{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T13:40:29Z","timestamp":1778334029834,"version":"3.51.4"},"posted":{"date-parts":[[2023,5,9]]},"group-title":"Genomics","reference-count":104,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,5,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization\n                  <jats:sup>1\u20133<\/jats:sup>\n                  . Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (&gt; 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.\n                <\/jats:p>","DOI":"10.1101\/2023.05.07.539762","type":"posted-content","created":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T10:08:10Z","timestamp":1683713290000},"source":"Crossref","is-referenced-by-count":25,"title":["High-resolution spatial multi-omics reveals cell-type specific nuclear compartments"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7226-5185","authenticated-orcid":false,"given":"Yodai","family":"Takei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan","family":"White","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jina","family":"Yun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meera","family":"Prasad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lincoln J","family":"Ombelets","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Schindler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Long","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023051104350929000_2023.05.07.539762v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2016.02.014"},{"key":"2023051104350929000_2023.05.07.539762v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00387-1"},{"key":"2023051104350929000_2023.05.07.539762v1.3","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a041268"},{"key":"2023051104350929000_2023.05.07.539762v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0890-0"},{"key":"2023051104350929000_2023.05.07.539762v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.07.032"},{"key":"2023051104350929000_2023.05.07.539762v1.6","doi-asserted-by":"crossref","unstructured":"Payne, A. 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