Bisulfite-seq: Analysis of CpG methylation at two CTCF binding sites flanking the CTG repeats of DMPK.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE148177 | GEO | 2020/04/07
REPOSITORIES: GEO
Similar Datasets
Project description:Bisulfite-seq: Analysis of CpG methylation at two CTCF binding sites flanking the CTG repeats of DMPK.
| PRJNA623381 | ENA
Project description:Myotonic dystrophy type 1 (DM1), the most frequent inherited muscular dystrophy in adults, is caused by the CTG repeat expansion in the 3’UTR of the DMPK gene. Mutant DMPK RNA accumulates in nuclear foci altering diverse cellular functions including alternative splicing regulation. DM1 is a multisystemic condition, with debilitating central nervous system alterations. Although a defective neuroglia communication has been described as a contributor of the brain pathology in DM1, the specific cellular and molecular events potentially affected in glia cells have not been totally recognized. Thus, to study the effects of DM1 mutation on glial physiology, in this work we have established an inducible DM1 model derived from the MIO-M1 cell line expressing 648 CUG repeats. This new model recreated the molecular hallmarks of DM1 elicited by a toxic RNA gain-of-function mechanism: accumulation of RNA foci colocalized with MBNL proteins and dysregulation of alternative splicing. By applying a microarray whole-transcriptome approach, we identified several gene changes associated with DM1 mutation in MIO-M1 cells, including the immune mediators CXCL10, CCL5, CXCL8, TNFAIP3, and TNFRSF9, as well as the microRNAs miR-222, miR-448, among others, as potential regulators. A gene ontology enrichment analyses revealed that inflammation and immune response emerged as major cellular deregulated processes in the MIO-M1 DM1 cells. Our findings indicate the involvement of an altered immune response in glia cells, opening new windows for the study of glia as potential contributor of the CNS symptoms in DM1. In this dataset, we include the expression data obtained from MIO-M1-CTG(648) and MIO-M1-CTG(0) with and witouth Doxycycline treatment (1µg/ml) by 8 days . These data are used to obtain genes that are differentially expressed in response to mutant (CUG expanded) DMPK RNA expression.
2023-10-31 | GSE164057 | GEO
Project description:RNA-seq on proliferating myoblasts of the DM11 line carrying 13 and 2600 CTG repeats in the DMPK gene, compared to their genome-edited counterparts without both the 13 and 2600 CTG repeat or just lacking the 2600 CTG repeat.
2019-04-11 | GSE127296 | GEO
Project description:Myotonic dystrophy type 1 (DM1) is a neuro-muscular disorder caused by CTG triplet expansion in the 3-UTR of the DMPK gene. Mutated transcripts aggregate in muscle nuclei and sequester the MBNL1 splicing factor. To assess the involvement of Mbl sequestration on transcriptpion deregulation in DM1, we performed genome wide analyses of gene expression of DM1 Drosophila model in three different genetic contexts: Mef>mblRNAi, Mef>600CTG, Mef>960CTG vs. Mef>lacZ control line.
2013-04-01 | E-MTAB-1469 | biostudies-arrayexpress
Project description:This study tested candidate therapeutic antimiRs in a comprehensive new collection of primary myoblasts derived from myotonic dystrophy type 1 (DM1) patients. DM1 is caused by genetically unstable CTG repeat expansions in the DMPK gene and has multiple clinical presentations, likely because of variable repeat sizes at the tissue and organ levels. Expanded DMPK transcripts deplete Muscleblind-Like Splicing Regulator protein MBNL1, which in turn causes DM1 symptoms. A promising therapeutic approach increases the expression of MBNL1 by blocking natural repressors miR-23b and miR-218 employing antimiRs with chemical modifications designed for a better pharmacological profile in humans. In untreated primary cells, we demonstrate that upregulated therapeutic targets miR-23b and miR-218 and reduced MBNL1 protein levels inversely correlate with CTG repeat size, supporting that active MBNL1 protein repression synergizes with the sequestration by CUG repeats in DM1. Upon treatment with novel antimiRs, multiple readouts of RNA toxicity associated with typical DM1 alterations improved. MBNL1-dependent exon inclusions, and myoblast fusion and myotube area defects, showed robust correction over a wide range of CTG expansions. Unexpectedly, antimiR treatment also reduced DMPK transcript levels and the number of ribonuclear aggregates. Based on these data, we selected a leading antimiR for further transcriptomics characterization and demonstrated that it reversed up to 68% of dysregulated genes. The study revealed that the candidate antimiRs could provide therapy to clinically relevant DM1 forms over a wide range of repeat sizes and genetic backgrounds by simultaneously reducing MBNL1 sequestration and derepressing protein synthesis.
2024-05-01 | GSE237411 | GEO
Project description:Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders.
2020-04-07 | GSE148176 | GEO
Project description:Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders. This SuperSeries is composed of the SubSeries listed below.
2020-04-07 | GSE148185 | GEO
Project description:The congenital form of myotonic dystrophy type 1 (cDM) is caused by large-scale expansion of a (CTG•CAG)n repeat in DMPK and DM1-AS. Production of toxic transcripts with long trinucleotide tracts from these genes results in impediment of myogenic differentiation capacity as cDM’s most prominent morpho-phenotypic hallmark. In the current in vitro study, we compared the early differentiation programs of isogenic cDM myoblasts with and without a (CTG)2600 repeat obtained by gene editing. We found that excision of the repeat restored the ability of cDM myoblasts to engage in myogenic fusion, preventing that the ensuing myotubes remained immature. Although the cDM-typical epigenetic status of the DM1 locus and the expression of genes therein were not altered upon removal of the repeat, analyses at the transcriptome and proteome level revealed that early abnormalities in the temporal expression of differentiation regulators, myogenic progression markers and alternative splicing patterns before and immediately after the onset of differentiation became normalized. Our observation that molecular and cellular features of cDM are reversible and can be corrected by repeat-directed genome editing in muscle progenitors is important information for future development of gene therapy for different forms of DM1.
2019-11-20 | PXD016056 | Pride
Project description:Myotonic dystrophy type 1 (DM1) is a neuro-muscular disorder caused by CTG triplet expansion in the 3'-UTR of the DMPK gene. Mutated transcripts aggregate in muscle nuclei and increase CUGBP1 stability by a not-yet determined mechanism. To assess the involvement of CUGBP1 in DM1, we used Drosophila as a model of the disease and we performed genome wide analyses of gene expression of bru-3 (CUGBP1 orthologue) gain of function line (Mef>bru-3) vs. Mef>lacZ control line.
2017-03-24 | E-MTAB-3231 | biostudies-arrayexpress
Project description:Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystem disorder mainly characterized by gradual muscle loss, weakness, and delayed relaxation after muscle contraction. It is caused by an expanded CTG repeat in the 3' UTR of DMPK, which is transcribed into a toxic gain-of-function mRNA that affects the splicing of a range of other genes. The repeat is unstable, with a bias towards expansions both in somatic cells and in the germline, which results in a tendency for earlier onset with each generation, as longer repeat lengths generally correlate with earlier onset. Previous studies have found hypermethylation in the regions flanking the repeat in congenital onset DM1 and in some patients with non-congenital DM1. We used pyrosequencing to investigate blood methylation levels in 68 patients with non-congenital DM1, compare the methylation levels between the blood and muscle, and assess whether methylation levels change over time in the blood. We found higher methylation levels in the blood of DM1 patients than in healthy controls and especially in the patients who had inherited the disease allele maternally. The methylation levels remained relatively stable over time and are a strong biomarker of the disease, as well as of the maternal inheritance of the disease.
| S-EPMC7465187 | biostudies-literature