{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T08:27:40Z","timestamp":1786955260054,"version":"build-2736575974"},"reference-count":50,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32130043"],"award-info":[{"award-number":["32130043"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai Municipality","doi-asserted-by":"publisher","award":["25ZR1401269"],"award-info":[{"award-number":["25ZR1401269"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["febs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The FEBS Journal"],"abstract":"<jats:p>\n                    A central question in gene regulation is the relationship between the nanoscale organization of chromatin and transcriptional activity. However, directly visualizing and quantifying this process in living cells at nanometer resolution remains challenging. Here, we integrate live\u2010cell MINFLUX nanoscopy with the DNA probe 5\u2010HMSiR\u2010Hoechst and a HaloTag system to map chromatin architecture at loci colabeled with RNA polymerase II (Pol II) and heterochromatin protein 1\n                    <jats:italic>\u03b1<\/jats:italic>\n                    (HP1\n                    <jats:italic>\u03b1<\/jats:italic>\n                    )\u2014markers of distinct transcriptional states. High\u2010resolution snapshots, captured via spatiotemporal segmentation of single\u2010molecule localizations, reveal that HP1\n                    <jats:italic>\u03b1<\/jats:italic>\n                    loci exhibit densely packed chromatin with high DNA localization density, indicating a stable, rigid state. In contrast, Pol II loci are predominantly open and extended and exhibit low DNA localization density, implying a highly flexible and dynamic conformation. Critically, we establish a direct positive correlation between the degree of HP1\n                    <jats:italic>\u03b1<\/jats:italic>\n                    aggregation and the level of local chromatin compaction. Our work thus provides nanoscale insight into how transcriptional activity is physically encoded in living cell chromatin.\n                  <\/jats:p>","DOI":"10.1111\/febs.70705","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T08:20:58Z","timestamp":1786954858000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>MINFLUX<\/scp>\n                    nanoscopy links chromatin nanostructure to transcriptional state in living cells"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-0656-7414","authenticated-orcid":false,"given":"Yi","family":"Hu","sequence":"first","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"},{"name":"School of Life Sciences and Technology ShanghaiTech University  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chong","family":"Zuo","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangnan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Technology ShanghaiTech University  China"},{"name":"ENT Institute and Department of Otorhinolaryngology Eye &amp; ENT Hospital, Fudan University  Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruixi","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaiyuan","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u2010Song","family":"Guan","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Technology ShanghaiTech University  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanhui","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Technology ShanghaiTech University  China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9165-8515","authenticated-orcid":false,"given":"Hong","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Science and Technology University of Shanghai for Science and Technology  China"},{"name":"Institute of Photonic Chips University of Shanghai for Science and Technology  China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1016\/j.cell.2019.01.020","article-title":"Extensive heterogeneity and intrinsic variation in spatial genome organization","volume":"176","author":"Finn EH","year":"2019","journal-title":"Cell"},{"key":"e_1_2_10_3_1","first-page":"327","article-title":"The role of transcription in shaping the spatial organization of the genome","volume":"20","author":"Steensel B","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long\u2010range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman\u2010Aiden E","year":"2009","journal-title":"Science"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"7175","DOI":"10.1016\/j.cell.2025.10.013","article-title":"Mapping chromatin structure at base\u2010pair resolution unveils a unified model of cis\u2010regulatory element interactions","volume":"188","author":"Li H","year":"2025","journal-title":"Cell"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1016\/j.cell.2020.07.032","article-title":"Genome\u2010scale imaging of the 3D organization and transcriptional activity of chromatin","volume":"182","author":"Su JH","year":"2020","journal-title":"Cell"},{"key":"e_1_2_10_7_1","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/j.cell.2015.01.054","article-title":"Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo","volume":"160","author":"Ricci MA","year":"2015","journal-title":"Cell"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s00412-023-00792-9","article-title":"Fluorescence\u2010based super\u2010resolution\u2010microscopy strategies for chromatin studies","volume":"132","author":"Burgers TCQ","year":"2023","journal-title":"Chromosoma"},{"key":"e_1_2_10_9_1","doi-asserted-by":"crossref","first-page":"4477","DOI":"10.1038\/srep04477","article-title":"Super\u2010resolution microscopy reveals decondensed chromatin structure at transcription sites","volume":"4","author":"Wang Y","year":"2014","journal-title":"Sci Rep"},{"key":"e_1_2_10_10_1","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/nature16496","article-title":"Super\u2010resolution imaging reveals distinct chromatin folding for different epigenetic states","volume":"529","author":"Boettiger AN","year":"2016","journal-title":"Nature"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","first-page":"8470","DOI":"10.1093\/nar\/gkz593","article-title":"Super\u2010resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo","volume":"47","author":"Otterstrom J","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"e_1_2_10_12_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.112567","article-title":"True\u2010to\u2010scale DNA\u2010density maps correlate with major accessibility differences between active and inactive chromatin","volume":"42","author":"Gelleri M","year":"2023","journal-title":"Cell Rep"},{"key":"e_1_2_10_13_1","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/s41377-025-01786-1","article-title":"Three\u2010color single\u2010molecule localization microscopy in chromatin","volume":"14","author":"Acosta N","year":"2025","journal-title":"Light Sci Appl"},{"key":"e_1_2_10_14_1","doi-asserted-by":"crossref","first-page":"5561","DOI":"10.3390\/cancers13215561","article-title":"Topological analysis of gammaH2AX and MRE11 clusters detected by localization microscopy during X\u2010ray\u2010induced DNA double\u2010Strand break repair","volume":"13","author":"Hahn H","year":"2021","journal-title":"Cancers (Basel)"},{"key":"e_1_2_10_15_1","doi-asserted-by":"crossref","first-page":"3636","DOI":"10.3390\/ijms22073636","article-title":"Elucidation of the clustered Nano\u2010architecture of radiation\u2010induced DNA damage sites and surrounding chromatin in cancer cells: a single molecule localization microscopy approach","volume":"22","author":"Hausmann M","year":"2021","journal-title":"Int J Mol Sci"},{"key":"e_1_2_10_16_1","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.3390\/ijms19082263","article-title":"Using persistent homology as a new approach for super\u2010resolution localization microscopy data analysis and classification of gammaH2AX foci\/clusters","volume":"19","author":"Hofmann A","year":"2018","journal-title":"Int J Mol Sci"},{"key":"e_1_2_10_17_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.sbi.2025.103021","article-title":"Super\u2010resolving chromatin in its own terms: recent approaches to portray genomic organization","volume":"92","author":"Merino MF","year":"2025","journal-title":"Curr Opin Struct Biol"},{"key":"e_1_2_10_18_1","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1002\/jemt.24765","article-title":"MINFLUX nanoscopy: a \u201cbrilliant\u201d technique promising major breakthrough","volume":"88","author":"Salerno M","year":"2025","journal-title":"Microsc Res Tech"},{"key":"e_1_2_10_19_1","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1126\/science.aak9913","article-title":"Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes","volume":"355","author":"Balzarotti F","year":"2017","journal-title":"Science"},{"key":"e_1_2_10_20_1","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/s41566-025-01625-0","article-title":"MINFLUX achieves molecular resolution with minimal photons","volume":"19","author":"Scheiderer L","year":"2025","journal-title":"Nat Photonics"},{"key":"e_1_2_10_21_1","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.ade2676","article-title":"Direct observation of motor protein stepping in living cells using MINFLUX","volume":"379","author":"Deguchi T","year":"2023","journal-title":"Science"},{"key":"e_1_2_10_22_1","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/s41586-025-08738-0","article-title":"Overlapping nuclear import and export paths unveiled by two\u2010colour MINFLUX","volume":"640","author":"Sau A","year":"2025","journal-title":"Nature"},{"key":"e_1_2_10_23_1","doi-asserted-by":"crossref","first-page":"8497","DOI":"10.1038\/ncomms9497","article-title":"SiR\u2010Hoechst is a far\u2010red DNA stain for live\u2010cell nanoscopy","volume":"6","author":"Lukinavicius G","year":"2015","journal-title":"Nat Commun"},{"key":"e_1_2_10_24_1","doi-asserted-by":"crossref","first-page":"14797","DOI":"10.1039\/D0CC06759H","article-title":"Far\u2010red switching DNA probes for live cell nanoscopy","volume":"56","author":"Bucevicius J","year":"2020","journal-title":"Chem Commun (Camb)"},{"key":"e_1_2_10_25_1","doi-asserted-by":"crossref","DOI":"10.1093\/nsr\/nwaf451","article-title":"MINFLUX dissects nucleosome and compacting chromatin structures in living cells","volume":"13","author":"Xie H","year":"2026","journal-title":"Natl Sci Rev"},{"key":"e_1_2_10_26_1","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/nrm1355","article-title":"HP1 and the dynamics of heterochromatin maintenance","volume":"5","author":"Maison C","year":"2004","journal-title":"Nat Rev Mol Cell Biol"},{"key":"e_1_2_10_27_1","doi-asserted-by":"crossref","first-page":"3303","DOI":"10.1038\/s41467-023-38429-1","article-title":"Chromatin alternates between a and B compartments at kilobase scale for subgenic organization","volume":"14","author":"Harris HL","year":"2023","journal-title":"Nat Commun"},{"key":"e_1_2_10_28_1","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/s41588-021-00784-4","article-title":"Liquid chromatin hi\u2010C characterizes compartment\u2010dependent chromatin interaction dynamics","volume":"53","author":"Belaghzal H","year":"2021","journal-title":"Nat Genet"},{"key":"e_1_2_10_29_1","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao SS","year":"2014","journal-title":"Cell"},{"key":"e_1_2_10_30_1","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1016\/j.cell.2013.12.001","article-title":"Dynamic imaging of genomic loci in living human cells by an optimized CRISPR\/Cas system","volume":"155","author":"Chen B","year":"2013","journal-title":"Cell"},{"key":"e_1_2_10_31_1","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1038\/nbt.3526","article-title":"Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow","volume":"34","author":"Ma H","year":"2016","journal-title":"Nat Biotechnol"},{"key":"e_1_2_10_32_1","doi-asserted-by":"crossref","first-page":"21301","DOI":"10.1073\/pnas.1213818110","article-title":"Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes","volume":"109","author":"Beliveau BJ","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_2_10_33_1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/978-1-60761-789-1_13","article-title":"COMBinatorial oligo FISH: directed labeling of specific genome domains in differentially fixed cell material and live cells","volume":"659","author":"Schmitt E","year":"2010","journal-title":"Methods Mol Biol"},{"key":"e_1_2_10_34_1","doi-asserted-by":"crossref","first-page":"4094","DOI":"10.3390\/ijms11104094","article-title":"COMBO\u2010FISH enables high precision localization microscopy as a prerequisite for nanostructure analysis of genome loci","volume":"11","author":"Muller P","year":"2010","journal-title":"Int J Mol Sci"},{"key":"e_1_2_10_35_1","doi-asserted-by":"crossref","first-page":"6506","DOI":"10.1073\/pnas.0601212103","article-title":"EM measurements define the dimensions of the 30\u2010nm chromatin fiber: evidence for a compact, interdigitated structure","volume":"103","author":"Robinson PJ","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_2_10_36_1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41594-019-0368-x","article-title":"Beads on a string\u2010nucleosome array arrangements and folding of the chromatin fiber","volume":"27","author":"Baldi S","year":"2020","journal-title":"Nat Struct Mol Biol"},{"key":"e_1_2_10_37_1","doi-asserted-by":"crossref","DOI":"10.1126\/science.aag0025","article-title":"ChromEMT: visualizing 3D chromatin structure and compaction in interphase and mitotic cells","volume":"357","author":"Ou HD","year":"2017","journal-title":"Science"},{"key":"e_1_2_10_38_1","doi-asserted-by":"crossref","first-page":"6324","DOI":"10.1038\/s41467-023-42072-1","article-title":"Structure of native chromatin fibres revealed by Cryo\u2010ET in situ","volume":"14","author":"Hou Z","year":"2023","journal-title":"Nat Commun"},{"key":"e_1_2_10_39_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113134","article-title":"Cryo\u2010ET study from in vitro to in vivo revealed a general folding mode of chromatin with two\u2010start helical architecture","volume":"42","author":"Li Y","year":"2023","journal-title":"Cell Rep"},{"key":"e_1_2_10_40_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adf1488","article-title":"Condensed but liquid\u2010like domain organization of active chromatin regions in living human cells","volume":"9","author":"Nozaki T","year":"2023","journal-title":"Sci Adv"},{"key":"e_1_2_10_41_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abn5626","article-title":"Single\u2010nucleosome imaging reveals steady\u2010state motion of interphase chromatin in living human cells","volume":"8","author":"Iida S","year":"2022","journal-title":"Sci Adv"},{"key":"e_1_2_10_42_1","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1007\/BF00284881","article-title":"Fluorometric properties of the bibenzimidazole derivative Hoechst 33258, a fluorescent probe specific for AT concentration in chromosomal DNA","volume":"46","author":"Weisblum B","year":"1974","journal-title":"Chromosoma"},{"key":"e_1_2_10_43_1","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.63972","article-title":"HP1alpha is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics","volume":"10","author":"Strom AR","year":"2021","journal-title":"elife"},{"key":"e_1_2_10_44_1","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1093\/jmcb\/mjy040","article-title":"LRIF1 interacts with HP1alpha to coordinate accurate chromosome segregation during mitosis","volume":"10","author":"Akram S","year":"2018","journal-title":"J Mol Cell Biol"},{"key":"e_1_2_10_45_1","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/nature22822","article-title":"Liquid droplet formation by HP1alpha suggests a role for phase separation in heterochromatin","volume":"547","author":"Larson AG","year":"2017","journal-title":"Nature"},{"key":"e_1_2_10_46_1","doi-asserted-by":"crossref","first-page":"6850","DOI":"10.1074\/jbc.M113.512137","article-title":"Human heterochromatin protein 1alpha promotes nucleosome associations that drive chromatin condensation","volume":"289","author":"Azzaz AM","year":"2014","journal-title":"J Biol Chem"},{"key":"e_1_2_10_47_1","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/s41586-019-1669-2","article-title":"HP1 reshapes nucleosome core to promote phase separation of heterochromatin","volume":"575","author":"Sanulli S","year":"2019","journal-title":"Nature"},{"key":"e_1_2_10_48_1","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature22989","article-title":"Phase separation drives heterochromatin domain formation","volume":"547","author":"Strom AR","year":"2017","journal-title":"Nature"},{"key":"e_1_2_10_49_1","doi-asserted-by":"crossref","first-page":"8152","DOI":"10.3390\/cimb45100515","article-title":"Microscopic analysis of heterochromatin, euchromatin and Cohesin in cancer cell models and under anti\u2010cancer treatment","volume":"45","author":"Fischer EF","year":"2023","journal-title":"Curr Issues Mol Biol"},{"key":"e_1_2_10_50_1","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1016\/j.neuron.2021.12.035","article-title":"ASH1L haploinsufficiency results in autistic\u2010like phenotypes in mice and links Eph receptor gene to autism spectrum disorder","volume":"110","author":"Yan Y","year":"2022","journal-title":"Neuron"},{"key":"e_1_2_10_51_1","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/s41380-019-0560-8","article-title":"Mutations in ASH1L confer susceptibility to Tourette syndrome","volume":"25","author":"Liu S","year":"2020","journal-title":"Mol Psychiatry"}],"container-title":["The FEBS Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/febs.70705","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/febs.70705","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/febs.70705","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T08:21:05Z","timestamp":1786954865000},"score":1,"resource":{"primary":{"URL":"https:\/\/febs.onlinelibrary.wiley.com\/doi\/10.1111\/febs.70705"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,17]]},"references-count":50,"alternative-id":["10.1111\/febs.70705"],"URL":"https:\/\/doi.org\/10.1111\/febs.70705","archive":["Portico"],"relation":{},"ISSN":["1742-464X","1742-4658"],"issn-type":[{"value":"1742-464X","type":"print"},{"value":"1742-4658","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,17]]},"assertion":[{"value":"2026-03-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-11","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"febs.70705"}}