Whole-genome DNA methylation profiling using MethylCap-seq

Brinkman, Arie B.; Simmer, Femke; Ma, Kelong; Kaan, Anita; Zhu, Jingde; Stunnenberg, Hendrik G.

doi:10.1016/j.ymeth.2010.06.012

Cited by 243 publications

(162 citation statements)

References 14 publications

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“…S2B,C). As shown previously (Bock et al 2010;Brinkman et al 2010), genomic regions identified by MethylCap-sequencing can be validated using MeDIP and bisulfite sequencing.…”

Section: Dna Methylation Profiles Of X Tropicalis Embryosmentioning

confidence: 71%

“…Genomic DNA isolated from blastula and gastrula (NieuwkoopFaber stages 9 and 12.5) embryos was purified by affinity capture (MethylCap) using the methyl-CpG-binding domain (MBD) of human MECP2 protein (Cross et al 1994;Kangaspeska et al 2008;Brinkman et al 2010;Martens et al 2010). MethylCap has been benchmarked as a robust, accurate, and effective approach to map DNA methylation (Bock et al 2010).…”

Section: Dna Methylation Profiles Of X Tropicalis Embryosmentioning

confidence: 99%

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Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

Bogdanović

Long²,

Heeringen³

et al. 2011

Genome Res.

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DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find both promoters and gene bodies of active genes robustly methylated. In contrast, DNA methylation is absent in large H3K27me3 domains, indicating that these two repression pathways have different roles. Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high DNA methylation. Therefore, we tested the repressive potential of DNA methylation using transient and transgenic approaches and show that methylated promoters are robustly transcribed in blastula-and gastrula-stage embryos, but not in oocytes or late embryos. These findings have implications for reprogramming and the epigenetic regulation of pluripotency and differentiation and suggest a relatively open, pliable chromatin state in early embryos followed by reestablished methylation-dependent transcriptional repression during organogenesis and differentiation.

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“…S2B,C). As shown previously (Bock et al 2010;Brinkman et al 2010), genomic regions identified by MethylCap-sequencing can be validated using MeDIP and bisulfite sequencing.…”

Section: Dna Methylation Profiles Of X Tropicalis Embryosmentioning

confidence: 71%

Section: Dna Methylation Profiles Of X Tropicalis Embryosmentioning

confidence: 99%

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

Bogdanović

Long²,

Heeringen³

et al. 2011

Genome Res.

Self Cite

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“…This method involves capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation Illumina sequencing of eluted DNA as schematically outlined in Figure S1. 9 MethylCapseq was performed on 24 tumors and an equal number of matched normal samples (48 DNA methylation profiles in total).…”

Section: Dna Methylation Profiles Of Crc Cases and Matched Controlsmentioning

confidence: 99%

“…[9][10][11][12] To validate the current MethylCap-seq, four fragments were selected and assessed in two sample pairs. These fragments overlap with the promoters of SDC2, SIM2, ROBO1 and CYP1B1.…”

Section: Dna Methylation Profiles Of Crc Cases and Matched Controlsmentioning

confidence: 99%

“…[5][6][7][8] Here, we investigated DNA methylation in CRC genomewide using MethylCap-seq. 9 Our study provides comprehensive DNA methylation maps of CRC and matched normal colon tissue, and identifies differentially methylated regions (DMRs). We determined characteristics of these DMRs using publically available expression and epigenetic data sets, and select a list of candidate biomarkers for CRC detection.…”

Section: Introductionmentioning

confidence: 99%

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Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

et al. 2012

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Unlocking the potential of tumor‐derived DNA in urine for cancer detection: methodological challenges and opportunities

Wever,

Steenbergen

2024

Molecular Oncology

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High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self‐collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine‐based cancer detection, with a focus on non‐urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor‐derived cell‐free DNA. We also provide future recommendations for technical advancements in urine‐based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell‐free DNA.

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Whole-genome DNA methylation profiling using MethylCap-seq

Cited by 243 publications

References 14 publications

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

Unlocking the potential of tumor‐derived DNA in urine for cancer detection: methodological challenges and opportunities

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