Percy AK, Lane JB. Rett syndrome: model of neurodevelopmental disorders. J Child Neurol. 2005;20:718–21.
Article
PubMed
Google Scholar
Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet. 1999;23:185–8.
Article
CAS
PubMed
Google Scholar
Cuddapah VA, Pillai RB, Shekar KV, Lane JB, Motil KJ, Skinner SA, Tarquinio DC, Glaze DG, McGwin G, Kaufmann WE, et al. Methyl-CpG-binding protein 2 (MECP2) mutation type is associated with disease severity in Rett syndrome. J Med Genet. 2014;51:152–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chahrour M, Jung SY, Shaw C, Zhou X, Wong ST, Qin J, Zoghbi HY. MeCP2, a key contributor to neurological disease, activates and represses transcription. Science. 2008;320:1224–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, Lasalle JM. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A. 2007;104:19416–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet. 2005;37:31–40.
Article
CAS
PubMed
Google Scholar
Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY. Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci U S A. 2005;102:17551–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghosh RP, Horowitz-Scherer RA, Nikitina T, Shlyakhtenko LS, Woodcock CL. MeCP2 binds cooperatively to its substrate and competes with histone H1 for chromatin binding sites. Mol Cell Biol. 2010;30:4656–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li R, Dong Q, Yuan X, Zeng X, Gao Y, Chiao C, Li H, Zhao X, Keles S, Wang Z, Chang Q. Misregulation of alternative splicing in a mouse model of Rett syndrome. PLoS Genet. 2016;12:e1006129.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jung BP, Jugloff DG, Zhang G, Logan R, Brown S, Eubanks JH. The expression of methyl CpG binding factor MeCP2 correlates with cellular differentiation in the developing rat brain and in cultured cells. J Neurobiol. 2003;55:86–96.
Article
CAS
PubMed
Google Scholar
Zachariah RM, Olson CO, Ezeonwuka C, Rastegar M. Novel MeCP2 isoform-specific antibody reveals the endogenous MeCP2E1 expression in murine brain, primary neurons and astrocytes. PLoS One. 2012;7:e49763.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kishi N, Macklis JD. MECP2 is progressively expressed in post-migratory neurons and is involved in neuronal maturation rather than cell fate decisions. Mol Cell Neurosci. 2004;27:306–21.
Article
CAS
PubMed
Google Scholar
Skene PJ, Illingworth RS, Webb S, Kerr AR, James KD, Turner DJ, Andrews R, Bird AP. Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell. 2010;37:457–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ballas N, Lioy DT, Grunseich C, Mandel G. Non-cell autonomous influence of MeCP2-deficient glia on neuronal dendritic morphology. Nat Neurosci. 2009;12:311–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maezawa I, Swanberg S, Harvey D, LaSalle JM, Jin LW. Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions. J Neurosci. 2009;29:5051–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Derecki NC, Cronk JC, Lu Z, Xu E, Abbott SB, Guyenet PG, Kipnis J. Wild-type microglia arrest pathology in a mouse model of Rett syndrome. Nature. 2012;484:105–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen MV, Felice CA, Du F, Covey MV, Robinson JK, Mandel G, Ballas N. Oligodendrocyte lineage cells contribute unique features to Rett syndrome neuropathology. J Neurosci. 2013;33:18764–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lioy DT, Garg SK, Monaghan CE, Raber J, Foust KD, Kaspar BK, Hirrlinger PG, Kirchhoff F, Bissonnette JM, Ballas N, Mandel G. A role for glia in the progression of Rett’s syndrome. Nature. 2011;475:497–500.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J. Gene expression profiling in postmortem Rett syndrome brain: differential gene expression and patient classification. Neurobiol Dis. 2001;8:847–65.
Article
CAS
PubMed
Google Scholar
Tudor M, Akbarian S, Chen RZ, Jaenisch R. Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci U S A. 2002;99:15536–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nuber UA, Kriaucionis S, Roloff TC, Guy J, Selfridge J, Steinhoff C, Schulz R, Lipkowitz B, Ropers HH, Holmes MC, Bird A. Up-regulation of glucocorticoid-regulated genes in a mouse model of Rett syndrome. Hum Mol Genet. 2005;14:2247–56.
Article
CAS
PubMed
Google Scholar
Peddada S, Yasui DH, LaSalle JM. Inhibitors of differentiation (ID1, ID2, ID3 and ID4) genes are neuronal targets of MeCP2 that are elevated in Rett syndrome. Hum Mol Genet. 2006;15:2003–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jordan C, Li HH, Kwan HC, Francke U. Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets. BMC Med Genet. 2007;8:36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Urdinguio RG, Lopez-Serra L, Lopez-Nieva P, Alaminos M, Diaz-Uriarte R, Fernandez AF, Esteller M. Mecp2-null mice provide new neuronal targets for Rett syndrome. PLoS One. 2008;3:e3669.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ben-Shachar S, Chahrour M, Thaller C, Shaw CA, Zoghbi HY. Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus. Hum Mol Genet. 2009;18:2431–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gibson JH, Slobedman B, K NH, Williamson SL, Minchenko D, El-Osta A, Stern JL, Christodoulou J. Downstream targets of methyl CpG binding protein 2 and their abnormal expression in the frontal cortex of the human Rett syndrome brain. BMC Neurosci. 2010;11:53.
Article
PubMed
PubMed Central
CAS
Google Scholar
Urdinguio RG, Fernandez AF, Lopez-Nieva P, Rossi S, Huertas D, Kulis M, Liu CG, Croce CM, Calin GA, Esteller M. Disrupted microRNA expression caused by Mecp2 loss in a mouse model of Rett syndrome. Epigenetics. 2010;5:656–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu H, Tao J, Chen PJ, Shahab A, Ge W, Hart RP, Ruan X, Ruan Y, Sun YE. Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome. Proc Natl Acad Sci U S A. 2010;107:18161–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petazzi P, Sandoval J, Szczesna K, Jorge OC, Roa L, Sayols S, Gomez A, Huertas D, Esteller M. Dysregulation of the long non-coding RNA transcriptome in a Rett syndrome mouse model. RNA Biol. 2013;10:1197–203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sugino K, Hempel CM, Okaty BW, Arnson HA, Kato S, Dani VS, Nelson SB. Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes. J Neurosci. 2014;34:12877–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen L, Chen K, Lavery LA, Baker SA, Shaw CA, Li W, Zoghbi HY. MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome. Proc Natl Acad Sci U S A. 2015;112:5509–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME. Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature. 2015;522:89–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin P, Nicholls L, Assareh H, Fang Z, Amos TG, Edwards RJ, Assareh AA, Voineagu I. Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q genes in Rett syndrome. BMC Genomics. 2016;17:427.
Article
PubMed
PubMed Central
CAS
Google Scholar
Veeraragavan S, Wan YW, Connolly DR, Hamilton SM, Ward CS, Soriano S, Pitcher MR, McGraw CM, Huang SG, Green JR, et al. Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome. Hum Mol Genet. 2016;25:3284–302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maxwell SS, Pelka GJ, Tam PP, El-Osta A. Chromatin context and ncRNA highlight targets of MeCP2 in brain. RNA Biol. 2013;10:1741–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matarazzo V, Ronnett GV. Temporal and regional differences in the olfactory proteome as a consequence of MeCP2 deficiency. Proc Natl Acad Sci U S A. 2004;101:7763–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cortelazzo A, Pietri T, De Felice C, Leoncini S, Guerranti R, Signorini C, Timperio AM, Zolla L, Ciccoli L, Hayek J. Proteomic analysis of the Rett syndrome experimental model mecp2Q63X mutant zebrafish. J Proteome. 2017;154:128–33.
Article
CAS
Google Scholar
Cortelazzo A, Guerranti R, De Felice C, Signorini C, Leoncini S, Pecorelli A, Landi C, Bini L, Montomoli B, Sticozzi C, et al. A plasma proteomic approach in Rett syndrome: classical versus preserved speech variant. Mediat Inflamm. 2013;2013:438653.
Article
CAS
Google Scholar
Cortelazzo A, De Felice C, Guerranti R, Signorini C, Leoncini S, Pecorelli A, Zollo G, Landi C, Valacchi G, Ciccoli L, et al. Subclinical inflammatory status in Rett syndrome. Mediat Inflamm. 2014;2014:480980.
Article
CAS
Google Scholar
Chen RZ, Akbarian S, Tudor M, Jaenisch R. Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat Genet. 2001;27:327–31.
Article
CAS
PubMed
Google Scholar
Calfa G, Percy AK, Pozzo-Miller L. Experimental models of Rett syndrome based on Mecp2 dysfunction. Exp Biol Med (Maywood). 2011;236:3–19.
Article
CAS
Google Scholar
Liu Y, Zhou J, White KP. RNA-seq differential expression studies: more sequence or more replication? Bioinformatics. 2014;30:301–4.
Article
CAS
PubMed
Google Scholar
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Eberhard C, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44:W3–W10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trim Galore! [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/].
FastQC: a quality control tool for high throughput sequence data [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Illumina iGenomes [https://support.illumina.com/sequencing/sequencing_software/igenome.html ].
Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem. 2009;81:6481–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, Dianes JA, Sun Z, Farrah T, Bandeira N, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;32:223–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vizcaino JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44:D447–56.
Article
CAS
PubMed
Google Scholar
Heaven MR, Funk AJ, Cobbs AL, Haffey WD, Norris JL, McCullumsmith RE, Greis KD. Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics—a prototype design for a single injection assay. J Mass Spectrom. 2016;51:1–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Norris JL, Farrow MA, Gutierrez DB, Palmer LD, Muszynski N, Sherrod SD, Pino JC, Allen JL, Spraggins JM, Lubbock AL, et al. Integrated, high-throughput, multiomics platform enables data-driven construction of cellular responses and reveals global drug mechanisms of action. J Proteome Res. 2017;16:1364–75.
Article
CAS
PubMed
Google Scholar
Deng V, Matagne V, Banine F, Frerking M, Ohliger P, Budden S, Pevsner J, Dissen GA, Sherman LS, Ojeda SR. FXYD1 is an MeCP2 target gene overexpressed in the brains of Rett syndrome patients and Mecp2-null mice. Hum Mol Genet. 2007;16:640–50.
Article
CAS
PubMed
Google Scholar
Miyake K, Hirasawa T, Soutome M, Itoh M, Goto Y, Endoh K, Takahashi K, Kudo S, Nakagawa T, Yokoi S, et al. The protocadherins, PCDHB1 and PCDH7, are regulated by MeCP2 in neuronal cells and brain tissues: implication for pathogenesis of Rett syndrome. BMC Neurosci. 2011;12:81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nadler JJ, Zou F, Huang H, Moy SS, Lauder J, Crawley JN, Threadgill DW, Wright FA, Magnuson TR. Large-scale gene expression differences across brain regions and inbred strains correlate with a behavioral phenotype. Genetics. 2006;174:1229–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, et al. Spatio-temporal transcriptome of the human brain. Nature. 2011;478:483–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007;445:168–76.
Article
CAS
PubMed
Google Scholar
Sharma K, Schmitt S, Bergner CG, Tyanova S, Kannaiyan N, Manrique-Hoyos N, Kongi K, Cantuti L, Hanisch UK, Philips MA, et al. Cell type- and brain region-resolved mouse brain proteome. Nat Neurosci. 2015;18:1819–31.
Article
CAS
PubMed
Google Scholar
Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 2013;29:600–8.
Article
CAS
PubMed
Google Scholar
Liu Y, Zhao D, Dong R, Yang X, Zhang Y, Tammimies K, Uddin M, Scherer SW, Gai Z. De novo exon 1 deletion of AUTS2 gene in a patient with autism spectrum disorder and developmental delay: a case report and a brief literature review. Am J Med Genet A. 2015;167:1381–5.
Article
CAS
PubMed
Google Scholar
Leblond CS, Nava C, Polge A, Gauthier J, Huguet G, Lumbroso S, Giuliano F, Stordeur C, Depienne C, Mouzat K, et al. Meta-analysis of SHANK mutations in autism spectrum disorders: a gradient of severity in cognitive impairments. PLoS Genet. 2014;10:e1004580.
Article
PubMed
PubMed Central
CAS
Google Scholar
O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, Mackenzie AP, Ng SB, Baker C, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011;43:585–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hamdan FF, Daoud H, Rochefort D, Piton A, Gauthier J, Langlois M, Foomani G, Dobrzeniecka S, Krebs MO, Joober R, et al. De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment. Am J Hum Genet. 2010;87:671–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang P, Lin M, Pedrosa E, Hrabovsky A, Zhang Z, Guo W, Lachman HM, Zheng D. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. Mol Autism. 2015;6:55.
Article
PubMed
PubMed Central
CAS
Google Scholar
King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, et al. Topoisomerases facilitate transcription of long genes linked to autism. Nature. 2013;501:58–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang HS, Allen JA, Mabb AM, King IF, Miriyala J, Taylor-Blake B, Sciaky N, Dutton JW Jr, Lee HM, Chen X, et al. Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature. 2011;481:185–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 2014;34:11929–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Q, Wang YZ, Zhang W, Chen X, Wang J, Chen J, Luo W. Involvement of cold inducible RNA-binding protein in severe hypoxia-induced growth arrest of neural stem cells in vitro. Mol Neurobiol. 2017;54:2143–53.
Article
CAS
PubMed
Google Scholar
Ure K, Lu H, Wang W, Ito-Ishida A, Wu Z, He LJ, Sztainberg Y, Chen W, Tang J, Zoghbi HY. Restoration of Mecp2 expression in GABAergic neurons is sufficient to rescue multiple disease features in a mouse model of Rett syndrome. elife. 2016;5:e14198.
Nguyen MV, Du F, Felice CA, Shan X, Nigam A, Mandel G, Robinson JK, Ballas N. MeCP2 is critical for maintaining mature neuronal networks and global brain anatomy during late stages of postnatal brain development and in the mature adult brain. J Neurosci. 2012;32:10021–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao D, Mokhtari R, Pedrosa E, Birnbaum R, Zheng D, Lachman HM. Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress. Mol Autism. 2017;8:17.
Article
PubMed
PubMed Central
Google Scholar
Lisowski P, Wieczorek M, Goscik J, Juszczak GR, Stankiewicz AM, Zwierzchowski L, Swiergiel AH. Effects of chronic stress on prefrontal cortex transcriptome in mice displaying different genetic backgrounds. J Mol Neurosci. 2013;50:33–57.
Article
CAS
PubMed
Google Scholar
Uzturk BG, Jin SX, Rubin B, Bartolome C, Feig LA. RasGRF1 regulates the hypothalamic-pituitary-adrenal axis specifically in early-adolescent female mice. J Endocrinol. 2015;227:1–12.
Article
CAS
PubMed
Google Scholar
Buchovecky CM, Turley SD, Brown HM, Kyle SM, McDonald JG, Liu B, Pieper AA, Huang W, Katz DM, Russell DW, et al. A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome. Nat Genet. 2013;45:1013–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sticozzi C, Belmonte G, Pecorelli A, Cervellati F, Leoncini S, Signorini C, Ciccoli L, De Felice C, Hayek J, Valacchi G. Scavenger receptor B1 post-translational modifications in Rett syndrome. FEBS Lett. 2013;587:2199–204.
Article
CAS
PubMed
Google Scholar
Justice MJ, Buchovecky CM, Kyle SM, Djukic A. A role for metabolism in Rett syndrome pathogenesis: new clinical findings and potential treatment targets. Rare Dis. 2013;1:e27265.
Article
PubMed
PubMed Central
Google Scholar
Zoghbi HY, Milstien S, Butler IJ, Smith EO, Kaufman S, Glaze DG, Percy AK. Cerebrospinal fluid biogenic amines and biopterin in Rett syndrome. Ann Neurol. 1989;25:56–60.
Article
CAS
PubMed
Google Scholar
Ehrhart F, Coort SL, Cirillo E, Smeets E, Evelo CT, Curfs LM. Rett syndrome—biological pathways leading from MECP2 to disorder phenotypes. Orphanet J Rare Dis. 2016;11:158.
Article
PubMed
PubMed Central
Google Scholar
Mato JM, Martinez-Chantar ML, SC L. S-adenosylmethionine metabolism and liver disease. Ann Hepatol. 2013;12:183–9.
CAS
PubMed
PubMed Central
Google Scholar
McBreairty LE, Bertolo RF. The dynamics of methionine supply and demand during early development. Appl Physiol Nutr Metab. 2016;41:581–7.
Article
CAS
PubMed
Google Scholar
Mellen M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell. 2012;151:1417–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kinde B, DY W, Greenberg ME, Gabel HW. DNA methylation in the gene body influences MeCP2-mediated gene repression. Proc Natl Acad Sci U S A. 2016;113:15114–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kaufmann WE, Stallworth JL, Everman DB, Skinner SA. Neurobiologically-based treatments in Rett syndrome: opportunities and challenges. Expert Opin Orphan Drugs. 2016;4:1043–55.
Article
PubMed
PubMed Central
Google Scholar
Dougherty JD, Geschwind DH. Progress in realizing the promise of microarrays in systems neurobiology. Neuron. 2005;45:183–5.
Article
CAS
PubMed
Google Scholar
Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, Wu C, Huang ZJ, Nelson SB. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci. 2006;9:99–107.
Article
CAS
PubMed
Google Scholar
Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, Goodlett DR, Kruglyak L. Genetic basis of proteome variation in yeast. Nat Genet. 2007;39:1369–75.
Article
CAS
PubMed
Google Scholar
Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, Farber CR, Sinsheimer J, Kang HM, Furlotte N, et al. Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet. 2011;7:e1001393.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 2012;13:227–32.
CAS
PubMed
PubMed Central
Google Scholar
Haider S, Pal R. Integrated analysis of transcriptomic and proteomic data. Curr Genomics. 2013;14:91–110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fang X, Kaduce TL, Weintraub NL, Harmon S, Teesch LM, Morisseau C, Thompson DA, Hammock BD, Spector AA. Pathways of epoxyeicosatrienoic acid metabolism in endothelial cells. Implications for the vascular effects of soluble epoxide hydrolase inhibition. J Biol Chem. 2001;276:14867–74.
Article
CAS
PubMed
Google Scholar
Yamaguchi Y, Shirai Y, Matsubara T, Sanse K, Kuriyama M, Oshiro N, Yoshino K, Yonezawa K, Ono Y, Saito N. Phosphorylation and up-regulation of diacylglycerol kinase gamma via its interaction with protein kinase C gamma. J Biol Chem. 2006;281:31627–37.
Article
CAS
PubMed
Google Scholar
Hasan NM, Longacre MJ, Stoker SW, Kendrick MA, MacDonald MJ. Mitochondrial malic enzyme 3 is important for insulin secretion in pancreatic beta-cells. Mol Endocrinol. 2015;29:396–410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu F, Sudo Y, Sanechika S, Yamashita J, Shimaguchi S, Honda S, Sumi-Ichinose C, Mori-Kojima M, Nakata R, Furuta T, et al. Disturbed biopterin and folate metabolism in the Qdpr-deficient mouse. FEBS Lett. 2014;588:3924–31.
Article
CAS
PubMed
Google Scholar
Li XF, Lytton J. An essential role for the K+-dependent Na+/Ca2+-exchanger, NCKX4, in melanocortin-4-receptor-dependent satiety. J Biol Chem. 2014;289:25445–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Narayan S, Head SR, Gilmartin TJ, Dean B, Thomas EA. Evidence for disruption of sphingolipid metabolism in schizophrenia. J Neurosci Res. 2009;87:278–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ohgami M, Takahashi N, Yamasaki M, Fukui T. Expression of acetoacetyl-CoA synthetase, a novel cytosolic ketone body-utilizing enzyme, in human brain. Biochem Pharmacol. 2003;65:989–94.
Article
CAS
PubMed
Google Scholar
Balogh A, Cadel S, Foulon T, Picart R, Der Garabedian A, Rousselet A, Tougard C, Cohen P. Aminopeptidase B: a processing enzyme secreted and associated with the plasma membrane of rat pheochromocytoma (PC12) cells. J Cell Sci. 1998;111(Pt 2):161–9.
CAS
PubMed
Google Scholar
Friedman J. Sepiapterin reductase deficiency. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Ledbetter N, Mefford HC, RJH S, Stephens K, editors. GeneReviews(R). Seattle: University of Washington; 1993.
Bost F, Diarra-Mehrpour M, Martin JP. Inter-alpha-trypsin inhibitor proteoglycan family—a group of proteins binding and stabilizing the extracellular matrix. Eur J Biochem. 1998;252:339–46.
Article
CAS
PubMed
Google Scholar
Sun C, Zheng J, Cheng S, Feng D, He J. EBP50 phosphorylation by Cdc2/cyclin B kinase affects actin cytoskeleton reorganization and regulates functions of human breast cancer cell line MDA-MB-231. Mol Cells. 2013;36:47–54.
Article
PubMed
PubMed Central
CAS
Google Scholar
Weinman EJ, Steplock D, Zhang Y, Biswas R, Bloch RJ, Shenolikar S. Cooperativity between the phosphorylation of Thr95 and Ser77 of NHERF-1 in the hormonal regulation of renal phosphate transport. J Biol Chem. 2010;285:25134–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mullershausen F, Craveiro LM, Shin Y, Cortes-Cros M, Bassilana F, Osinde M, Wishart WL, Guerini D, Thallmair M, Schwab ME, et al. Phosphorylated FTY720 promotes astrocyte migration through sphingosine-1-phosphate receptors. J Neurochem. 2007;102:1151–61.
Article
CAS
PubMed
Google Scholar
Coe H, Michalak M. Calcium binding chaperones of the endoplasmic reticulum. Gen Physiol Biophys. 2009;28 Spec No Focus:F96–F103.
PubMed
Google Scholar
Tzingounis AV, Kobayashi M, Takamatsu K, Nicoll RA. Hippocalcin gates the calcium activation of the slow after hyperpolarization in hippocampal pyramidal cells. Neuron. 2007;53:487–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feig LA. Regulation of neuronal function by Ras-GRF exchange factors. Genes Cancer. 2011;2:306–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brunton H, Goodarzi AA, Noon AT, Shrikhande A, Hansen RS, Jeggo PA, Shibata A. Analysis of human syndromes with disordered chromatin reveals the impact of heterochromatin on the efficacy of ATM-dependent G2/M checkpoint arrest. Mol Cell Biol. 2011;31:4022–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Babbio F, Castiglioni I, Cassina C, Gariboldi MB, Pistore C, Magnani E, Badaracco G, Monti E, Bonapace IM. Knock-down of methyl CpG-binding protein 2 (MeCP2) causes alterations in cell proliferation and nuclear lamins expression in mammalian cells. BMC Cell Biol. 2012;13:19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bergo A, Strollo M, Gai M, Barbiero I, Stefanelli G, Sertic S, Cobolli Gigli C, Di Cunto F, Kilstrup-Nielsen C, Landsberger N. Methyl-CpG binding protein 2 (MeCP2) localizes at the centrosome and is required for proper mitotic spindle organization. J Biol Chem. 2015;290:3223–37.
Article
CAS
PubMed
Google Scholar
Armstrong DD. Neuropathology of Rett syndrome. J Child Neurol. 2005;20:747–53.
Article
PubMed
Google Scholar
Chapleau CA, Calfa GD, Lane MC, Albertson AJ, Larimore JL, Kudo S, Armstrong DL, Percy AK, Pozzo-Miller L. Dendritic spine pathologies in hippocampal pyramidal neurons from Rett syndrome brain and after expression of Rett-associated MECP2 mutations. Neurobiol Dis. 2009;35:219–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Villemagne PM, Naidu S, Villemagne VL, Yaster M, Wagner HN Jr, ., Harris JC, Moser HW, Johnston MV, Dannals RF, Wong DF: Brain glucose metabolism in Rett syndrome. Pediatr Neurol 2002, 27:117-122.
Article
PubMed
Google Scholar
Pitcher MR, Ward CS, Arvide EM, Chapleau CA, Pozzo-Miller L, Hoeflich A, Sivaramakrishnan M, Saenger S, Metzger F, Neul JL. Insulinotropic treatments exacerbate metabolic syndrome in mice lacking MeCP2 function. Hum Mol Genet. 2013;22:2626–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park MJ, Aja S, Li Q, Degano AL, Penati J, Zhuo J, Roe CR, Ronnett GV. Anaplerotic triheptanoin diet enhances mitochondrial substrate use to remodel the metabolome and improve lifespan, motor function, and sociability in MeCP2-null mice. PLoS One. 2014;9:e109527.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lekman AY, Hagberg BA, Svennerholm LT. Membrane cerebral lipids in Rett syndrome. Pediatr Neurol. 1991;7:186–90.
Article
CAS
PubMed
Google Scholar
Viola A, Saywell V, Villard L, Cozzone PJ, Lutz NW. Metabolic fingerprints of altered brain growth, osmoregulation and neurotransmission in a Rett syndrome model. PLoS One. 2007;2:e157.
Article
PubMed
PubMed Central
CAS
Google Scholar
Braun S, Kottwitz D, Nuber UA. Pharmacological interference with the glucocorticoid system influences symptoms and lifespan in a mouse model of Rett syndrome. Hum Mol Genet. 2012;21:1673–80.
Article
CAS
PubMed
Google Scholar
Segatto M, Trapani L, Di Tunno I, Sticozzi C, Valacchi G, Hayek J, Pallottini V. Cholesterol metabolism is altered in Rett syndrome: a study on plasma and primary cultured fibroblasts derived from patients. PLoS One. 2014;9:e104834.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lopez AM, Chuang JC, Posey KS, Turley SD. Suppression of brain cholesterol synthesis in male Mecp2-deficient mice is age dependent and not accompanied by a concurrent change in the rate of fatty acid synthesis. Brain Res. 2017;1654:77–84.
Article
CAS
PubMed
Google Scholar
De Felice C, Signorini C, Durand T, Oger C, Guy A, Bultel-Ponce V, Galano JM, Ciccoli L, Leoncini S, D'Esposito M, et al. F2-dihomo-isoprostanes as potential early biomarkers of lipid oxidative damage in Rett syndrome. J Lipid Res. 2011;52:2287–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahashi S, Matsumoto N, Okayama A, Suzuki N, Araki A, Okajima K, Tanaka H, Miyamoto A. FOXG1 mutations in Japanese patients with the congenital variant of Rett syndrome. Clin Genet. 2012;82:569–73.
Article
CAS
PubMed
Google Scholar
Sharma K, Singh J, Pillai PP, Frost EE. Involvement of MeCP2 in regulation of myelin-related gene expression in cultured rat oligodendrocytes. J Mol Neurosci. 2015;57:176–84.
Article
CAS
PubMed
Google Scholar
De Felice C, Leoncini S, Signorini C, Cortelazzo A, Rovero P, Durand T, Ciccoli L, Papini AM, Hayek J. Rett syndrome: an autoimmune disease? Autoimmun Rev. 2016;15:411–6.
Article
CAS
PubMed
Google Scholar
Pecorelli A, Cervellati C, Hayek J, Valacchi G. OxInflammation in Rett syndrome. Int J Biochem Cell Biol. 2016;81:246–53.
Article
CAS
PubMed
Google Scholar
Goubau C, Devriendt K, Van der Aa N, Crepel A, Wieczorek D, Kleefstra T, Willemsen MH, Rauch A, Tzschach A, de Ravel T, et al. Platelet defects in congenital variant of Rett syndrome patients with FOXG1 mutations or reduced expression due to a position effect at 14q12. Eur J Hum Genet. 2013;21:1349–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Panighini A, Duranti E, Santini F, Maffei M, Pizzorusso T, Funel N, Taddei S, Bernardini N, Ippolito C, Virdis A, Costa M. Vascular dysfunction in a mouse model of Rett syndrome and effects of curcumin treatment. PLoS One. 2013;8:e64863.
Article
PubMed
PubMed Central
Google Scholar
Tu-Sekine B, Raben DM. Regulation and roles of neuronal diacylglycerol kinases: a lipid perspective. Crit Rev Biochem Mol Biol. 2011;46:353–64.
Article
CAS
PubMed
Google Scholar
Jentarra GM, Olfers SL, Rice SG, Srivastava N, Homanics GE, Blue M, Naidu S, Narayanan V. Abnormalities of cell packing density and dendritic complexity in the MeCP2 A140V mouse model of Rett syndrome/X-linked mental retardation. BMC Neurosci. 2010;11:19.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schilling K, Oberdick J. The treasury of the commons: making use of public gene expression resources to better characterize the molecular diversity of inhibitory interneurons in the cerebellar cortex. Cerebellum. 2009;8:477–89.
Article
CAS
PubMed
Google Scholar
The UniProt C. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158–69.
Article
Google Scholar
Llorens F, Del Rio JA. Unraveling the neuroprotective mechanisms of PrP (C) in excitotoxicity. Prion. 2012;6:245–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hall EA, Nahorski MS, Murray LM, Shaheen R, Perkins E, Dissanayake KN, Kristaryanto Y, Jones RA, Vogt J, Rivagorda M, et al. PLAA mutations cause a lethal infantile epileptic encephalopathy by disrupting ubiquitin-mediated endolysosomal degradation of synaptic proteins. Am J Hum Genet. 2017;100:706–24.
Article
CAS
PubMed
Google Scholar
Chapleau CA, Larimore JL, Theibert A, Pozzo-Miller L. Modulation of dendritic spine development and plasticity by BDNF and vesicular trafficking: fundamental roles in neurodevelopmental disorders associated with mental retardation and autism. J Neurodev Disord. 2009;1:185–96.
Article
PubMed
PubMed Central
Google Scholar
Chahrour M, Zoghbi HY. The story of Rett syndrome: from clinic to neurobiology. Neuron. 2007;56:422–37.
Article
CAS
PubMed
Google Scholar
Haustein MD, Kracun S, XH L, Shih T, Jackson-Weaver O, Tong X, Xu J, Yang XW, O'Dell TJ, Marvin JS, et al. Conditions and constraints for astrocyte calcium signaling in the hippocampal mossy fiber pathway. Neuron. 2014;82:413–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang R, Diaz-Castro B, Looger LL, Khakh BS. Dysfunctional calcium and glutamate signaling in striatal astrocytes from Huntington’s disease model mice. J Neurosci. 2016;36:3453–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carmignoto G, Haydon PG. Astrocyte calcium signaling and epilepsy. Glia. 2012;60:1227–33.
Article
PubMed
PubMed Central
Google Scholar
Nectoux J, Florian C, Delepine C, Bahi-Buisson N, Khelfaoui M, Reibel S, Chelly J, Bienvenu T. Altered microtubule dynamics in Mecp2-deficient astrocytes. J Neurosci Res. 2012;90:990–8.
Article
CAS
PubMed
Google Scholar
Delepine C, Nectoux J, Letourneur F, Baud V, Chelly J, Billuart P, Bienvenu T. Astrocyte transcriptome from the Mecp2(308)-truncated mouse model of Rett syndrome. NeuroMolecular Med. 2015;17:353–63.
Article
CAS
PubMed
Google Scholar
Lee A, Rayfield A, Hryciw DH, Ma TA, Wang D, Pow D, Broer S, Yun C, Poronnik P. Na+-H+ exchanger regulatory factor 1 is a PDZ scaffold for the astroglial glutamate transporter GLAST. Glia. 2007;55:119–29.
Article
PubMed
PubMed Central
Google Scholar
Molina JR, Morales FC, Hayashi Y, Aldape KD, Georgescu MM. Loss of PTEN binding adapter protein NHERF1 from plasma membrane in glioblastoma contributes to PTEN inactivation. Cancer Res. 2010;70:6697–703.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen JY, Lin YY, Jou TS. Phosphorylation of EBP50 negatively regulates beta-PIX-dependent Rac1 activity in anoikis. Cell Death Differ. 2012;19:1027–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahashi Y, Morales FC, Kreimann EL, Georgescu MM. PTEN tumor suppressor associates with NHERF proteins to attenuate PDGF receptor signaling. EMBO J. 2006;25:910–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schafer DP, Heller CT, Gunner G, Heller M, Gordon C, Hammond T, Wolf Y, Jung S, Stevens B. Microglia contribute to circuit defects in Mecp2 null mice independent of microglia-specific loss of Mecp2 expression. elife. 2016;5:e15224.
Cronk JC, Derecki NC, Ji E, Xu Y, Lampano AE, Smirnov I, Baker W, Norris GT, Marin I, Coddington N, et al. Methyl-CpG binding protein 2 regulates microglia and macrophage gene expression in response to inflammatory stimuli. Immunity. 2015;42:679–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chao HT, Zoghbi HY, Rosenmund C. MeCP2 controls excitatory synaptic strength by regulating glutamatergic synapse number. Neuron. 2007;56:58–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bosio A, Binczek E, Stoffel W. Functional breakdown of the lipid bilayer of the myelin membrane in central and peripheral nervous system by disrupted galactocerebroside synthesis. Proc Natl Acad Sci U S A. 1996;93:13280–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coetzee T, Fujita N, Dupree J, Shi R, Blight A, Suzuki K, Suzuki K, Popko B. Myelination in the absence of galactocerebroside and sulfatide: normal structure with abnormal function and regional instability. Cell. 1996;86:209–19.
Article
CAS
PubMed
Google Scholar
Heanue TA, Pachnis V. Expression profiling the developing mammalian enteric nervous system identifies marker and candidate Hirschsprung disease genes. Proc Natl Acad Sci U S A. 2006;103:6919–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwartzman F, Vitolo MR, Schwartzman JS, Morais MB. Eating practices, nutritional status and constipation in patients with Rett syndrome. Arq Gastroenterol. 2008;45:284–9.
Article
PubMed
Google Scholar
Motil KJ, Caeg E, Barrish JO, Geerts S, Lane JB, Percy AK, Annese F, McNair L, Skinner SA, Lee HS, et al. Gastrointestinal and nutritional problems occur frequently throughout life in girls and women with Rett syndrome. J Pediatr Gastroenterol Nutr. 2012;55:292–8.
Article
PubMed
PubMed Central
Google Scholar
Wang J, Pantopoulos K. Regulation of cellular iron metabolism. Biochem J. 2011;434:365–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ohba C, Nabatame S, Iijima Y, Nishiyama K, Tsurusaki Y, Nakashima M, Miyake N, Tanaka F, Ozono K, Saitsu H, Matsumoto N. De novo WDR45 mutation in a patient showing clinically Rett syndrome with childhood iron deposition in brain. J Hum Genet. 2014;59:292–5.
Article
CAS
PubMed
Google Scholar
Crisp SJ, Meyer E, Gregory A, Archer H, Hayflick S, Kurian MA, de Silva R. WDR45 mutation in atypical Rett syndrome with brain iron accumulation. Movement Disorders Clinical Practice. 2015;2:81–3.
Article
Google Scholar
Haack TB, Hogarth P, Kruer MC, Gregory A, Wieland T, Schwarzmayr T, Graf E, Sanford L, Meyer E, Kara E, et al. Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA. Am J Hum Genet. 2012;91:1144–9.
Article
CAS
PubMed
PubMed Central
Google Scholar