Xiromerisiou G, Dadouli K, Marogianni C, Provatas A, Ntellas P, Rikos D, et al. A novel homozygous SACS mutation identified by whole exome sequencing-genotype phenotype correlations of all published cases. J Mol Neurosci. 2020;70:131–41.

Article  CAS  PubMed  Google Scholar 

Bagaria J, Bagyinszky E, An SSA. Genetics of autosomal recessive spastic Ataxia of Charlevoix-Saguenay (ARSACS) and role of Sacsin in Neurodegeneration. Int J Mol Sci. 2022;23:552.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Delgado-Morales R, Agís-Balboa RC, Esteller M, Berdasco M. Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders. Clin Epigenetics. 2017;9:67.

Article  PubMed  PubMed Central  Google Scholar 

Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev. 2021;125:503–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. 2013;38:23–38.

Article  CAS  PubMed  Google Scholar 

Greenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019;20:590–607.

Article  CAS  PubMed  Google Scholar 

Greene E, Mahishi L, Entezam A, Kumari D, Usdin K. Repeat-induced epigenetic changes in intron 1 of the frataxin gene and its consequences in Friedreich ataxia. Nucleic Acids Res. 2007;35:3383–90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Castaldo I, Pinelli M, Monticelli A, Acquaviva F, Giacchetti M, Filla A, et al. DNA methylation in intron 1 of the frataxin gene is related to GAA repeat length and age of onset in Friedreich ataxia patients. J Med Genet. 2008;45:808–12.

Article  CAS  PubMed  Google Scholar 

Rodden LN, Chutake YK, Gilliam K, Lam C, Soragni E, Hauser L, et al. Methylated and unmethylated epialleles support variegated epigenetic silencing in Friedreich ataxia. Hum Mol Genet. 2021;29:3818–29.

Article  PubMed  PubMed Central  Google Scholar 

McGrath-Morrow SA, Ndeh R, Helmin KA, Khuder B, Rothblum-Oviatt C, Collaco JM, et al. DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype. Sci Rep. 2020;10:7479.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laffita-Mesa JM, Bauer PO, Kourí V, Serrano LP, Roskams J, Gotay DA, et al. Epigenetics DNA methylation in the core ataxin-2 gene promoter: novel physiological and pathological implications. Hum Genet. 2012;131:625–38.

Article  CAS  PubMed  Google Scholar 

Wang C, Peng H, Li J, Ding D, Chen Z, Long Z, et al. Alteration of methylation status in the ATXN3 gene promoter region is linked to the SCA3/MJD. Neurobiol Aging. 2017;53:e1925–19210.

Article  Google Scholar 

Ding D, Wang C, Chen Z, Xia K, Tang B, Qiu R, et al. Polyglutamine-expanded ataxin3 alter specific gene expressions through changing DNA methylation status in SCA3/MJD. Aging. 2020;13:3680–98.

Article  PubMed  PubMed Central  Google Scholar 

Masliah E, Dumaop W, Galasko D, Desplats P. Distinctive patterns of DNA methylation associated with Parkinson disease: identification of concordant epigenetic changes in brain and peripheral blood leukocytes. Epigenetics. 2013;8:1030–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Di Francesco A, Arosio B, Falconi A, Di Micioni MV, Karimi M, Mari D, et al. Global changes in DNA methylation in Alzheimer’s disease peripheral blood mononuclear cells. Brain Behav Immun. 2015;45:139–44.

Article  PubMed  Google Scholar 

Sun Y, Zhu J, Yang Y, Zhang Z, Zhong H, Zeng G, et al. Identification of candidate DNA methylation biomarkers related to Alzheimer’s disease risk by integrating genome and blood methylome data. Transl Psychiatry. 2023;13:387.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krueger F, Andrews SR, Bismark. A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571–2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013;341:1237905.

Article  PubMed  PubMed Central  Google Scholar 

Park Y, Wu H. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics. 2016;32:1446–53.

Article  CAS  PubMed  Google Scholar 

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:480–4.

Article  Google Scholar 

Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics. 2005;21:3787–93.

Article  CAS  PubMed  Google Scholar 

Acha B, Corroza J, Sanchez-Ruiz De Gordoa J, Cabello C, Robles M, Mendez-Lopez I, et al. Association of blood-based DNA methylation markers with late-onset Alzheimer Disease: a potential Diagnostic Approach. Neurology. 2023;101:e2434–47.

Article  PubMed  PubMed Central  Google Scholar 

Breen C, Papale LA, Clark LR, Bergmann PE, Madrid A, Asthana S, et al. Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late-onset dementia due to Alzheimer’s disease. Alzheimer’s Dement. 2024;20:1050–62.

Article  CAS  Google Scholar 

Mitsumori R, Sakaguchi K, Shigemizu D, Mori T, Akiyama S, Ozaki K, et al. Lower DNA methylation levels in CpG island shores of CR1, CLU, and PICALM in the blood of Japanese Alzheimer’s disease patients. PLoS ONE. 2020;15:e0239196.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20:320–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brenet F, Moh M, Funk P, Feierstein E, Viale AJ, Socci ND, et al. DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS ONE. 2011;6:e14524.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, Dsouza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes Dev. 2003;17:419–37.

Article