{"entity": "researcher", "timestamp": "2026-07-22T17:40:30.132Z", "family": "Mihai", "given": "Ionut Sebastian", "initials": "IS", "orcid": "0000-0002-9322-5879", "affiliations": ["Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Biomedicinbyggnaden 6K och 6L, Ume\u00e5 universitetssjukhus, 901 87, Ume\u00e5, Sweden.", "Ume\u00e5 Centre for Microbial Research (UCMR), Universitetstorget 4, 901 87, Ume\u00e5, Sweden.", "Department of Molecular Biology, Ume\u00e5 University, Biomedicinbyggnaden 6K och 6L, Ume\u00e5 universitetssjukhus, 901 87, Ume\u00e5, Sweden.", "Industrial Doctoral School, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/a992010c915b42e8a5d3b1ab8e6302ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/a992010c915b42e8a5d3b1ab8e6302ee"}}, "publications": [{"entity": "publication", "iuid": "bb208e8865fc4192b2c539f6a8e46c82", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bb208e8865fc4192b2c539f6a8e46c82.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bb208e8865fc4192b2c539f6a8e46c82"}}, "title": "Telomemore enables single-cell analysis of cell cycle and chromatin condensation.", "authors": [{"family": "Yakovenko", "given": "Iryna", "initials": "I", "orcid": "0009-0003-5235-2999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03c9f5e054fb4eaaadec42a6e484df3b.json"}}, {"family": "Mihai", "given": "Ionut Sebastian", "initials": "IS", "orcid": "0000-0002-9322-5879", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a992010c915b42e8a5d3b1ab8e6302ee.json"}}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/178f194601f84780a0cdee01ab25a12d.json"}}, {"family": "Rosenbaum", "given": "William", "initials": "W", "orcid": "0000-0003-2274-7343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/452d1628f9ca4fb88ccc432a0258c517.json"}}, {"family": "Dernstedt", "given": "Andy", "initials": "A", "orcid": "0000-0001-6048-5300", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63ec9ea5d1d64327a301381d7496561a.json"}}, {"family": "Gr\u00f6ning", "given": "Remigius", "initials": "R", "orcid": "0000-0001-5384-8038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/554e7b2b64da4db890e3330c3766b1d6.json"}}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e227e1e1bb84083b9534f4124830f6d.json"}}, {"family": "Carroll", "given": "Laura", "initials": "L", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Forsell", "given": "Mattias", "initials": "M", "orcid": "0000-0001-6904-742X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3209b86680246b898a8442ea43bba0e.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/598b7031d1c9448a91de58d8544af7fa.json"}}], "type": "journal article", "published": "2025-01-24", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "3", "issn-l": "0305-1048"}, "abstract": "Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.", "doi": "10.1093/nar/gkaf031", "pmid": "39878215", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11775621"}, {"db": "pii", "key": "7986050"}], "notes": [], "created": "2025-03-18T17:32:33.811Z", "modified": "2025-03-18T17:32:34.241Z"}]}