{"entity": "researcher", "timestamp": "2026-08-11T14:05:57.492Z", "family": "Luzon", "given": "Carmen Navarro", "initials": "CN", "orcid": "0000-0001-5438-9654", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85"}}, "publications": [{"entity": "publication", "iuid": "ead989ea22be400abf08c96a2de3f6c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0"}}, "title": "RNA transcripts regulate G-quadruplex landscapes through G-loop formation.", "authors": [{"family": "Sato", "given": "Koichi", "initials": "K", "orcid": "0000-0002-0574-774X", "researcher": {"href": "https://publications.scilifelab.se/researcher/419db8b1c9a142d8994dc12727020ed4.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "van den Berg", "given": "Jeroen", "initials": "J", "orcid": "0000-0002-9430-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81ddd6ecb4e4654aef53c4388448204.json"}}, {"family": "Braat", "given": "Diana", "initials": "D", "orcid": "0009-0003-1086-7185", "researcher": {"href": "https://publications.scilifelab.se/researcher/8028609fa976407c9f756fa4640b9012.json"}}, {"family": "Cruz", "given": "Victoria M", "initials": "VM", "orcid": "0000-0001-5385-1472", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d30dbce78446cc8b327a0df98ce69c.json"}}, {"family": "Navarro Luz\u00f3n", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Schimmel", "given": "Joost", "initials": "J", "orcid": "0000-0002-2620-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a37bb4f3de34d3c8c9fffab2d3a6d0c.json"}}, {"family": "Esteban-Jurado", "given": "Clara", "initials": "C"}, {"family": "Alemany", "given": "Ma\u00eblys", "initials": "M", "orcid": "0009-0004-3277-6206", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc9d305d46084a598ff3eeb47127d700.json"}}, {"family": "Dreyer", "given": "Jan", "initials": "J"}, {"family": "Hendrikx", "given": "Aiko", "initials": "A"}, {"family": "Mattiroli", "given": "Francesca", "initials": "F", "orcid": "0000-0002-1574-7217", "researcher": {"href": "https://publications.scilifelab.se/researcher/0afa3a260bfb4e49b2ed1ef9b3af3357.json"}}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A", "orcid": "0000-0002-9442-3551", "researcher": {"href": "https://publications.scilifelab.se/researcher/86e54078e6ea45949e7468b2653601d9.json"}}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Knipscheer", "given": "Puck", "initials": "P", "orcid": "0000-0003-4198-0132", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b1d8281b234a30b7e450f2759559c2.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6752", "pages": "1225-1231", "issn-l": "0036-8075"}, "abstract": "G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics are controlled remains poorly understood. Here, we report that RNA transcripts govern G4 landscapes through coordinated G-loop assembly and disassembly. G-loop assembly involves activation of the ATM and ATR kinases, followed by homology-directed invasion of RNA opposite the G4 strand mediated by BRCA2 and RAD51. Disassembly of the G-loop resolves the G4 structure through DHX36-FANCJ-mediated G4 unwinding, which triggers nucleolytic incision and subsequent hybrid strand renewal by DNA synthesis. Inhibition of G-loop disassembly causes global G4 and R-loop accumulation, leading to transcriptome dysregulation, replication stress, and genome instability. These findings establish an intricate G-loop assembly-disassembly mechanism that controls G4 landscapes and is essential for cellular homeostasis and survival.", "doi": "10.1126/science.adr0493", "pmid": "40504899", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:51:58.676Z", "modified": "2025-11-28T10:51:59.081Z"}, {"entity": "publication", "iuid": "6821d1cd51294efd9c8abd81faf7a73a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a"}}, "title": "Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.", "authors": [{"family": "Kumar", "given": "Banushree", "initials": "B", "orcid": "0000-0001-9200-6773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd7494dc4ea43d9b493fd6a099fc675.json"}}, {"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Yung", "given": "Philip Yuk Kwong", "initials": "PYK", "orcid": "0000-0003-2926-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/97f9b0c8cf5a4f3ab22629842c2b08dd.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "Salazar Mantero", "given": "Angelo", "initials": "A"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Hannah", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2024-10-03", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.", "doi": "10.1038/s41596-024-01058-z", "pmid": "39363107", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-024-01058-z"}], "notes": [], "created": "2025-02-28T14:15:54.627Z", "modified": "2025-11-28T20:16:06.367Z"}, {"entity": "publication", "iuid": "e980f00b87dd45d3ab9ceb6c3c4cca0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c"}}, "title": "An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.", "authors": [{"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J", "orcid": "0000-0001-9529-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbe28157081c49debba23f0b9ebd9c74.json"}}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Caridha", "given": "Rozina", "initials": "R"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5095", "issn-l": "2041-1723"}, "abstract": "Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.", "doi": "10.1038/s41467-020-18863-1", "pmid": "33037201", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7547087"}, {"db": "pii", "key": "10.1038/s41467-020-18863-1"}], "notes": [], "created": "2024-04-03T14:21:34.373Z", "modified": "2024-04-03T14:22:37.597Z"}]}