{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T14:38:47Z","timestamp":1788446327526,"version":"build-2803163510"},"reference-count":42,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:00:00Z","timestamp":1746662400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Rett syndrome (RTT) is a rare X-linked dominant neurodevelopmental disorder caused by pathogenic variants in the methyl-CpG-binding protein 2 (MECP2) gene, which encodes a methyl-CpG-binding protein (MeCP2) that acts as a repressor of gene expression, crucial in neurons. Dysfunction of MeCP2 due to its pathogenic variants explains the clinical features of RTT. Here, we performed histological and RNA analyses on a post-mortem brain sample from an RTT patient carrying the p.Arg106Trp missense mutation. This patient is part of a cohort of 56 genetically and clinically characterized RTT patients, for whom we provide an overview of the mutation landscape. In the RTT brain specimen, RT-PCR analysis detected preferential transcription of the mutated mRNA. X-inactivation studies revealed a skewed X-chromosome inactivation ratio (95:5), supporting the transcriptional findings. We also mapped the MECP2 transcript in control human brain regions (temporal cortex and cerebellum) using the RNAscope assay, confirming its high expression. This study reports the MECP2 transcript representation in a post-mortem RTT brain and, for the first time, the in situ MECP2 transcript localization in a human control brain, offering insights into how specific MECP2 mutations may differentially impact neuronal functions. We suggest these findings are crucial for developing RNA-based therapies for Rett syndrome.<\/jats:p>","DOI":"10.3390\/biom15050687","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T07:41:47Z","timestamp":1746690107000},"page":"687","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["MECP2 mRNA Profile in Brain Tissues from a Rett Syndrome Patient and Three Human Controls: Mutated Allele Preferential Transcription and In Situ RNA Mapping"],"prefix":"10.3390","volume":"15","author":[{"given":"Martina","family":"Mietto","sequence":"first","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3189-9353","authenticated-orcid":false,"given":"Silvia","family":"Montanari","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5619-628X","authenticated-orcid":false,"given":"Maria Sofia","family":"Falzarano","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Manzati","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Rimessi","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Fabris","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3099-0100","authenticated-orcid":false,"given":"Rita","family":"Selvatici","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9551-057X","authenticated-orcid":false,"given":"Francesca","family":"Gualandi","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6133-9831","authenticated-orcid":false,"given":"Marcella","family":"Neri","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0232-196X","authenticated-orcid":false,"given":"Fernanda","family":"Fortunato","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0335-5862","authenticated-orcid":false,"given":"Miryam Rosa Stella","family":"Foti","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefania","family":"Bigoni","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Gessi","sequence":"additional","affiliation":[{"name":"Pathology Institute, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5495-9183","authenticated-orcid":false,"given":"Marcella","family":"Vacca","sequence":"additional","affiliation":[{"name":"Institute of Genetics and Biophysics \u201cA. Buzzati-Traverso\u201d, CNR, 80131 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8840-6835","authenticated-orcid":false,"given":"Silvia","family":"Torelli","sequence":"additional","affiliation":[{"name":"The Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London WC1E 6BT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joussef","family":"Hayek","sequence":"additional","affiliation":[{"name":"Child Neuropsychiatry Unit, University Hospital, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8385-9870","authenticated-orcid":false,"given":"Alessandra","family":"Ferlini","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Kyle, S.M., Vashi, N., and Justice, M.J. (2018). Rett syndrome: A neurological disorder with metabolic components. Open Biol., 8.","DOI":"10.1098\/rsob.170216"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/brain\/awy323","article-title":"Towards a better diagnosis and treatment of Rett syndrome: A model synaptic disorder","volume":"142","author":"Banerjee","year":"2019","journal-title":"Brain"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Bin Akhtar, G., Buist, M., and Rastegar, M. (2022). MeCP2 and transcriptional control of eukaryotic gene expression. Eur. J. Cell Biol., 101.","DOI":"10.1016\/j.ejcb.2022.151237"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Vidal, S., Xiol, C., Pascual-Alonso, A., O\u2019Callaghan, M., Pineda, M., and Armstrong, J. (2019). Genetic Landscape of Rett Syndrome Spectrum: Improvements and Challenges. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20163925"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Pejhan, S., and Rastegar, M. (2021). Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease. Biomolecules, 11.","DOI":"10.3390\/biom11010075"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s12017-014-8295-9","article-title":"Rett syndrome and MeCP2","volume":"16","author":"Liyanage","year":"2014","journal-title":"Neuromol. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1016\/j.neuron.2024.11.006","article-title":"Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis","volume":"113","author":"Bajikar","year":"2025","journal-title":"Neuron"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e2312757121","DOI":"10.1073\/pnas.2312757121","article-title":"Variable expression of MECP2, CDKL5, and FMR1 in the human brain: Implications for gene restorative therapies","volume":"121","author":"Zito","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.neubiorev.2021.07.014","article-title":"The neuropathology of autism: A systematic review of post-mortem studies of autism and related disorders","volume":"129","author":"Fetit","year":"2021","journal-title":"Neurosci. Biobehav. Rev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1111\/nan.12619","article-title":"Differential brain region-specific expression of MeCP2 and BDNF in Rett Syndrome patients: A distinct grey-white matter variation","volume":"46","author":"Pejhan","year":"2020","journal-title":"Neuropathol. Appl. Neurobiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1002\/ana.22124","article-title":"Rett syndrome: Revised diagnostic criteria and nomenclature","volume":"68","author":"Neul","year":"2010","journal-title":"Ann. Neurol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S246","DOI":"10.1016\/S0387-7604(01)00343-6","article-title":"MECP2 gene mutation analysis in the British and Italian Rett Syndrome patients: Hot spot map of the most recurrent mutations and bioinformatic analysis of a new MECP2 conserved region","volume":"23","author":"Vacca","year":"2001","journal-title":"Brain Dev."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Brioschi, S., Gualandi, F., Scotton, C., Armaroli, A., Bovolenta, M., Falzarano, M.S., Sabatelli, P., Selvatici, R., D\u2019Amico, A., and Pane, M. (2012). Genetic characterization in symptomatic female DMD carriers: Lack of relationship between X-inactivation, transcriptional DMD allele balancing and phenotype. BMC Med. Genet., 13.","DOI":"10.1186\/1471-2350-13-73"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/0003-2697(87)90021-2","article-title":"Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction","volume":"162","author":"Chomczynski","year":"1987","journal-title":"Anal. Biochem."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Pepe, G., Fioriniello, S., Marracino, F., Capocci, L., Maglione, V., D\u2019Esposito, M., Di Pardo, A., and Della Ragione, F. (2023). Blood-Brain Barrier Integrity Is Perturbed in a Mecp2-Null Mouse Model of Rett Syndrome. Biomolecules, 13.","DOI":"10.3390\/biom13040606"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/hmg\/ddad150","article-title":"MeCP2 ubiquitination and sumoylation, in search of a function","volume":"33","author":"Kalani","year":"2023","journal-title":"Hum. Mol. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1038\/s41572-024-00568-0","article-title":"Rett syndrome","volume":"10","author":"Gold","year":"2024","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Pejhan, S., Del Bigio, M.R., and Rastegar, M. (2020). The MeCP2E1\/E2-BDNF-miR132 Homeostasis Regulatory Network Is Region-Dependent in the Human Brain and Is Impaired in Rett Syndrome Patients. Front. Cell Dev. Biol., 8.","DOI":"10.3389\/fcell.2020.00763"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2679","DOI":"10.1093\/hmg\/ddh282","article-title":"Mild overexpression of MeCP2 causes a progressive neurological disorder in mice","volume":"13","author":"Collins","year":"2004","journal-title":"Hum. Mol. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s00412-016-0591-8","article-title":"Post-translational modifications of the intrinsically disordered terminal domains of histone H1: Effects on secondary structure and chromatin dynamics","volume":"126","author":"Roque","year":"2017","journal-title":"Chromosoma"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Schmidt, A., Zhang, H., and Cardoso, M.C. (2020). MeCP2 and Chromatin Compartmentalization. Cells, 9.","DOI":"10.3390\/cells9040878"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Claveria-Gimeno, R., Lanuza, P.M., Morales-Chueca, I., Jorge-Torres, O.C., Vega, S., Abian, O., Esteller, M., and Velazquez-Campoy, A. (2017). The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site. Sci. Rep., 7.","DOI":"10.1038\/srep41635"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"20523","DOI":"10.1074\/jbc.M803021200","article-title":"Rett syndrome-causing mutations in human MeCP2 result in diverse structural changes that impact folding and DNA interactions","volume":"283","author":"Ghosh","year":"2008","journal-title":"J. Biol. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Ortega-Alarcon, D., Claveria-Gimeno, R., Vega, S., Jorge-Torres, O.C., Esteller, M., Abian, O., and Velazquez-Campoy, A. (2020). Molecular Context-Dependent Effects Induced by Rett Syndrome-Associated Mutations in MeCP2. Biomolecules, 10.","DOI":"10.3390\/biom10111533"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Bueno, C., Tabares-Seisdedos, R., Moraleda, J.M., and Martinez, S. (2016). Rett Syndrome Mutant Neural Cells Lacks MeCP2 Immunoreactive Bands. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0153262"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/B978-0-444-64189-2.00015-9","article-title":"Epigenetic cerebellar diseases","volume":"155","author":"Serrano","year":"2018","journal-title":"Handb. Clin. Neurol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"113559","DOI":"10.1016\/j.celrep.2023.113559","article-title":"Purkinje-cell-specific MeCP2 deficiency leads to motor deficits and autistic-like behavior due to aberrations in PTP1B-TrkB-SK signaling","volume":"42","author":"Xu","year":"2023","journal-title":"Cell Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/s41597-020-0527-2","article-title":"Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain","volume":"7","author":"Aldinger","year":"2020","journal-title":"Sci. Data"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1002\/ajmg.10557","article-title":"Balanced X chromosome inactivation patterns in the Rett syndrome brain","volume":"111","author":"Shahbazian","year":"2002","journal-title":"Am. J. Med. Genet."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.braindev.2004.07.002","article-title":"X chromosome inactivation patterns in brain in Rett syndrome: Implications for the disease phenotype","volume":"27","author":"Gibson","year":"2005","journal-title":"Brain Dev."},{"key":"ref_31","unstructured":"Xiol, C., Vidal, S., Pascual-Alonso, A., Blasco, L., Brandi, N., Pacheco, P., Gerotina, E., O\u2019Callaghan, M., Pineda, M., and Armstrong, J. (2019). X chromosome inactivation does not necessarily determine the severity of the phenotype in Rett syndrome patients. Sci. Rep., 9."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1126\/science.1068663","article-title":"Genetics. Do X chromosomes set boundaries?","volume":"295","author":"Percec","year":"2002","journal-title":"Science"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"129","DOI":"10.2174\/138920207780368141","article-title":"The Human Pseudoautosomal Region (PAR): Origin, Function and Future","volume":"8","author":"Morris","year":"2007","journal-title":"Curr. Genom."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1016\/j.gendis.2022.04.007","article-title":"Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities","volume":"9","author":"Li","year":"2022","journal-title":"Genes Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/S1097-2765(00)80248-8","article-title":"A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation","volume":"5","author":"Wutz","year":"2000","journal-title":"Mol. Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"6634","DOI":"10.1073\/pnas.97.12.6634","article-title":"Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis","volume":"97","author":"Bailey","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1146\/annurev.genet.35.102401.091032","article-title":"Biology of mammalian L1 retrotransposons","volume":"35","author":"Ostertag","year":"2001","journal-title":"Annu. Rev. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nature09544","article-title":"L1 retrotransposition in neurons is modulated by MeCP2","volume":"468","author":"Muotri","year":"2010","journal-title":"Nature"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/cr.2018.8","article-title":"Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders","volume":"28","author":"Eyal","year":"2018","journal-title":"Cell Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/s41583-018-0006-3","article-title":"Rett syndrome: Insights into genetic, molecular and circuit mechanisms","volume":"19","author":"Ip","year":"2018","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1007\/s001090000155","article-title":"Mutation analysis of the MECP2 gene in British and Italian Rett syndrome females","volume":"78","author":"Vacca","year":"2001","journal-title":"J. Mol. Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4490","DOI":"10.1073\/pnas.90.10.4490","article-title":"The retroviral oncogene qin belongs to the transcription factor family that includes the homeotic gene fork head","volume":"90","author":"Li","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/5\/687\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:29:30Z","timestamp":1760030970000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/5\/687"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,8]]},"references-count":42,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["biom15050687"],"URL":"https:\/\/doi.org\/10.3390\/biom15050687","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,8]]}}}