almost every biological process, across all domains of life. The characterization of native RNAs of unknown function and structure is particularly challenging due to their typical low abundance in the cell and the inherent sensitivity toward ubiquitous RNA degrading enzymes. Therefore, robust in vitro synthesis and extensive work-up methods are often needed to obtain samples amenable for biochemical, biophysical, and structural studies. Here, we present a protocol that combines the most recent advances in T7 in vitro transcription methodology with reverse phase ion pairing and ion exchange HPLC purification of RNAs for the production of yield-optimized large-scale samples. The method is easy to follow, robust and suitable for users with little or no experience within the field of biochemistry or chromatography. The complete execution of this method, for example, for production of isotopically labeled NMR samples, can be performed in less than a week.", "doi": "10.1261/rna.075697.120", "pmid": "32354720", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7373988"}, {"db": "pii", "key": "rna.075697.120"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2024-04-03T14:25:24.689Z", "modified": "2024-04-03T14:25:24.694Z"}, {"entity": "publication", "iuid": "3500d5de886449048814de1ef449a274", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3500d5de886449048814de1ef449a274.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3500d5de886449048814de1ef449a274"}}, "title": "Molecular barcoding of viral vectors enables mapping and optimization of mRNAtrans-splicing", "authors": [{"family": "Davidsson", "given": "Marcus", "initials": "M"}, {"family": "D\u00edaz-Fern\u00e1ndez", "given": "Paula", "initials": "P"}, {"family": "Torroba", "given": "Marcos", "initials": "M"}, {"family": "Schwich", "given": "Oliver D", "initials": "OD"}, {"family": "Aldrin-Kirk", "given": "Patrick", "initials": "P"}, {"family": "Quintino", "given": "Luis", "initials": "L"}, {"family": "Heuer", "given": "Andreas", "initials": "A"}, {"family": "Wang", "given": "Gang", "initials": "G"}, {"family": "Lundberg", "given": "Cecilia", "initials": "C"}, {"family": "Bj\u00f6rklund", "given": "Tomas", "initials": "T"}], "type": "journal-article", "published": "2018-05-00", "journal": {"volume": "24", "issn": "1469-9001", "issue": "5", "pages": "673-687", "title": "RNA", "issn-l": "1355-8382"}, "abstract": "Genome editing has proven to be highly potent in the generation of functional gene knockouts in dividing cells. In the CNS however, efficient technologies to repair sequences are yet to materialize. Reprogramming on the mRNA level is an attractive alternative as it provides means to perform in situ editing of coding sequences without nuclease dependency. Furthermore, de novo sequences can be inserted without the requirement of homologous recombination. Such reprogramming would enable efficient editing in quiescent cells (e.g., neurons) with an attractive safety profile for translational therapies. In this study, we applied a novel molecular-barcoded screening assay to investigate RNA \n                trans-splicing in mammalian neurons. Through three alternative screening systems in cell culture and in vivo, we demonstrate that factors determining trans-splicing are reproducible regardless of the screening system. With this screening, we have located the most permissive trans-splicing sequences targeting an intron in the Synapsin I gene. Using viral vectors, we were able to splice full-length fluorophores into the mRNA while retaining very low off-target expression. Furthermore, this approach also showed evidence of functionality in the mouse striatum. However, in its current form, the trans-splicing events are stochastic and the overall activity lower than would be required for therapies targeting loss-of-function mutations. Nevertheless, the herein described barcode-based screening assay provides a unique possibility to screen and map large libraries in single animals or cell assays with very high precision.", "doi": "10.1261/rna.063925.117", "pmid": "29386333", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:23:25.926Z", "modified": "2020-01-21T13:56:12.103Z"}, {"entity": "publication", "iuid": "f19861f2021c485c8460562c82beb902", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f19861f2021c485c8460562c82beb902.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f19861f2021c485c8460562c82beb902"}}, "title": "MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.", "authors": [{"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "18", "issn": "1469-9001", "issue": "10", "pages": "1771-1782", "title": "RNA", "issn-l": "1355-8382"}, "abstract": "The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.", "doi": "10.1261/rna.033175.112", "pmid": "22875808", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "rna.033175.112"}, {"db": "pmc", "key": "PMC3446702"}], "notes": [], "created": "2017-05-04T14:57:45.715Z", "modified": "2020-01-21T13:56:10.526Z"}], "created": "2017-05-09T09:12:51.097Z", "modified": "2020-11-27T13:14:03.307Z"}