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CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

ABSTRACT: Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, expression levels, expression correlations and regulatory regions of the three genes.Our investigations reveal the predominantly used transcription start sites (TSSs) for each gene including novel transcription start sites for FOXG1. We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5. We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes. Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.Our analyses provide a comprehensive picture of the regulatory regions of the three genes involved in Rett Syndrome.

SUBMITTER: Vitezic M

PROVIDER: S-EPMC4522966 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Vitezic Morana M Bertin Nicolas N Andersson Robin R Lipovich Leonard L Kawaji Hideya H Lassmann Timo T Sandelin Albin A Heutink Peter P Goldowitz Dan D Ha Thomas T Zhang Peter P Patrizi Annarita A Fagiolini Michela M Forrest Alistair R R AR Carninci Piero P Saxena Alka A

BMC genomics 20141224

<h4>Background</h4>Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, exp ...[more]

PMID: 25539566

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Project description:BACKGROUND:Rett Syndrome (RTT) is a complex neurodevelopmental disorder, frequently associated with epilepsy. Despite increasing recognition of the clinical heterogeneity of RTT and its variants (e.g Classical, Hanefeld and PSV(Preserved Speech Variant)), the link between causative mutations and observed clinical phenotypes remains unclear. Quantitative analysis of electroencephalogram (EEG) recordings may further elucidate important differences between the different clinical and genetic forms of RTT. METHODS:Using a large cohort (n?=?42) of RTT patients, we analysed the electrophysiological profiles of RTT variants (genetic and clinical) in addition to epilepsy status (no epilepsy/treatment-responsive epilepsy/treatment-resistant epilepsy). The distribution of spectral power and inter-electrode coherence measures were derived from continuous resting-state EEG recordings. RESULTS:RTT genetic variants (MeCP2/CDLK5) were characterised by significant differences in network architecture on comparing first principal components of inter-electrode coherence across all frequency bands (p?<?0.0001). Greater coherence in occipital and temporal pairs were seen in MeCP2 vs CDLK5 variants, the main drivers in between group differences. Similarly, clinical phenotypes (Classical RTT/Hanefeld/PSV) demonstrated significant differences in network architecture (p?<?0.0001). Right tempero-parietal connectivity was found to differ between groups (p?=?0.04), with greatest coherence in the Classical RTT phenotype. PSV demonstrated a significant difference in left-sided parieto-occipital coherence (p?=?0.026). Whilst overall power decreased over time, there were no difference in asymmetry and inter-electrode coherence profiles over time. There was a significant difference in asymmetry in the overall power spectra between epilepsy groups (p?=?0.04) in addition to occipital asymmetry across all frequency bands. Significant differences in network architecture were also seen across epilepsy groups (p?=?0.044). CONCLUSIONS:Genetic and clinical variants of RTT are characterised by discrete patterns of inter-electrode coherence and network architecture which remain stable over time. Further, hemispheric distribution of spectral power and measures of network dysfunction are associated with epilepsy status and treatment responsiveness. These findings support the role of discrete EEG profiles as non-invasive biomarkers in RTT and its genetic/clinical variants.

Project description:More than 90% of Rett syndrome (RTT) patients have heterozygous mutations in the X-linked methyl-CpG binding protein 2 (MECP2) gene that encodes the methyl-CpG-binding protein 2, a transcriptional modulator. Because MECP2 is subjected to X chromosome inactivation (XCI), girls with RTT either express the wild-type or mutant allele in each individual cell. To test the consequences of MECP2 mutations resulting from a genome-wide transcriptional dysregulation and to identify its target genes in a system that circumvents the functional mosaicism resulting from XCI, we carried out gene expression profiling of clonal populations derived from fibroblast primary cultures expressing exclusively either the wild-type or the mutant MECP2 allele. Clonal cultures were obtained from skin biopsy of three RTT patients carrying either a non-sense or a frameshift MECP2 mutation. For each patient, gene expression profiles of wild-type and mutant clones were compared by oligonucleotide expression microarray analysis. Firstly, clustering analysis classified the RTT patients according to their genetic background and MECP2 mutation. Secondly, expression profiling by microarray analysis and quantitative RT-PCR indicated four up-regulated genes and five down-regulated genes significantly dysregulated in all our statistical analysis, including excellent potential candidate genes for the understanding of the pathophysiology of this neurodevelopmental disease. Thirdly, chromatin immunoprecipitation analysis confirmed MeCP2 binding to respective CpG islands in three out of four up-regulated candidate genes and sequencing of bisulphite-converted DNA indicated that MeCP2 preferentially binds to methylated-DNA sequences. Most importantly, the finding that at least two of these genes (BMCC1 and RNF182) were shown to be involved in cell survival and/or apoptosis may suggest that impaired MeCP2 function could alter the survival of neurons thus compromising brain function without inducing cell death.

Dataset Information

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Publications

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

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