{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T06:30:48Z","timestamp":1786516248288,"version":"build-2736575974"},"reference-count":41,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004774","name":"New England Biolabs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004774","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    <jats:italic>Wolbachia pipientis<\/jats:italic>\n                    is a widespread obligate intracellular bacterium and an effective biocontrol agent being deployed in the field against mosquito-borne viral diseases. Investigating the transcriptomic dynamics of\n                    <jats:italic>Wolbachia<\/jats:italic>\n                    within host cells is highly desired but is fundamentally challenged by the overwhelming abundance of eukaryotic host RNA and bacterial ribosomal RNA. Here, we demonstrate that Cappable-seq specifically captures the active, primary transcriptome of\n                    <jats:italic>Wolbachia<\/jats:italic>\n                    while drastically reducing host background. We applied this methodology to monitor\n                    <jats:italic>Wolbachia<\/jats:italic>\n                    gene expression changes over a single host cell passage cycle, tracking the transition from early infection to a high-titer maintenance phase. Differential gene expression analysis identified the upregulation of\n                    <jats:italic>rpoH<\/jats:italic>\n                    transcription factor, stress-response chaperones and WO prophage elements. This was coupled with a continuous downregulation of key host-manipulation effectors, including Ankyrin-repeat domain-containing proteins and secretion systems, alongside the broad suppression of metabolic transporters over the time-course. In addition, we discovered that Cappable-seq concurrently co-enriches the transcripts and genomes from various single-stranded RNA viruses that are known to be present in these mosquito cells. In summary, Cappable-seq technology provides a robust framework to investigate complex, tripartite host-microbe-virus interactions, demonstrating that\n                    <jats:italic>Wolbachia<\/jats:italic>\n                    actively senses and adapts to the dynamic constraints of its intracellular environment by regulating its transcriptome.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1860204","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T05:55:44Z","timestamp":1786514144000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Primary transcript enrichment reveals a density-dependent Wolbachia transcriptome and active mosquito RNA viruses"],"prefix":"10.3389","volume":"17","author":[{"given":"Amit","family":"Sinha","sequence":"first","affiliation":[{"name":"New England Biolabs, Inc.","place":["Ipswich, MA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clotilde K. 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