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Wojciechowska M, Sobczak K, Kozlowski P, Sedehizadeh S, Wojtkowiak-Szlachcic A, Czubak K, Markus R, Lusakowska A, Kaminska A, Brook JD. Quantitative Methods to Monitor RNA Biomarkers in Myotonic Dystrophy. Sci Rep 2018; 8:5885. [PMID: 29651162 PMCID: PMC5897446 DOI: 10.1038/s41598-018-24156-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/22/2018] [Indexed: 12/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs. We present two quantitative methods, Multiplex Ligation-Dependent Probe Amplification and droplet digital PCR, for studying the mutant DMPK transcript (DMPKexpRNA) and the aberrant alternative splicing in DM1 and DM2 human tissues and cells. We demonstrate that in DM1, the DMPKexpRNA is detected in higher copy number than its normal counterpart. Moreover, the absolute number of the mutant transcript indicates its low abundance with only a few copies per cell in DM1 fibroblasts. Most importantly, in conjunction with fluorescence in-situ hybridization experiments, our results suggest that in DM1 fibroblasts, the vast majority of nuclear RNA foci consist of a few molecules of DMPKexpRNA.
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Affiliation(s)
- Marzena Wojciechowska
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland.
| | - Krzysztof Sobczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Department of Gene Expression, Poznan, 60-614, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland
| | - Saam Sedehizadeh
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom
| | - Agnieszka Wojtkowiak-Szlachcic
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Department of Gene Expression, Poznan, 60-614, Poland
| | - Karol Czubak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland
| | - Robert Markus
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom
| | - Anna Lusakowska
- Medical University of Warsaw, Department of Neurology, Warsaw, 02-097, Poland
| | - Anna Kaminska
- Medical University of Warsaw, Department of Neurology, Warsaw, 02-097, Poland
| | - J David Brook
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom.
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Zhang Y, Song J, Day K, Absher D. dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization. BMC Genomics 2017; 18:811. [PMID: 29061109 PMCID: PMC5653981 DOI: 10.1186/s12864-017-4159-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Targeted sequencing is a powerful tool with broad application in both basic and translational sciences. Relatively low on-target rates for most current targeted sequencing studies influence the required coverage and data quality for subsequent applications. RESULTS We present an improved targeted sequencing method that uses two rounds of in solution hybridization with probes synthesized from genomic clone templates, termed dCATCH-Seq. Independent captures of two large continuous genomic regions across three cell types within the human major histocompatibility complex (MHC) that spans ~3.5 Mb and a ~250 kb region on chromosome 11 demonstrated that dCATCH-Seq was highly reproducible with ~95% capture specificity. Comprehensive analyses of sequencing data generated using the dCATCH-Seq approach also showed high accuracy in the detection of genetic variants and HLA typing. The double hybridization capture approach can also be coupled with bisulfite sequencing for DNA methylation profiling of both CpG and non-CpG sites. CONCLUSIONS Altogether, dCATCH-Seq is a powerful and scalable targeted sequencing approach to investigate both genetic and epigenetic features.
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Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Jun Song
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, USA. .,Ubiquity Genomics Inc., Huntsville, USA.
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Kaur P, Gaikwad K. From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:2164. [PMID: 29312405 PMCID: PMC5742236 DOI: 10.3389/fpls.2017.02164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Exome sequencing represents targeted capture and sequencing of 1-2% of 'high-value genomic regions' (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.
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