Cargando…
Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing
Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)(n) domain that acts as a genetic modifier...
Autores principales: | , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775018/ https://www.ncbi.nlm.nih.gov/pubmed/35052466 http://dx.doi.org/10.3390/genes13010126 |
_version_ | 1784636480702906368 |
---|---|
author | Lüth, Theresa Laβ, Joshua Schaake, Susen Wohlers, Inken Pozojevic, Jelena Jamora, Roland Dominic G. Rosales, Raymond L. Brüggemann, Norbert Saranza, Gerard Diesta, Cid Czarina E. Schlüter, Kathleen Tse, Ronnie Reyes, Charles Jourdan Brand, Max Busch, Hauke Klein, Christine Westenberger, Ana Trinh, Joanne |
author_facet | Lüth, Theresa Laβ, Joshua Schaake, Susen Wohlers, Inken Pozojevic, Jelena Jamora, Roland Dominic G. Rosales, Raymond L. Brüggemann, Norbert Saranza, Gerard Diesta, Cid Czarina E. Schlüter, Kathleen Tse, Ronnie Reyes, Charles Jourdan Brand, Max Busch, Hauke Klein, Christine Westenberger, Ana Trinh, Joanne |
author_sort | Lüth, Theresa |
collection | PubMed |
description | Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)(n) domain that acts as a genetic modifier of disease onset and expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach. Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus. Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif. |
format | Online Article Text |
id | pubmed-8775018 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-87750182022-01-21 Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing Lüth, Theresa Laβ, Joshua Schaake, Susen Wohlers, Inken Pozojevic, Jelena Jamora, Roland Dominic G. Rosales, Raymond L. Brüggemann, Norbert Saranza, Gerard Diesta, Cid Czarina E. Schlüter, Kathleen Tse, Ronnie Reyes, Charles Jourdan Brand, Max Busch, Hauke Klein, Christine Westenberger, Ana Trinh, Joanne Genes (Basel) Article Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)(n) domain that acts as a genetic modifier of disease onset and expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach. Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus. Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif. MDPI 2022-01-11 /pmc/articles/PMC8775018/ /pubmed/35052466 http://dx.doi.org/10.3390/genes13010126 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Lüth, Theresa Laβ, Joshua Schaake, Susen Wohlers, Inken Pozojevic, Jelena Jamora, Roland Dominic G. Rosales, Raymond L. Brüggemann, Norbert Saranza, Gerard Diesta, Cid Czarina E. Schlüter, Kathleen Tse, Ronnie Reyes, Charles Jourdan Brand, Max Busch, Hauke Klein, Christine Westenberger, Ana Trinh, Joanne Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title | Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title_full | Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title_fullStr | Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title_full_unstemmed | Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title_short | Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing |
title_sort | elucidating hexanucleotide repeat number and methylation within the x-linked dystonia-parkinsonism (xdp)-related sva retrotransposon in taf1 with nanopore sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775018/ https://www.ncbi.nlm.nih.gov/pubmed/35052466 http://dx.doi.org/10.3390/genes13010126 |
work_keys_str_mv | AT luththeresa elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT labjoshua elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT schaakesusen elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT wohlersinken elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT pozojevicjelena elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT jamorarolanddominicg elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT rosalesraymondl elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT bruggemannnorbert elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT saranzagerard elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT diestacidczarinae elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT schluterkathleen elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT tseronnie elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT reyescharlesjourdan elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT brandmax elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT buschhauke elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT kleinchristine elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT westenbergerana elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing AT trinhjoanne elucidatinghexanucleotiderepeatnumberandmethylationwithinthexlinkeddystoniaparkinsonismxdprelatedsvaretrotransposonintaf1withnanoporesequencing |