Genetics: profiling DNA methylation and beyond

Marx, Vivien

doi:10.1038/nmeth.3736

Cited by 10 publications

(5 citation statements)

References 8 publications

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“…(2) immunoprecipitation of methylated DNA; and (3) bisulfite treatment that converts unmethylated cytosines to uracils while leaving methylated cytosines unchanged. Among them, WGBS is currently the most popular method; however, as we mentioned before, WGBS bioinformatics analysis is usually based on either wild-card or three-letter aligners and tends to waste a large proportion of the sequencing reads (Kunde-Ramamoorthy et al 2014;Plongthongkum et al 2014;Marx 2016). To reconcile this problem, we developed the GPS method, in which the first part of the pair-ended read is the original DNA sequence and the second part of the read pair is bisulfite-converted sequence.…”

Section: Discussionmentioning

confidence: 99%

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Jin

et al. 2019

Genome Res.

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Aberrant DNA methylation is a distinguishing feature of cancer. Yet, how methylation affects immune surveillance and tumor metastasis remains ambiguous. We introduce a novel method, Guide Positioning Sequencing (GPS), for precisely detecting whole-genome DNA methylation with cytosine coverage as high as 96% and unbiased coverage of GC-rich and repetitive regions. Systematic comparisons of GPS with whole-genome bisulfite sequencing (WGBS) found that methylation difference between gene body and promoter is an effective predictor of gene expression with a correlation coefficient of 0.67 (GPS) versus 0.33 (WGBS). Moreover, Methylation Boundary Shift (MBS) in promoters or enhancers is capable of modulating expression of genes associated with immunity and tumor metabolism. Furthermore, aberrant DNA methylation results in tissue-specific enhancer switching, which is responsible for altering cell identity during liver cancer development. Altogether, we demonstrate that GPS is a powerful tool with improved accuracy and efficiency over WGBS in simultaneously detecting genome-wide DNA methylation and genomic variation. Using GPS, we show that aberrant DNA methylation is associated with altering cell identity and immune surveillance networks, which may contribute to tumorigenesis and metastasis.

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Section: Discussionmentioning

confidence: 99%

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Jin

et al. 2019

Genome Res.

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“…Sequencing platforms like Oxford Nanopore Technologies' MinION, which has recently been demonstrated in the Dry Valleys as a proof of principle for future in situ analyses (Johnson et al, 2017), and PacBio may also open new ways to interrogate DNA damage and repair via base modification detection. Base modifications, like cytosine methylation, are directly detectable in PacBio data by measuring kinetic variation during base incorporation (Marx, 2016) and have also been detected in nanopore sequencing data (Simpson et al, 2017). As DNA does not have to be amplified before sequencing, this method opens the door to analyzing rare sequence variants in situ.…”

Section: Future Workmentioning

confidence: 99%

Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics

et al. 2019

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“…Altogether, these studies implicate a role for 5-hmC in disease and suggest that 5-hmC may be a useful clinical marker of diseases depending on its genomic localization. We anticipate further, more precise mechanistic insight into the role of 5-hmC as improvements in evaluating DNA methylation states genome-wide are currently being investigated (112). …”

Section: Implications Of 5-hmc In Diseasementioning

confidence: 99%

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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Genetics: profiling DNA methylation and beyond

Cited by 10 publications

References 8 publications

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics

High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

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