{"entity": "researcher", "timestamp": "2026-06-15T17:05:03.771Z", "family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "affiliations": ["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.", "Science for Life Laboratory, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae"}}, "publications": [{"entity": "publication", "iuid": "6448eef2b2ba45f08ede2ebd059ea9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8"}}, "title": "FRET-FISH probes chromatin compaction at individual genomic loci in single cells.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Berezicki", "given": "Szymon", "initials": "S", "orcid": "0000-0003-3980-6290", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8794ceeb3bf405a8125545b49f7ebc7.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Gradin", "given": "Katarina", "initials": "K"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2022-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6680"}, "abstract": "Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.", "doi": "10.1038/s41467-022-34183-y", "pmid": "36335096", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9637210"}, {"db": "pii", "key": "10.1038/s41467-022-34183-y"}], "notes": [], "created": "2023-06-26T12:49:38.233Z", "modified": "2023-11-29T16:29:33.698Z"}, {"entity": "publication", "iuid": "26b36e84d7ee4479848b114b7c51ba21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21"}}, "title": "An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.", "authors": [{"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications.scilifelab.se/researcher/7933c49c5e6448408159ddb654286127.json"}}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "dataset", "published": "2022-07-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "400"}, "abstract": "Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.", "doi": "10.1038/s41597-022-01508-x", "pmid": "35821502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9276747"}, {"db": "pii", "key": "10.1038/s41597-022-01508-x"}], "notes": [], "created": "2022-08-19T08:38:43.514Z", "modified": "2023-10-16T11:44:09.152Z"}, {"entity": "publication", "iuid": "d71873c329c7421db086762eddcf7cb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7"}}, "title": "GPSeq reveals the radial organization of chromatin in the cell nucleus.", "authors": [{"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Kallas", "given": "Tomasz", "initials": "T"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Spanjaard", "given": "Bastiaan", "initials": "B"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Kolbeinsdottir", "given": "Solrun", "initials": "S"}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "10", "pages": "1184-1193", "issn-l": "1087-0156"}, "abstract": "With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.", "doi": "10.1038/s41587-020-0519-y", "pmid": "32451505", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0519-y"}, {"db": "pmc", "key": "PMC7610410"}, {"db": "mid", "key": "EMS118404"}], "notes": [], "created": "2020-05-26T07:12:39.312Z", "modified": "2021-11-10T12:46:51.496Z"}]}