Advances in measuring DNA methylation

Sun, Ruixia; Zhu, Ping

doi:10.1097/bs9.0000000000000098

Cited by 11 publications

(8 citation statements)

References 65 publications

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“…With the development of high-throughput sequencing technology, we can analyze events such as 5′-methylcytosine and histone modification at the whole-genome level using “DNA methylation sequencing” to provide more in-depth results than those obtainable by genomics research [ 161 ]. Moreover, with the continuous decline of sequencing costs and the iterative updating of sequencing technology in recent years, DNA methylation sequencing methods can be more selective [ 162 ]. At present, there are six common sequencing methods for epigenetic DNA methylation research: whole-genome bisulfite methylation sequencing (WGBS), precise DNA methylation and hydroxymethylation sequencing (oxidation combined with bisulfite transformation sequencing (oxBS-Seq)), optimized simplified methylation sequencing (RRBS/dRRBS/XRS), single/micro cell whole-genome methylation sequencing (scWGBS), amplification (hydroxy) methylation sequencing, and (hydroxy) methylated DNA immunoprecipitation sequencing ((h) MeDIP-seq), with each solution suitable for different DNA methylation research directions [ 163 ].…”

Section: Methods For Studying the Epigenetic Modificationmentioning

confidence: 99%

Targeting the chromatin structural changes of antitumor immunity

Li,

Lun,

Gong

et al. 2024

Journal of Pharmaceutical Analysis

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Section: Methods For Studying the Epigenetic Modificationmentioning

confidence: 99%

Targeting the chromatin structural changes of antitumor immunity

Li,

Lun,

Gong

et al. 2024

Journal of Pharmaceutical Analysis

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“…New developments in bisulfite-free sequencing approaches Enzymatic methyl-seq (EM-seq) EM-seq utilizes two biological enzymes, first to convert 5mC to 5hmC with TET2, then to deaminate unmethylated cytosine to uracil with APOBEC3A [151,154] Advantages • By eliminating the use of bisufite, DNA is less damaged, allowing DNA inputs down to 100 pg. 40…”

Section: Advantagesmentioning

confidence: 99%

Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder

LaSalle

2023

Mol Psychiatry

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Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental outcomes in children with a commonality in deficits in social communication and language combined with repetitive behaviors and interests. The etiology of ASD is heterogeneous, as several hundred genes have been implicated as well as multiple in utero environmental exposures. Over the past two decades, epigenetic investigations, including DNA methylation, have emerged as a novel way to capture the complex interface of multivariate ASD etiologies. More recently, epigenome-wide association studies using human brain and surrogate accessible tissues have revealed some convergent genes that are epigenetically altered in ASD, many of which overlap with known genetic risk factors. Unlike transcriptomes, epigenomic signatures defined by DNA methylation from surrogate tissues such as placenta and cord blood can reflect past differences in fetal brain gene transcription, transcription factor binding, and chromatin. For example, the discovery of NHIP (neuronal hypoxia inducible, placenta associated) through an epigenome-wide association in placenta, identified a common genetic risk for ASD that was modified by prenatal vitamin use. While epigenomic signatures are distinct between different genetic syndromic causes of ASD, bivalent chromatin and some convergent gene pathways are consistently epigenetically altered in both syndromic and idiopathic ASD, as well as some environmental exposures. Together, these epigenomic signatures hold promising clues towards improved early prediction and prevention of ASD as well genes and gene pathways to target for pharmacological interventions. Future advancements in single cell and multi-omic technologies, machine learning, as well as non-invasive screening of epigenomic signatures during pregnancy or newborn periods are expected to continue to impact the translatability of the recent discoveries in epigenomics to precision public health.

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“…A range of technologies are available for quantifying DNA methylation [ 9 , 10 ]. The most common approaches to distinguish methylated from unmethylated DNA include: sodium bisulphite treatment, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged [ 11 ] (used in clonal bisulphite sequencing, pyrosequencing, Illumina BeadChips, Whole Genome Bisulphite Sequencing (WGBS)); endonuclease digestion-based methods, which use methylation-sensitive restriction enzymes to fragment double stranded DNA according to its methylation status (e.g.…”

Section: Introductionmentioning

confidence: 99%

Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling

Peters,

Meyer,

Ryan

et al. 2024

BMC Genomics

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Background The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. Results We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer’s recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2’s new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. Conclusions Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.

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Advances in measuring DNA methylation

Cited by 11 publications

References 65 publications

Targeting the chromatin structural changes of antitumor immunity

Targeting the chromatin structural changes of antitumor immunity

Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder

Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling

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