{"entity": "researcher", "timestamp": "2026-07-19T18:51:18.194Z", "family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "affiliations": ["Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.", "Science for Life Laboratory, Tomtebodav\u00e4gen 23 A, Solna, SE-17165, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510"}}, "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": "05430c40833b4be3b4985f41f27377d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6"}}, "title": "Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Schweitzer", "given": "Maud", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"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"}], "type": "dataset", "published": "2022-02-10", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "47", "issn-l": "2052-4463"}, "abstract": "Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.", "doi": "10.1038/s41597-022-01139-2", "pmid": "35145120", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8831585"}, {"db": "pii", "key": "10.1038/s41597-022-01139-2"}], "notes": [], "created": "2023-06-26T12:49:04.953Z", "modified": "2023-06-26T12:49:05.083Z"}]}