High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1
Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder caused by the expansion of a CTG repeat in the 3′-UTR of <i>DMPK</i>, which is transcribed to a toxic gain-of-function RNA that affects splicing of a range of genes. The expanded repeat is unstable in both germline...
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MDPI AG
2022-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/6/970 |
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| author | Astrid Rasmussen Mathis Hildonen John Vissing Morten Duno Zeynep Tümer Ulf Birkedal |
| author_facet | Astrid Rasmussen Mathis Hildonen John Vissing Morten Duno Zeynep Tümer Ulf Birkedal |
| author_sort | Astrid Rasmussen |
| collection | DOAJ |
| description | Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder caused by the expansion of a CTG repeat in the 3′-UTR of <i>DMPK</i>, which is transcribed to a toxic gain-of-function RNA that affects splicing of a range of genes. The expanded repeat is unstable in both germline and somatic cells. The variable age at disease onset and severity of symptoms have been linked to the inherited CTG repeat length, non-CTG interruptions, and methylation levels flanking the repeat. In general, the genetic biomarkers are investigated separately with specific methods, making it tedious to obtain an overall characterisation of the repeat for a given individual. In the present study, we employed Oxford nanopore sequencing in a pilot study to simultaneously determine the repeat lengths, investigate the presence and nature of repeat interruptions, and quantify methylation levels in the regions flanking the CTG-repeats in four patients with DM1. We determined the repeat lengths, and in three patients, we observed interruptions which were not detected using repeat-primed PCR. Interruptions may thus be more common than previously anticipated and should be investigated in larger cohorts. Allele-specific analyses enabled characterisation of aberrant methylation levels specific to the expanded allele, which greatly increased the sensitivity and resolved cases where the methylation levels were ambiguous. |
| first_indexed | 2024-03-09T23:43:51Z |
| format | Article |
| id | doaj.art-6ba5e956fa1047c6a5d0ff8a196057c4 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T23:43:51Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-6ba5e956fa1047c6a5d0ff8a196057c42023-11-23T16:47:07ZengMDPI AGGenes2073-44252022-05-0113697010.3390/genes13060970High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1Astrid Rasmussen0Mathis Hildonen1John Vissing2Morten Duno3Zeynep Tümer4Ulf Birkedal5Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, DenmarkKennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, DenmarkCopenhagen Neuromuscular Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, DenmarkDepartment of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, DenmarkKennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, DenmarkKennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, DenmarkMyotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder caused by the expansion of a CTG repeat in the 3′-UTR of <i>DMPK</i>, which is transcribed to a toxic gain-of-function RNA that affects splicing of a range of genes. The expanded repeat is unstable in both germline and somatic cells. The variable age at disease onset and severity of symptoms have been linked to the inherited CTG repeat length, non-CTG interruptions, and methylation levels flanking the repeat. In general, the genetic biomarkers are investigated separately with specific methods, making it tedious to obtain an overall characterisation of the repeat for a given individual. In the present study, we employed Oxford nanopore sequencing in a pilot study to simultaneously determine the repeat lengths, investigate the presence and nature of repeat interruptions, and quantify methylation levels in the regions flanking the CTG-repeats in four patients with DM1. We determined the repeat lengths, and in three patients, we observed interruptions which were not detected using repeat-primed PCR. Interruptions may thus be more common than previously anticipated and should be investigated in larger cohorts. Allele-specific analyses enabled characterisation of aberrant methylation levels specific to the expanded allele, which greatly increased the sensitivity and resolved cases where the methylation levels were ambiguous.https://www.mdpi.com/2073-4425/13/6/970Oxford nanoporelong-read sequencingDM1epigeneticsmethylationdiagnostics |
| spellingShingle | Astrid Rasmussen Mathis Hildonen John Vissing Morten Duno Zeynep Tümer Ulf Birkedal High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 Genes Oxford nanopore long-read sequencing DM1 epigenetics methylation diagnostics |
| title | High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 |
| title_full | High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 |
| title_fullStr | High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 |
| title_full_unstemmed | High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 |
| title_short | High Resolution Analysis of <i>DMPK</i> Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1 |
| title_sort | high resolution analysis of i dmpk i hypermethylation and repeat interruptions in myotonic dystrophy type 1 |
| topic | Oxford nanopore long-read sequencing DM1 epigenetics methylation diagnostics |
| url | https://www.mdpi.com/2073-4425/13/6/970 |
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