{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:04:57Z","timestamp":1790082297099,"version":"4.0.1"},"posted":{"date-parts":[[2026,9,17]]},"group-title":"Microbiology","reference-count":40,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["AI140167"],"award-info":[{"award-number":["AI140167"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AI154305"],"award-info":[{"award-number":["AI154305"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AI182210"],"award-info":[{"award-number":["AI182210"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["CA054174"],"award-info":[{"award-number":["CA054174"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["S10OD030311"],"award-info":[{"award-number":["S10OD030311"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The developmental cycle of\n                  <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                  requires coordinated transitions between infectious elementary bodies (EBs) and replicative reticulate bodies (RBs), yet the temporal organization of the underlying transcriptional programs remains incompletely resolved. We performed high-coverage RNA sequencing from 0 to 32 h post-infection (hpi), with closely spaced early sampling, and used unsupervised clustering of temporal expression profiles to identify four coordinated programs: immediate-early host adaptation and developmental program, RB formation and maintenance, RB proliferation and secondary differentiation, and EB formation and invasion. The immediate-early program peaked at 1 hpi and contained a strong representation of inclusion-membrane and intracellular-trafficking genes, together with the developmental regulator gene euo. The RB formation and maintenance program peaked at approximately 3 hpi and sustained expression throughout much of the cycle, encompassing genes that support transcription, translation, and core metabolism. The RB proliferation and secondary differentiation program combined DNA replication and cell-division genes with alternative sigma factors, partner-switching components, and type III secretion apparatus genes, consistent with developmental preparation during proliferation. The EB formation and invasion program contained genes associated with structural maturation, host-cell interaction, and infectious competence. These findings distinguish transient host-adaptation expression from sustained early biosynthetic expression, separate RB establishment from population expansion, and differentiate regulatory preparation for the RB-to-EB transition from later EB maturation. Together, the four programs define partially overlapping transcriptional priorities that provide a framework for investigating how gene expression coordinates chlamydial growth, differentiation, and preparation for the next infection cycle.\n                <\/jats:p>","DOI":"10.64898\/2026.09.15.751914","type":"posted-content","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T03:40:20Z","timestamp":1789702820000},"source":"Crossref","is-referenced-by-count":0,"title":["A Refined Developmental Transcriptomic Landscape Reveals Four Coordinated Programs in\n                  <i>Chlamydia trachomatis<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8262-8173","authenticated-orcid":false,"given":"Danny","family":"Wan","sequence":"first","affiliation":[{"name":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, 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