{"entity": "researcher", "timestamp": "2026-05-12T22:03:01.237Z", "family": "Marmol-Sanchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "affiliations": ["Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19"}}, "publications": [{"entity": "publication", "iuid": "0b7420c798754417bc3361852666e5e0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0b7420c798754417bc3361852666e5e0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0b7420c798754417bc3361852666e5e0"}}, "title": "Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.", "authors": [{"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P"}, {"family": "Stanicek", "given": "Laura", "initials": "L"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA", "orcid": "0000-0001-9984-2985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76bc874436644ebe8276f29414866635.json"}}, {"family": "Widmark", "given": "Albin", "initials": "A"}, {"family": "Doukoumopoulos", "given": "Evangelos", "initials": "E"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d61f8576ba87431d90b18fe5110c993d.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2023-09-21", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156"}, "abstract": "MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.", "doi": "10.1038/s41587-023-01951-0", "pmid": "37735263", "labels": {"SciLifeLab Fellow": null, "Marc Friedl\u00e4nder": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-023-01951-0"}], "notes": [], "created": "2023-12-04T12:44:49.220Z", "modified": "2023-12-04T12:44:49.277Z"}, {"entity": "publication", "iuid": "d34c9ee3e4074662aede0c94ccde1c03", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d34c9ee3e4074662aede0c94ccde1c03.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d34c9ee3e4074662aede0c94ccde1c03"}}, "title": "Historical RNA expression profiles from the extinct Tasmanian tiger.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86bda59888834d6889a108f8abbdb0fa.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6717-5011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b014c8406dd4e4a84635a9d33db07ef.json"}}, {"family": "Eriksson", "given": "Eli", "initials": "E", "orcid": "0000-0002-0340-3062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d889bc237534609b80b92d2d0fb46fd.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d61f8576ba87431d90b18fe5110c993d.json"}}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V", "orcid": "0000-0002-6810-1591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9092f71803fa45a98082b2b79b423a58.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9475506c96f34614ad7cece42a4559b9.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2975-9400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/869d72720cd9462dba09cbc861556de6.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/070030648e52418abda45f9f79688168.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Genome Res", "issn": "1549-5469", "volume": "33", "issue": "8", "pages": "1299-1316", "issn-l": "1088-9051"}, "abstract": "Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a \u223c130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.", "doi": "10.1101/gr.277663.123", "pmid": "37463752", "labels": {"SciLifeLab Fellow": null, "Marc Friedl\u00e4nder": null}, "xrefs": [{"db": "pmc", "key": "PMC10552650"}, {"db": "pii", "key": "gr.277663.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-12-04T12:45:17.431Z", "modified": "2023-12-04T12:45:17.750Z"}, {"entity": "publication", "iuid": "62fc60e776784e35bd5c86ae88877a4f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62fc60e776784e35bd5c86ae88877a4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62fc60e776784e35bd5c86ae88877a4f"}}, "title": "Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene.", "authors": [{"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdc4c42e06604b759dd6225c5f8362b5.json"}}, {"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9678d0797def441e9870afe6ffbb08d0.json"}}, {"family": "Smith", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0146-9244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b114f019dad43c580e985932e10a586.json"}}, {"family": "Marmol-Sanchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4afc80fe64684cd2b75c9c0a13630e19.json"}}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "Gilbert", "given": "Tom P", "initials": "TP", "orcid": "0000-0002-2570-3963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7445eeb9df23401ab9e8522b9520f370.json"}}, {"family": "Friedlander", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a2794be7c4cab89d1e4f1570c9417.json"}}], "type": "journal article", "published": "2020-12-15", "journal": {"title": "RNA", "issn": "1469-9001", "issn-l": "1355-8382"}, "abstract": "DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .", "doi": "10.1261/rna.078410.120", "pmid": "33323528", "labels": {"Marc Friedl\u00e4nder": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "rna.078410.120"}, {"db": "pmc", "key": "PMC7901840"}], "notes": [], "created": "2021-11-30T16:02:53.166Z", "modified": "2022-11-04T11:32:13.932Z"}]}