{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T15:03:49Z","timestamp":1790348629762,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,22]]},"group-title":"Molecular Biology","reference-count":81,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["R35GM118051"],"award-info":[{"award-number":["R35GM118051"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>The promoter-proximal pause (PPP), at most metazoan genes, is believed to prime transcriptional activation by release of paused RNAPII into the gene. We tested the pause-release model by abolishing the PPP and monitoring gene activation. An LLM-guided AI discovered that upstream G\u2019s and a G T\/C dinucleotide robustly discriminates pauses from non-pauses. Insertion of G-less sequences into NDRG1 and HSP90AA1 abolished the PPP in an orientation-dependent way, but did not impair activation by hypoxia or heat-shock. Hence pause-release is dispensable for these responses. The 5\u2032 peak of RNAPII detected by ChIP persisted even when pausing, detected by NET-seq was absent. Instead of pausing, these promoter-proximal polymerases may undergo abortive initiation. RNAPII C-terminal domain (CTD) deletion suppresses the PPP and shifts it upstream without affecting sequence-dependent pausing, consistent with promoter-tethering by this IDR. We propose that PPP formation is initiated by G-dependent arrest, and stabilized by multiple factors including CTD-dependent tethering.<\/jats:p>","DOI":"10.64898\/2026.09.18.752771","type":"posted-content","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T10:50:18Z","timestamp":1790074218000},"source":"Crossref","is-referenced-by-count":0,"title":["AI discovery of sequence rules for RNA polymerase II pausing revises the pause-release model of gene activation"],"prefix":"10.64898","author":[{"given":"Nova","family":"Fong","sequence":"first","affiliation":[{"name":"Centre for Mathematical Sciences, Cambridge University, Wilberforce Rd, Cambridge CB3 0WA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Huynh","sequence":"additional","affiliation":[{"name":"Centre for Mathematical Sciences, Cambridge University, Wilberforce Rd, Cambridge CB3 0WA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Erickson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan M.","family":"Sheridan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2929-1377","authenticated-orcid":false,"given":"Srinivas","family":"Ramachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihaela","family":"van der Schaar","sequence":"additional","affiliation":[{"name":"Centre for Mathematical Sciences, Cambridge University, Wilberforce Rd, Cambridge CB3 0WA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Bentley","sequence":"additional","affiliation":[{"name":"Dept. 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