{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T19:09:50Z","timestamp":1793387390646,"version":"4.5.0"},"posted":{"date-parts":[[2026,2,6]]},"group-title":"Cell Biology","reference-count":52,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T00:00:00Z","timestamp":1770336000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Subcellular RNA localization is a fundamental layer of gene regulation, yet its heterogeneity across individual cells remains poorly understood. Here, we introduce the RNA Localization Profiler (RLP), a proximity-based RNA-editing strategy that maps compartment-specific RNAs in living cells. Across the cytoplasm, endoplasmic reticulum (ER), and plasma membrane, RLP identifies robust and highly specific RNA localization programs linked to translation and membrane organization. Single-cell RLP (scRLP) reveals that individual cells harbor roughly 5,000-7,000 cytoplasmic RNAs, with &lt;10% associated with the ER. These measurements uncover pervasive subcellular heterogeneity in RNA localization that is undetectable by bulk assays. Spatial RNA patterns define an orthogonal axis of cell-state identity that is independent of gene expression. For example, ZWINT mRNA relocalizes to the cytoplasm in a cell cycle-dependent manner. These findings establish heterogeneous levels of subcellular RNA localization as a variable dimension of intracellular organization and cell identity.<\/jats:p>","DOI":"10.64898\/2026.02.04.703776","type":"posted-content","created":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T02:00:11Z","timestamp":1770429611000},"source":"Crossref","is-referenced-by-count":1,"title":["Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9255-1544","authenticated-orcid":false,"given":"Xiaojuan","family":"Fan","sequence":"first","affiliation":[{"name":"RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4336-6518","authenticated-orcid":false,"given":"Markus","family":"Hafner","sequence":"additional","affiliation":[{"name":"RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026020911302085000_2026.02.04.703776v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2017.7"},{"key":"2026020911302085000_2026.02.04.703776v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.05.027"},{"key":"2026020911302085000_2026.02.04.703776v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-02021-1"},{"key":"2026020911302085000_2026.02.04.703776v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2025.01.040"},{"key":"2026020911302085000_2026.02.04.703776v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.11.025"},{"key":"2026020911302085000_2026.02.04.703776v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-019-0263-5"},{"key":"2026020911302085000_2026.02.04.703776v1.7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1176488"},{"key":"2026020911302085000_2026.02.04.703776v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/nature06888"},{"key":"2026020911302085000_2026.02.04.703776v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2015.10.005"},{"key":"2026020911302085000_2026.02.04.703776v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.01.044"},{"key":"2026020911302085000_2026.02.04.703776v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.06.036"},{"key":"2026020911302085000_2026.02.04.703776v1.12","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.44752"},{"key":"2026020911302085000_2026.02.04.703776v1.13","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0586-4"},{"key":"2026020911302085000_2026.02.04.703776v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01829-8"},{"key":"2026020911302085000_2026.02.04.703776v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06868-w"},{"key":"2026020911302085000_2026.02.04.703776v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2012.02.036"},{"key":"2026020911302085000_2026.02.04.703776v1.17","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.312280"},{"key":"2026020911302085000_2026.02.04.703776v1.18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1185"},{"key":"2026020911302085000_2026.02.04.703776v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0220-y"},{"key":"2026020911302085000_2026.02.04.703776v1.20","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaa6090"},{"key":"2026020911302085000_2026.02.04.703776v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1049-y"},{"key":"2026020911302085000_2026.02.04.703776v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.03.007"},{"key":"2026020911302085000_2026.02.04.703776v1.23","doi-asserted-by":"crossref","first-page":"20709","DOI":"10.1016\/S0021-9258(19)36836-X","article-title":"The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase","volume":"268","year":"1993","journal-title":"J Biol Chem"},{"key":"2026020911302085000_2026.02.04.703776v1.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2021.12.038"},{"key":"2026020911302085000_2026.02.04.703776v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01128-0"},{"key":"2026020911302085000_2026.02.04.703776v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-45009-4"},{"key":"2026020911302085000_2026.02.04.703776v1.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01587-6"},{"key":"2026020911302085000_2026.02.04.703776v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81517-2"},{"key":"2026020911302085000_2026.02.04.703776v1.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.03.009"},{"key":"2026020911302085000_2026.02.04.703776v1.30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1912459116"},{"key":"2026020911302085000_2026.02.04.703776v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.05.001"},{"key":"2026020911302085000_2026.02.04.703776v1.32","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf277"},{"key":"2026020911302085000_2026.02.04.703776v1.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2023.09.001"},{"key":"2026020911302085000_2026.02.04.703776v1.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2020.10.006"},{"key":"2026020911302085000_2026.02.04.703776v1.35","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.200667"},{"key":"2026020911302085000_2026.02.04.703776v1.36","doi-asserted-by":"publisher","DOI":"10.1161\/01.RES.83.6.629"},{"key":"2026020911302085000_2026.02.04.703776v1.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2023.168384"},{"key":"2026020911302085000_2026.02.04.703776v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109407"},{"key":"2026020911302085000_2026.02.04.703776v1.39","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.01.043"},{"key":"2026020911302085000_2026.02.04.703776v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2014.006"},{"key":"2026020911302085000_2026.02.04.703776v1.41","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M407588200"},{"key":"2026020911302085000_2026.02.04.703776v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2017.08.018"},{"key":"2026020911302085000_2026.02.04.703776v1.43","doi-asserted-by":"publisher","DOI":"10.1101\/gad.247361.114"},{"key":"2026020911302085000_2026.02.04.703776v1.44","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.10288"},{"key":"2026020911302085000_2026.02.04.703776v1.45","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2021.12.010"},{"key":"2026020911302085000_2026.02.04.703776v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3179"},{"key":"2026020911302085000_2026.02.04.703776v1.47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab011"},{"key":"2026020911302085000_2026.02.04.703776v1.48","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004"},{"key":"2026020911302085000_2026.02.04.703776v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2017.04.042"},{"key":"2026020911302085000_2026.02.04.703776v1.50","doi-asserted-by":"publisher","DOI":"10.1101\/2022.04.08.487609"},{"key":"2026020911302085000_2026.02.04.703776v1.51","doi-asserted-by":"publisher","DOI":"10.1261\/rna.073239.119"},{"key":"2026020911302085000_2026.02.04.703776v1.52","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac835"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.02.04.703776","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T19:30:30Z","timestamp":1770665430000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.02.04.703776"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,6]]},"references-count":52,"URL":"https:\/\/doi.org\/10.64898\/2026.02.04.703776","relation":{},"subject":[],"published":{"date-parts":[[2026,2,6]]},"subtype":"preprint"}}