{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:41Z","timestamp":1792790321217,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,30]]},"group-title":"Molecular Biology","reference-count":53,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["R35GM143532"],"award-info":[{"award-number":["R35GM143532"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01EB036003"],"award-info":[{"award-number":["R01EB036003"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"U.S. National Science Foundation","award":["2041107"],"award-info":[{"award-number":["2041107"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"crossref"}]},{"name":"U.S. National Science Foundation","award":["2236422"],"award-info":[{"award-number":["2236422"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Welch Foundation","award":["C-2240"],"award-info":[{"award-number":["C-2240"]}],"id":[{"id":"https:\/\/ror.org\/00np6vq88","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Transcriptional memory is a phenomenon that allows cells to \u2018remember\u2019 prior stimulatory history, which can alter subsequent gene expression patterns and shape development, immunity, and disease. Although various epigenetic adaptations have been implicated, it remains unclear whether the mechanics of transcription alone are sufficient to install durable memory independently of complex activation and global phenotypic changes induced by inflammatory and environmental stimuli. Here, we employ CRISPR activation (CRISPRa) to uncouple gene activation from global signaling and test whether memory can be established selectively by a local transcriptional pulse in primary mesenchymal stromal cells (MSCs). Key stimulus-responsive genes (\n                  <jats:italic>IDO1, CXCL11<\/jats:italic>\n                  ) remain sensitized for weeks after either IFN\u03b3 exposure or locus-specific CRISPRa perturbations. Histone PTM profiling links this memory to epigenetic hysteresis involving persistent loss of promoter H3K27me3. Single-molecule chromatin mapping by DAF-seq showed that this adaptation does not coincide with gains in promoter accessibility, but suggests it supports increased transcription factor reacquisition in rechallenged cells. Finally, while H3K27me3 loss appears to be a key hallmark of strongly induced memory genes, multi-omic analyses showed that persistent H3K27me3 hysteresis also occurs at a small subset of non-memory genes. Coordination of H3K27me3 hysteresis with additional cis factors therefore likely shapes transcriptional memory in a locus-specific fashion, underscoring the utility of targeted CRISPRa perturbations for dissecting these responses.\n                <\/jats:p>","DOI":"10.64898\/2026.09.29.755468","type":"posted-content","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:00:22Z","timestamp":1790787622000},"source":"Crossref","is-referenced-by-count":0,"title":["Induction of hysteretic chromatin states by CRISPRa reveals locus-specific encoding of transcriptional memory"],"prefix":"10.64898","author":[{"given":"Guy C.","family":"Bedford","sequence":"first","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangrok","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek L.","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of BioSciences, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devika","family":"Dua","sequence":"additional","affiliation":[{"name":"Department of BioSciences, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hakeem","family":"Shitta-Bey","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Beauregard","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew R.","family":"DiNardo","sequence":"additional","affiliation":[{"name":"Global Tuberculosis Program, Division of Global Health, Baylor College of Medicine and Texas Children\u2019s Hospital, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3064-8532","authenticated-orcid":false,"given":"Isaac B.","family":"Hilton","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"},{"name":"Department of BioSciences, Rice University, Houston, TX 77030, United States"},{"name":"Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77030, United States"},{"name":"Rice Synthetic Biology Institute, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Diehl","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Rice University, Houston, TX 77030, United States"},{"name":"Department of Chemistry, Rice University, Houston, TX 77030, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100505400926000_2026.09.29.755468v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41418-023-01200-6"},{"key":"2026100505400926000_2026.09.29.755468v1.2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1146\/annurev-genet-012825-093148","article-title":"Epigenetic Preparation of Future Gene Induction Kinetics","volume":"59","year":"2025","journal-title":"Annual Review of Genetics"},{"key":"2026100505400926000_2026.09.29.755468v1.3","doi-asserted-by":"crossref","first-page":"e2600693123","DOI":"10.1073\/pnas.2600693123","article-title":"Regulation of immune signal integration and memory by inflammation-induced chromosome conformation","volume":"123","year":"2026","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2026100505400926000_2026.09.29.755468v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.09.034"},{"key":"2026100505400926000_2026.09.29.755468v1.5","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA118.006255"},{"key":"2026100505400926000_2026.09.29.755468v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.10.005"},{"key":"2026100505400926000_2026.09.29.755468v1.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1720930115"},{"key":"2026100505400926000_2026.09.29.755468v1.8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0050081"},{"key":"2026100505400926000_2026.09.29.755468v1.9","doi-asserted-by":"crossref","first-page":"eadz6830","DOI":"10.1126\/science.adz6830","article-title":"Distinctive DNA sequence features define epigenetic longevity of inflammatory memory","volume":"391","year":"2026","journal-title":"Science"},{"key":"2026100505400926000_2026.09.29.755468v1.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-020-0285-6"},{"key":"2026100505400926000_2026.09.29.755468v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2012.06.006"},{"key":"2026100505400926000_2026.09.29.755468v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2021.07.001"},{"key":"2026100505400926000_2026.09.29.755468v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/nature24271"},{"key":"2026100505400926000_2026.09.29.755468v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2025.05.002"},{"key":"2026100505400926000_2026.09.29.755468v1.15","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/s41577-025-01132-x","article-title":"Trained immunity in chronic inflammatory diseases and cancer","volume":"25","year":"2025","journal-title":"Nat Rev Immunol"},{"key":"2026100505400926000_2026.09.29.755468v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41584-023-01009-0"},{"key":"2026100505400926000_2026.09.29.755468v1.17","doi-asserted-by":"crossref","unstructured":"L. C. Hinte , D. Castellano-Castillo , A. Ghosh , K. Melrose , E. Gasser , F. No\u00e9 , L. Massier , H. Dong , W. Sun , A. Hoffmann , C. Wolfrum , M. Ryd\u00e9n , N. Mejhert , M. Bl\u00fcher , F. von Meyenn , Adipose tissue retains an epigenetic memory of obesity after weight loss. Nature, 1\u20139 (2024).","DOI":"10.1038\/s41586-024-08165-7"},{"key":"2026100505400926000_2026.09.29.755468v1.18","doi-asserted-by":"crossref","unstructured":"P. Mikulski , S. S. H. Tehrani , A. Kogan , I. Abdul-Zani , E. Shell , L. James , B. J. Ryan , L. E. T. Jansen , Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-\u03b3 signaling. Nat Struct Mol Biol, 1\u201313 (2025).","DOI":"10.1038\/s41594-025-01522-8"},{"key":"2026100505400926000_2026.09.29.755468v1.19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001524"},{"key":"2026100505400926000_2026.09.29.755468v1.20","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1016\/j.cmet.2016.10.008","article-title":"Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity","volume":"24","year":"2016","journal-title":"Cell Metabolism"},{"key":"2026100505400926000_2026.09.29.755468v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(03)00092-3"},{"key":"2026100505400926000_2026.09.29.755468v1.22","doi-asserted-by":"crossref","first-page":"9565","DOI":"10.1038\/s41467-025-65439-y","article-title":"Molecular mechanism of co-transcriptional H3K36 methylation by SETD2","volume":"16","year":"2025","journal-title":"Nat Commun"},{"key":"2026100505400926000_2026.09.29.755468v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.01.052"},{"key":"2026100505400926000_2026.09.29.755468v1.24","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2022112259"},{"key":"2026100505400926000_2026.09.29.755468v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00964-2"},{"key":"2026100505400926000_2026.09.29.755468v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2020.10.012"},{"key":"2026100505400926000_2026.09.29.755468v1.27","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2003-11-3909"},{"key":"2026100505400926000_2026.09.29.755468v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcyt.2015.11.008"},{"key":"2026100505400926000_2026.09.29.755468v1.29","doi-asserted-by":"crossref","first-page":"D1779","DOI":"10.1093\/nar\/gkaf1292","article-title":"The Gene Ontology knowledgebase in 2026","volume":"54","author":"Gene Ontology Consortium","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"2026100505400926000_2026.09.29.755468v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(03)00048-4"},{"key":"2026100505400926000_2026.09.29.755468v1.31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M608451200"},{"key":"2026100505400926000_2026.09.29.755468v1.32","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/cdg619"},{"key":"2026100505400926000_2026.09.29.755468v1.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2005.03.013"},{"key":"2026100505400926000_2026.09.29.755468v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-019-0466-2"},{"key":"2026100505400926000_2026.09.29.755468v1.35","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3274"},{"key":"2026100505400926000_2026.09.29.755468v1.36","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.05.009"},{"key":"2026100505400926000_2026.09.29.755468v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00398-y"},{"key":"2026100505400926000_2026.09.29.755468v1.38","doi-asserted-by":"crossref","unstructured":"E. G. Swanson , Y. Mao , B. J. Mallory , M. R. Vollger , S. C. Bohaczuk , C. B. Oliveira , D. B. Lyon , J. Ranchalis , N. L. Parmalee , B. A. Cohen , J. T. Bennett , A. B. Stergachis , Mapping single-cell diploid chromatin fiber architectures using DAF-seq. Nat Biotechnol, 1\u201312 (2025).","DOI":"10.1038\/s41587-025-02914-3"},{"key":"2026100505400926000_2026.09.29.755468v1.39","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.61965"},{"key":"2026100505400926000_2026.09.29.755468v1.40","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.07.019"},{"key":"2026100505400926000_2026.09.29.755468v1.41","doi-asserted-by":"publisher","DOI":"10.1126\/science.aab2956"},{"key":"2026100505400926000_2026.09.29.755468v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.03.025"},{"key":"2026100505400926000_2026.09.29.755468v1.43","doi-asserted-by":"crossref","first-page":"eaeb0060","DOI":"10.1126\/sciadv.aeb0060","article-title":"Single-cell chromatin state transitions during epigenetic memory formation","volume":"12","year":"2026","journal-title":"Science Advances"},{"key":"2026100505400926000_2026.09.29.755468v1.44","doi-asserted-by":"publisher","DOI":"10.1126\/science.aai8236"},{"key":"2026100505400926000_2026.09.29.755468v1.45","doi-asserted-by":"publisher","DOI":"10.1126\/science.1231382"},{"key":"2026100505400926000_2026.09.29.755468v1.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2011.03.025"},{"key":"2026100505400926000_2026.09.29.755468v1.47","doi-asserted-by":"crossref","unstructured":"T. Cookis , A. Lydecker , P. Sauer , V. Kasinath , E. Nogales , Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications. Nat Struct Mol Biol, 1\u201312 (2025).","DOI":"10.1101\/2024.02.09.579730"},{"key":"2026100505400926000_2026.09.29.755468v1.48","doi-asserted-by":"crossref","unstructured":"J. Jeong , S. Hausmann , H. Dong , K. Szczepski , N. M. Flores , A. Garcia Gonzalez , L. Shi , X. Lu , J. Lempi\u00e4inen , M. Jakab , L. Zeng , T. Chasan , E. Bareke , R. Dong , E. Carlson , R. Padilla , D. Husmann , J. Thompson , G. A. Shipman , E. Zahn , C. A. Barnes , L. F. Khan , L. M. Albertorio-S\u00e1ez , E. Brill , V. U. S. Kumary , M. R. Marunde , D. N. Maryanski , C. C. Szany , B. J. Venters , C. L. Windham , M. E. Nowakowski , I. Czaban , M. Jaremko , M.-C. Keogh , K. Le , M. J. Soth , B. A. Garcia , \u0141. Jaremko , J. Majewski , P. K. Mazur , O. Gozani , NSD2 inhibitors rewire chromatin to treat lung and pancreatic cancers. Nature, 1\u201311 (2025).","DOI":"10.1038\/s41586-025-09299-y"},{"key":"2026100505400926000_2026.09.29.755468v1.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-019-0298-7"},{"key":"2026100505400926000_2026.09.29.755468v1.50","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.08.692984"},{"key":"2026100505400926000_2026.09.29.755468v1.51","doi-asserted-by":"crossref","unstructured":"Z.-S. Chong , S. Ohnishi , K. Yusa , G. J. Wright , Pooled extracellular receptor-ligand interaction screening using CRISPR activation. Genome Biol 19, 205 (2018).","DOI":"10.1186\/s13059-018-1581-3"},{"key":"2026100505400926000_2026.09.29.755468v1.52","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07901-8"},{"key":"2026100505400926000_2026.09.29.755468v1.53","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1089\/crispr.2019.0077","article-title":"A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions","volume":"3","year":"2020","journal-title":"CRISPR J"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.29.755468","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T12:40:28Z","timestamp":1791204028000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.29.755468"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":53,"URL":"https:\/\/doi.org\/10.64898\/2026.09.29.755468","relation":{},"subject":[],"published":{"date-parts":[[2026,9,30]]},"subtype":"preprint"}}