Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology
Abstract DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (...
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BMC
2024-12-01
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| Series: | Epigenetics & Chromatin |
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| Online Access: | https://doi.org/10.1186/s13072-024-00558-2 |
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| author | Alexandra Chera Mircea Stancu-Cretu Nicolae Radu Zabet Octavian Bucur |
| author_facet | Alexandra Chera Mircea Stancu-Cretu Nicolae Radu Zabet Octavian Bucur |
| author_sort | Alexandra Chera |
| collection | DOAJ |
| description | Abstract DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties. Out of all genomic regions, long read sequencing provides advantages in studying repetitive elements, which are difficult to characterize through other sequencing methods. Transposable elements are repetitive regions of the genome that are silenced and usually display high levels of DNA methylation. Their demethylation and activation have been observed in many cancers. Due to their repetitive nature, it is challenging to accurately estimate DNA methylation levels within transposable elements using short sequencing technologies. The advantage to sequence native DNA (without PCR amplification biases or harsh bisulfite treatment) and long and ultra long reads coupled with epigenetic states of the DNA allows to accurately estimate DNA methylation levels in transposable elements. This is a big step forward for epigenomic studies, and unsolved questions regarding gene expression and transposable elements silencing through DNA methylation can now be answered. |
| format | Article |
| id | doaj-art-df5d5e2e478740e0b35e91f4f0d18d5c |
| institution | Kabale University |
| issn | 1756-8935 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | Epigenetics & Chromatin |
| spelling | doaj-art-df5d5e2e478740e0b35e91f4f0d18d5c2025-01-05T12:46:25ZengBMCEpigenetics & Chromatin1756-89352024-12-0117111510.1186/s13072-024-00558-2Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technologyAlexandra Chera0Mircea Stancu-Cretu1Nicolae Radu Zabet2Octavian Bucur3Carol Davila University of Medicine and PharmacyGenomics Research and Development InstituteBlizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of LondonCarol Davila University of Medicine and PharmacyAbstract DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties. Out of all genomic regions, long read sequencing provides advantages in studying repetitive elements, which are difficult to characterize through other sequencing methods. Transposable elements are repetitive regions of the genome that are silenced and usually display high levels of DNA methylation. Their demethylation and activation have been observed in many cancers. Due to their repetitive nature, it is challenging to accurately estimate DNA methylation levels within transposable elements using short sequencing technologies. The advantage to sequence native DNA (without PCR amplification biases or harsh bisulfite treatment) and long and ultra long reads coupled with epigenetic states of the DNA allows to accurately estimate DNA methylation levels in transposable elements. This is a big step forward for epigenomic studies, and unsolved questions regarding gene expression and transposable elements silencing through DNA methylation can now be answered.https://doi.org/10.1186/s13072-024-00558-2Nanopore sequencingLong-read sequencingDNA methylationEpigenomicsMethylome |
| spellingShingle | Alexandra Chera Mircea Stancu-Cretu Nicolae Radu Zabet Octavian Bucur Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology Epigenetics & Chromatin Nanopore sequencing Long-read sequencing DNA methylation Epigenomics Methylome |
| title | Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology |
| title_full | Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology |
| title_fullStr | Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology |
| title_full_unstemmed | Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology |
| title_short | Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology |
| title_sort | shedding light on dna methylation and its clinical implications the impact of long read based nanopore technology |
| topic | Nanopore sequencing Long-read sequencing DNA methylation Epigenomics Methylome |
| url | https://doi.org/10.1186/s13072-024-00558-2 |
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