{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:52:12Z","timestamp":1782280332054,"version":"3.54.5"},"posted":{"date-parts":[[2025,4,24]]},"group-title":"Genomics","reference-count":93,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T00:00:00Z","timestamp":1745452800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Epigenetic mechanisms, including histones and their post-translational modifications, play a crucial role in regulating programs integral to a cell\u2019s identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells\n                  <jats:italic>in vivo<\/jats:italic>\n                  remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst stem cells (CySCs), the\n                  <jats:italic>Drosophila<\/jats:italic>\n                  testis provides an excellent\n                  <jats:italic>in vivo<\/jats:italic>\n                  model for studying adult stem cells. However, the small number of stem cells and cellular heterogeneity of this tissue have limited comprehensive genomic studies.\n                <\/jats:p>\n                <jats:p>\n                  In this study, we developed cell type-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing of GSC-like and CySC-like cells. Single cell RNA sequencing validated previous findings on GSC-CySC intercellular communication and revealed high expression of chromatin regulators in GSC-like cells. To characterize chromatin landscapes, we developed a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3- enriched regions, corresponding to euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined cell type-specific replication timing profiles, integrating our\n                  <jats:italic>in vivo<\/jats:italic>\n                  datasets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program compared to somatic lineages, that aligns with chromatin state differences. Collectively, our integrated transcriptomic, chromatin, and replication datasets provide a comprehensive framework for understanding genome regulation differences between these\n                  <jats:italic>in vivo<\/jats:italic>\n                  stem cell populations, demonstrating the power of multi-omics in uncovering cell type- specific regulatory features.\n                <\/jats:p>","DOI":"10.1101\/2025.04.19.649648","type":"posted-content","created":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T11:20:29Z","timestamp":1745493629000},"source":"Crossref","is-referenced-by-count":0,"title":["Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of\n                  <i>Drosophila<\/i>\n                  testis tumor stem cell-like cells"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6621-8358","authenticated-orcid":false,"given":"Jennifer A.","family":"Urban","sequence":"first","affiliation":[{"name":"Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2728-3933","authenticated-orcid":false,"given":"Daniel","family":"Ringwalt","sequence":"additional","affiliation":[{"name":"Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9270-6569","authenticated-orcid":false,"given":"John M.","family":"Urban","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Baltimore, MD 21218, USA"},{"name":"Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9076-5829","authenticated-orcid":false,"given":"Wingel","family":"Xue","sequence":"additional","affiliation":[{"name":"Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3859-1390","authenticated-orcid":false,"given":"Ryan","family":"Gleason","sequence":"additional","affiliation":[{"name":"Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keji","family":"Zhao","sequence":"additional","affiliation":[{"name":"Systems Biology Center, National Heart, Lung and Blood Institute, NIH, 10 Center Dr., MSC 1674, Building 10, Room 7B05, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6990-0926","authenticated-orcid":false,"given":"Xin","family":"Chen","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Baltimore, MD 21218, USA"},{"name":"Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041205263198000_2025.04.19.649648v2.1","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/s41592-023-01814-1","article-title":"Comparison of transformations for single-cell RNA-seq data","volume":"20","year":"2023","journal-title":"Nature Methods"},{"key":"2026041205263198000_2025.04.19.649648v2.2","doi-asserted-by":"publisher","DOI":"10.1093\/BIOINFORMATICS\/BTAA1009"},{"key":"2026041205263198000_2025.04.19.649648v2.3","first-page":"176","article-title":"Functions of the Drosophila JAK-STAT pathway: Lessons from stem cells","volume":"1","year":"2012","journal-title":"JAKSTAT"},{"key":"2026041205263198000_2025.04.19.649648v2.4","doi-asserted-by":"crossref","unstructured":"Anderson JT , Henikoff S , Ahmad K . 2023. 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