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It is made of 10 subunits organized in core-TFIIH and CAK sub-complexes bridged by XPD. Pathogenic variants in the ERCC2\/XPD gene give rise to xeroderma pigmentosum (XP) or trichothiodystrophy (TTD), two distinct clinical entities with opposite skin cancer proneness. Here, we show that TTD variants cause a partial dissociation of the CAK from the chromatin and from the core-TFIIH. Mass spectrometry analysis reveals that the chromatin-bound CAK, as a\u00a0component of the entire TFIIH, participates in a protein assembly containing the RNA-binding proteins DDX1, SFPQ, NONO\u00a0as well as RNA polymerase II (Pol II). Gene silencing experiments demonstrate that the protein assembly is required to process the DNA:RNA hybrids formed during Pol II extension and to protect the cell from transcriptional stress. TTD-specific variants in ERCC2\/XPD result in TFIIH instability, altered interaction of the CAK with DDX1-SFPQ-NONO, and R-loop\u00a0accumulation. Therefore, the limited amount of TFIIH that distinguishes TTD from XP gives rise to transcriptional stress and extensive gene expression deregulations, thus accounting for the wide spectrum of TTD clinical features.<\/jats:p>","DOI":"10.1093\/nar\/gkaf745","type":"journal-article","created":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T10:25:47Z","timestamp":1754303147000},"source":"Crossref","is-referenced-by-count":5,"title":["Trichothiodystrophy-causative pathogenic variants impair a cooperative action of TFIIH and DDX1 in R-loop processing"],"prefix":"10.1093","volume":"53","author":[{"given":"Debora","family":"Ferri","sequence":"first","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]},{"name":"Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) , Illkirch Cedex 67404 Strasbourg ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Branca","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0456-1134","authenticated-orcid":false,"given":"Manuela","family":"Lanzafame","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica","family":"Gandolfi","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7686-4230","authenticated-orcid":false,"given":"Valentina","family":"Riva","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8092-1552","authenticated-orcid":false,"given":"Giovanni","family":"Maga","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiziana","family":"Nardo","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0410-8038","authenticated-orcid":false,"given":"Claudia","family":"Landi","sequence":"additional","affiliation":[{"name":"University of Siena Department of Life Sciences, , 53100 Siena ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Bini","sequence":"additional","affiliation":[{"name":"University of Siena Department of Life Sciences, , 53100 Siena ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lavinia","family":"Arseni","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiorenzo\u00a0A","family":"Peverali","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. Cavalli Sforza, CNR , 27100 Pavia ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Compe","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC) , Illkirch Cedex 67404 Strasbourg ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3830-3408","authenticated-orcid":false,"given":"Donata","family":"Orioli","sequence":"additional","affiliation":[{"name":"Istituto di Genetica Molecolare (IGM) L.L. 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