Semiconductor-based sequencing of genome-wide DNA methylation states

Corley, Michael J.; Zhang, Wei; Zheng, Xin; Lum-Jones, Annette; Maunakea, Alika K.

doi:10.1080/15592294.2014.1003747

Cited by 7 publications

(11 citation statements)

References 69 publications

(82 reference statements)

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“…However, genome-wide studies have revealed that DNA methylation within gene bodies is far more frequent than at promoters (5, 59–61), playing a role in tissue-specific alternative promoter usage (5). Preferential positioning of DNA methylation over exons compared with introns (62–65) prompted speculation for its potential role in pre-mRNA splicing, which has been confirmed by further studies (6, 66, 67). Interestingly, readers of DNA methylation including MeCP2 and methylation-sensitive proteins such as CTCF play roles in exon recognition and alternative splicing (6, 66).…”

Section: Role Of 5-hmc In Demethylationmentioning

confidence: 88%

“…As has been described for 5-mC (6), such exonic patterns of 5-hmC appears to be a common observation (84, 85) and suggest it may play a role in pre-mRNA splicing. In contrast to 5-mC where depletion is typically observed (5, 29, 67), 5-hmC appears significantly enriched at TES regions (67, 81–83) (Figure 2). Although the functional role of 5-hmC at TES has not been explicitly examined, integrating this distribution with studies of RNA revealing tissue-specific transcription initiation near TES (88, 89) and novel post-transcriptional RNA methylation at 3′-UTRs (90) implicate additional roles for 5-hmC in transcription and RNA methylation, respectively.…”

Section: Genomic Localization Of 5-hmc and Potential Functional Rolesmentioning

confidence: 95%

“…In particular, the abundance of 5-hmC at transcription end sites (TES) is substantially higher than neighboring regions within genes (67). MeDIP-Seq results of 5-hmC levels in brain tissue from our lab clearly show depletion of the mark in transcription start sites (TSS) and enrichment precisely over exons (Figure 2), similarly to 5-mC distribution (5, 6).…”

Section: Genomic Localization Of 5-hmc and Potential Functional Rolesmentioning

confidence: 99%

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High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

Pang¹,

Sugai²,

Maunakea

2016

Biomolecular Concepts

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Chemical modifications of DNA comprise epigenetic mechanisms that contribute to the maintenance of cellular activities and memory. Although the function of 5-methylcytosine (5-mC) has been extensively studied, little is known about the function(s) of relatively rarer and underappreciated cytosine modifications including 5-hydroxymethylcytosine (5-hmC). The discovery that ten-eleven translocation (Tet) proteins mediate conversion of 5-mC to 5-hmC, and other oxidation derivatives, sparked renewed interest to understand the biological role of 5-hmC. Studies examining total 5-hmC levels revealed the highly dynamic yet tissue-specific nature of this modification, implicating a role in epigenetic regulation and development. Intriguingly, 5-hmC levels are highest during early development and in the brain where abnormal patterns of 5-hmC have been observed in disease conditions. Thus, 5-hmC adds to the growing list of epigenetic modifications with potential utility in clinical applications and warrants further investigation. This review discusses the emerging functional roles of 5-hmC in normal and disease states, focusing primarily on insights provided by recent studies exploring the genome-wide distribution of this modification in mammals.

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Section: Role Of 5-hmc In Demethylationmentioning

confidence: 88%

Section: Genomic Localization Of 5-hmc and Potential Functional Rolesmentioning

confidence: 95%

Section: Genomic Localization Of 5-hmc and Potential Functional Rolesmentioning

confidence: 99%

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High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

Pang¹,

Sugai²,

Maunakea

2016

Biomolecular Concepts

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“…Epigenomics is the study of heritable gene regulation that does not involve the DNA nucleotide coding sequence itself but acts on a genome-wide scale via DNA nucleotide methylation and posttranslational modifications of histones, the interaction between transcription factors and their targets, and nucleosome positioning [23][24][25][26][27][28][29][30]. Methylomics is the genome-wide analysis of DNA methylations and their effects on gene expression and heredity [28].…”

Section: Methylomics and Epigenomicsmentioning

confidence: 99%

“…However, WGS may be preferred over WES because it provides more data with better uniformity of read coverage on disease-associated variants and reveals polymorphisms outside coding regions and genomic rearrangements [19,22]. The analysis of the methylome by MeS complements WGS, WES, and CGS to determine the active methylation sites and the epigenetic markers that regulate gene expression, epistructural base variations, imprinting, development, differentiation, disease, and the epigenetic state [23][24][25][26][27][28][29][30]. The impact of NGS technology is indeed egalitarian in that it allows both small and large research groups the possibility to provide answers and solutions to many different problems and questions in the fields of genetics and biology, including those in medicine, agriculture, forensic science, virology, microbiology, and marine and plant biology.…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications

Kulski¹

2016

Next Generation Sequencing - Advances, Applications and Challenges

143

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Next-generation sequencing NGS technologies using DN", RN", or methylation sequencing have impacted enormously on the life sciences. NGS is the choice for large-scale genomic and transcriptomic sequencing because of the high-throughput production and outputs of sequencing data in the gigabase range per instrument run and the lower cost compared to the traditional Sanger first-generation sequencing method. The vast amounts of data generated by NGS have broadened our understanding of structural and functional genomics through the concepts of omics ranging from basic genomics to integrated systeomics, providing new insight into the workings and meaning of genetic conservation and diversity of living things. NGS today is more than ever about how different organisms use genetic information and molecular biology to survive and reproduce with and without mutations, disease, and diversity within their population networks and changing environments. In this chapter, the advances, applications, and challenges of NGS are reviewed starting with a history of first-generation sequencing followed by the major NGS platforms, the bioinformatics issues confronting NGS data storage and analysis, and the impacts made in the fields of genetics, biology, agriculture, and medicine in the brave, new world of omics.Keywords: Next-generation sequencing, tools, platforms, applications, omics . IntroductionNext-generation sequencing NGS refers to the deep, high-throughput, in-parallel DN" sequencing technologies developed a few decades after the Sanger DN" sequencing method first emerged in and then dominated for three decades [ , ]. The NGS technologies are different from the Sanger method in that they provide massively parallel analysis, extremely high-throughput from multiple samples at much reduced cost [ ]. Millions to billions of DN" © 2015 The A""hor(s). Licensee InTech. This chap"er is dis"rib""ed "nder "he "erms of "he Crea"ive Commons A""rib""ion License (h""p://crea"ivecommons.org/licenses/by/3.0), which permi"s "nres"ric"ed "se, dis"rib""ion, and reprod"c"ion in any medi"m, provided "he original work is properly ci"ed.nucleotides can be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragment-cloning methods that were used with Sanger sequencing [ ]. The second-generation sequencing methods are characterized by the need to prepare amplified sequencing libraries before undertaking sequencing of the amplified DN" clones, whereas third-generation single molecular sequencing can be done without the need for creating the time-consuming and costly amplification libraries [ ]. The parallelization of a high number of sequencing reactions by NGS was achieved by the miniaturization of sequencing reactions and, in some cases, the development of microfluidics and improved detection systems [ ]. The time needed to generate the gigabase Gb -sized sequences by NGS was reduced from many years to only a few days or hours, with an accompanying massive price reduction. For example, as part of the Human...

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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns

Tost

2016

Advances in Experimental Medicine and Biology

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DNA methylation is the most studied epigenetic modification, and altered DNA methylation patterns have been identified in cancer and more recently also in many other complex diseases. Furthermore, DNA methylation is influenced by a variety of environmental factors, and the analysis of DNA methylation patterns might allow deciphering previous exposure. Although a large number of techniques to study DNA methylation either genome-wide or at specific loci have been devised, they all are based on a limited number of principles for differentiating the methylation state, viz., methylation-specific/methylation-dependent restriction enzymes, antibodies or methyl-binding proteins, chemical-based enrichment, or bisulfite conversion. Second-generation sequencing has largely replaced microarrays as readout platform and is also becoming more popular for locus-specific DNA methylation analysis. In this chapter, the currently used methods for both genome-wide and locus-specific analysis of 5-methylcytosine and as its oxidative derivatives, such as 5-hydroxymethylcytosine, are reviewed in detail, and the advantages and limitations of each approach are discussed. Furthermore, emerging technologies avoiding PCR amplification and allowing a direct readout of DNA methylation are summarized, together with novel applications, such as the detection of DNA methylation in single cells or in circulating cell-free DNA.

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Semiconductor-based sequencing of genome-wide DNA methylation states

Cited by 7 publications

References 69 publications

High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications

Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns

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