{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:41Z","timestamp":1792790321094,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,29]]},"group-title":"Molecular Biology","reference-count":68,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"National Institute of General Medical Sciences","award":["R35GM149216"],"award-info":[{"award-number":["R35GM149216"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of Neurological Disorders and Stroke","award":["R01NS132935"],"award-info":[{"award-number":["R01NS132935"]}],"id":[{"id":"https:\/\/ror.org\/01s5ya894","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Fragile X Syndrome (FXS) is a neuro-developmental disorder caused by a CGG expansion in\n                  <jats:italic>FMR1<\/jats:italic>\n                  , leading to transcriptional silencing and loss of the encoded protein FMRP. Surprisingly, \u223c70% of FXS individuals express\n                  <jats:italic>FMR1<\/jats:italic>\n                  , but the RNA is mis-spliced to isoform\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  , composed of exon 1 spliced to a pseudo-exon in intron 1 and cannot produce FMRP. Splice-switching ASOs rescue proper\n                  <jats:italic>FMR1<\/jats:italic>\n                  splicing and restore FMRP.\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  mis-splicing increases with CGG repeat length and is negatively correlated with patient IQ.\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  is associated with ribosome footprints, indicating it is translated into a polypeptide that may impair cognition. R-loops form at the\n                  <jats:italic>FMR1<\/jats:italic>\n                  locus and extend into the pseudo-exon, but splice-switching ASOs reduce\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  and elevate FMRP independently of R-loop formation. DRB-based transcription analysis identified impaired Pol II elongation at the 5\u2019 region of\n                  <jats:italic>FMR1<\/jats:italic>\n                  in FXS cells, indicated by accumulation of hypophosphorylated Pol II at the transcription start site. Consistent with this, camptothecin-induced Pol II stalling increased\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  pseudo-exon inclusion. The splicing factors PTBP1 and PTBP2 regulate\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  splicing in a differentiation stage-dependent manner. Together, these findings indicate that\n                  <jats:italic>FMR1-217<\/jats:italic>\n                  mis-splicing in FXS is associated with CGG repeat expansion, R-loop formation, impaired co-transcriptional Pol II elongation and context-dependent regulation by PTBP1\/PTBP2.\n                <\/jats:p>","DOI":"10.64898\/2026.09.28.754997","type":"posted-content","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T08:30:21Z","timestamp":1790670621000},"source":"Crossref","is-referenced-by-count":1,"title":["Dysregulation of\n                  <i>FMR1<\/i>\n                  Splicing in Human Fragile X Syndrome"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4014-0337","authenticated-orcid":false,"given":"Suna","family":"Jung","sequence":"first","affiliation":[{"name":"Program in Molecular Medicine University of Massachusetts Chan Medical School Worcester, MA 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2753-2501","authenticated-orcid":false,"given":"Joel D.","family":"Richter","sequence":"additional","affiliation":[{"name":"Program in Molecular Medicine University of Massachusetts Chan Medical School Worcester, MA 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100107350728000_2026.09.28.754997v1.1","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1007\/s11940-019-0551-8","article-title":"New Therapeutic Options for Fragile X Syndrome","volume":"21","year":"2019","journal-title":"Curr Treat Options Neurol"},{"key":"2026100107350728000_2026.09.28.754997v1.2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002417"},{"key":"2026100107350728000_2026.09.28.754997v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.07.033"},{"key":"2026100107350728000_2026.09.28.754997v1.4","first-page":"12","article-title":"Neuron-specific regulation of class I PI3K catalytic subunits and their dysfunction in brain disorders","volume":"7","year":"2014","journal-title":"Front Mol Neurosci"},{"key":"2026100107350728000_2026.09.28.754997v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aam8572"},{"key":"2026100107350728000_2026.09.28.754997v1.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.122205699"},{"key":"2026100107350728000_2026.09.28.754997v1.7","doi-asserted-by":"crossref","first-page":"R298","DOI":"10.1016\/j.cub.2017.03.011","article-title":"Neural Circuits: Reduced Inhibition in Fragile X Syndrome","volume":"27","year":"2017","journal-title":"Curr Biol"},{"key":"2026100107350728000_2026.09.28.754997v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbd.2019.01.002"},{"key":"2026100107350728000_2026.09.28.754997v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.11.019"},{"key":"2026100107350728000_2026.09.28.754997v1.10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2302534120"},{"key":"2026100107350728000_2026.09.28.754997v1.11","doi-asserted-by":"publisher","DOI":"10.1002\/mds.21359"},{"key":"2026100107350728000_2026.09.28.754997v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.conb.2021.11.006"},{"key":"2026100107350728000_2026.09.28.754997v1.13","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac626"},{"key":"2026100107350728000_2026.09.28.754997v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1666"},{"key":"2026100107350728000_2026.09.28.754997v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb1135"},{"key":"2026100107350728000_2026.09.28.754997v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-020-0590-1"},{"key":"2026100107350728000_2026.09.28.754997v1.17","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2350710"},{"key":"2026100107350728000_2026.09.28.754997v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-019-0159-1"},{"key":"2026100107350728000_2026.09.28.754997v1.19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004318"},{"key":"2026100107350728000_2026.09.28.754997v1.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.04.035"},{"key":"2026100107350728000_2026.09.28.754997v1.21","doi-asserted-by":"crossref","unstructured":"Yamakawa, T. and Itakura, K . (2019) Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells. J Vis Exp.","DOI":"10.3791\/59375-v"},{"key":"2026100107350728000_2026.09.28.754997v1.22","doi-asserted-by":"publisher","DOI":"10.1126\/science.abq5622"},{"key":"2026100107350728000_2026.09.28.754997v1.23","doi-asserted-by":"publisher","DOI":"10.1126\/science.ado2403"},{"key":"2026100107350728000_2026.09.28.754997v1.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2015.11.013"},{"key":"2026100107350728000_2026.09.28.754997v1.25","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-6714-x"},{"key":"2026100107350728000_2026.09.28.754997v1.26","doi-asserted-by":"publisher","DOI":"10.1126\/science.1260793"},{"key":"2026100107350728000_2026.09.28.754997v1.27","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-3578-9_16"},{"key":"2026100107350728000_2026.09.28.754997v1.28","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy096"},{"key":"2026100107350728000_2026.09.28.754997v1.29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku406"},{"key":"2026100107350728000_2026.09.28.754997v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab702"},{"key":"2026100107350728000_2026.09.28.754997v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38273-3"},{"key":"2026100107350728000_2026.09.28.754997v1.32","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.50"},{"key":"2026100107350728000_2026.09.28.754997v1.33","doi-asserted-by":"publisher","DOI":"10.1021\/bi034909g"},{"key":"2026100107350728000_2026.09.28.754997v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-022-01164-9"},{"key":"2026100107350728000_2026.09.28.754997v1.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.105307"},{"key":"2026100107350728000_2026.09.28.754997v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms15025"},{"key":"2026100107350728000_2026.09.28.754997v1.37","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2009161117"},{"key":"2026100107350728000_2026.09.28.754997v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.02.076"},{"key":"2026100107350728000_2026.09.28.754997v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09553-8"},{"key":"2026100107350728000_2026.09.28.754997v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3525"},{"key":"2026100107350728000_2026.09.28.754997v1.41","doi-asserted-by":"publisher","DOI":"10.1101\/gad.325142.119"},{"key":"2026100107350728000_2026.09.28.754997v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3293"},{"key":"2026100107350728000_2026.09.28.754997v1.43","doi-asserted-by":"publisher","DOI":"10.1101\/gr.111070.110"},{"key":"2026100107350728000_2026.09.28.754997v1.44","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2008.06.028"},{"key":"2026100107350728000_2026.09.28.754997v1.45","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.08.071"},{"key":"2026100107350728000_2026.09.28.754997v1.46","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx901"},{"key":"2026100107350728000_2026.09.28.754997v1.47","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELREP.2016.11.034"},{"key":"2026100107350728000_2026.09.28.754997v1.48","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22098-z"},{"key":"2026100107350728000_2026.09.28.754997v1.49","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1016\/j.bbagrm.2017.08.007","article-title":"Altered expression of the FMR1 splicing variants landscape in premutation carriers","volume":"1860","year":"2017","journal-title":"Biochim Biophys Acta Gene Regul Mech"},{"key":"2026100107350728000_2026.09.28.754997v1.50","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.03.040"},{"key":"2026100107350728000_2026.09.28.754997v1.51","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddu586"},{"key":"2026100107350728000_2026.09.28.754997v1.52","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/s41598-017-01175-8","article-title":"The tandem Agenet domain of fragile X mental retardation protein interacts with FUS","volume":"7","year":"2017","journal-title":"Sci Rep"},{"key":"2026100107350728000_2026.09.28.754997v1.53","doi-asserted-by":"crossref","unstructured":"Zhang, B. , Li, S.L. , Zhu, X. , Yang, C.S. , Liu, Y. , He, X. , Zhou, P. , Feng, T. , Chen, L. , Liu, Y. et al. (2025) The stability and unfolding of DNA: RNA hybrid G-quadruplexes. Nucleic Acids Res, 53.","DOI":"10.1093\/nar\/gkaf1182"},{"key":"2026100107350728000_2026.09.28.754997v1.54","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1809588115"},{"key":"2026100107350728000_2026.09.28.754997v1.55","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004294"},{"key":"2026100107350728000_2026.09.28.754997v1.56","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.118.301672"},{"key":"2026100107350728000_2026.09.28.754997v1.57","doi-asserted-by":"crossref","unstructured":"Karati, S. , Rawat, S. , Kumari, A.P. , Das, S. , Shukla, S. and Kumar, A . (2026) The Tale of the Guanosine Tract in Repeat Expansion Disorders. Mol Neurobiol, 63.","DOI":"10.1007\/s12035-026-05735-w"},{"key":"2026100107350728000_2026.09.28.754997v1.58","first-page":"4691","article-title":"The CGG triplet repeat binding protein 1 counteracts R-loop induced transcription-replication stress","volume":"26","year":"2025","journal-title":"EMBO Rep"},{"key":"2026100107350728000_2026.09.28.754997v1.59","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2007.06.098"},{"key":"2026100107350728000_2026.09.28.754997v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-025-02263-6"},{"key":"2026100107350728000_2026.09.28.754997v1.61","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddh053"},{"key":"2026100107350728000_2026.09.28.754997v1.62","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M110.194035"},{"key":"2026100107350728000_2026.09.28.754997v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1691"},{"key":"2026100107350728000_2026.09.28.754997v1.64","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2021.03.011"},{"key":"2026100107350728000_2026.09.28.754997v1.65","doi-asserted-by":"publisher","DOI":"10.1261\/rna.041442.113"},{"key":"2026100107350728000_2026.09.28.754997v1.66","doi-asserted-by":"publisher","DOI":"10.3390\/ijms141122906"},{"key":"2026100107350728000_2026.09.28.754997v1.67","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-007-7378-2"},{"key":"2026100107350728000_2026.09.28.754997v1.68","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2009.12.003"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.28.754997","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T14:35:21Z","timestamp":1790865321000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.28.754997"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,29]]},"references-count":68,"URL":"https:\/\/doi.org\/10.64898\/2026.09.28.754997","relation":{},"subject":[],"published":{"date-parts":[[2026,9,29]]},"subtype":"preprint"}}