Exposing the DNA methylome iceberg

Ndlovu, Matladi N.; Denis, Hélène; Fuks, François

doi:10.1016/j.tibs.2011.03.002

Cited by 63 publications

(66 citation statements)

References 75 publications

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“…Intergenic regions are included as well. This seemed particularly important in the light of recent data suggesting that one should look beyond CGI promoter methylation [18]. It is noteworthy that, except for those located within CGIs, the methylation status of cytosines is more frequently assessed by the Infinium II than by the Infinium I assay Figure 3).…”

Section: Results N Design Of the Infinium Methylation 450k Arraymentioning

confidence: 99%

Evaluation of the Infinium Methylation 450K technology

et al. 2011

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Aims: Studies of DNA methylomes hold enormous promise for biomedicine but are hampered by the technological challenges of analyzing many samples cost-effectively. Recently, a major extension of the previous Infinium HumanMethylation27 BeadChip ® (Illumina, Inc. CA, USA), called Infinium HumanMethylation450 (Infinium Methylation 450K; Illumina, Inc. CA, USA) was developed. This upgraded technology is a hybrid of two different chemical assays, the Infinium I and Infinium II assays, allowing (for 12 samples in parallel) assessment of the methylation status of more than 480,000 cytosines distributed over the whole genome. In this article, we evaluate Infinium Methylation 450K on cell lines and tissue samples, highlighting some of its advantages but also some of its limitations. In particular, we compare the methylation values of the Infinium I and Infinium II assays. Materials & methods: We used Infinium Methylation 450K to profile: first, the well-characterized HCT116 wild-type and double-knockout cell lines and then, 16 breast tissue samples (including eight normal and eight primary tumor samples). Absolute methylation values (b-values) were extracted with the GenomeStudio TM software and then subjected to detailed analysis. Results: While this technology appeared highly robust as previously shown, we noticed a divergence between the b-values retrieved from the type I and type II Infinium assays. Specifically, the b-values obtained from Infinium II probes were less accurate and reproducible than those obtained from Infinium I probes. This suggests that data from the type I and type II assays should be considered separately in any downstream bioinformatic analysis. To be able to deal with the Infinium I and Infinium II data together, we developed and tested a new correction technique, which we called 'peak-based correction'. The idea was to rescale the Infinium II data on the basis of the Infinium I data. While this technique should be viewed as an approximation method, it significantly improves the quality of Infinium II data. Conclusion: Infinium 450K is a powerful technique in terms of reagent costs, time of labor, sample throughput and coverage. It holds great promise for the better understanding of the epigenetic component in health and disease. Yet, due to the nature of its design comprising two different chemical assays, analysis of the whole set of data is not as easy as initially anticipated. Correction strategies, such as the peak-based approach proposed here, are a step towards adequate output data analysis. keywoRds: bisulfite-based method n dNA methylation n dNA methylome n epigenetics n epigenomics n Infinium I n Infinium II n Infinium Methylation 450k n peak-based correction

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Section: Results N Design Of the Infinium Methylation 450k Arraymentioning

confidence: 99%

Evaluation of the Infinium Methylation 450K technology

et al. 2011

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“…It was recently reported, however, that neither method can distinguish 5-hydroxymethylcytosine from methylcytosine (47). The latter DNA modification is thought to be indicative of gene expression rather than repression.…”

Section: Discussionmentioning

confidence: 98%

Human Th1 and Th17 Cells Exhibit Epigenetic Stability at Signature Cytokine and Transcription Factor Loci

Cohen

Crome

MacDonald

et al. 2011

The Journal of Immunology

103

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The linear model of Th cell lineage commitment is being revised due to reports that mature Th cells can trans-differentiate into alternate lineages. This ability of Th cells to reprogram is thought to be regulated by epigenetic mechanisms that control expression of transcription factors characteristic of opposing lineages. It is unclear, however, to what extent this new model of Th cell plasticity holds true in human Th cell subsets that develop under physiological conditions in vivo. We isolated in vivo-differentiated human Th1 and Th17 cells, as well as intermediate Th1/17 cells, and identified distinct epigenetic signatures at cytokine (IFNG and IL17A) and transcription factor (TBX21, RORC, and RORA) loci. We also examined the phenotypic and epigenetic stability of human Th17 cells exposed to Th1-polarizing conditions and found that although they could upregulate TBX21 and IFN-γ, this occurred without loss of IL-17 or RORC expression, and resulted in cells with a Th1/17 phenotype. Similarly, Th1 cells could upregulate IL-17 upon enforced expression of RORC2, but did not lose expression of IFN-γ or TBX21. Despite alterations in expression of these signature genes, epigenetic modifications were remarkably stable aside from the acquisition of active histone methylation marks at cytokine gene promoters. The limited capacity of human Th17 and Th1 cells to undergo complete lineage conversion suggests that the bipotent Th1/17 cells may arise from Th1 and/or Th17 cells. These data also question the broad applicability of the new model of Th cell lineage plasticity to in vivo-polarized human Th cell subsets.

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“…Nevertheless, given the complex relationship between gene expression and DNA methylation marks, 30 this result is not so surprising. It is possible that some of these methylation marks may act in trans or through more complex molecular pathways, especially as enhancers have been often shown to act this way.…”

Section: Xa-specific Methylation Is Associated With Genesmentioning

confidence: 99%

Human active X-specific DNA methylation events showing stability across time and tissues

et al. 2014

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The phenomenon of X chromosome inactivation in female mammals is well characterised and remains the archetypal example of dosage compensation via monoallelic expression. The temporal series of events that culminates in inactive X-specific gene silencing by DNA methylation has revealed a 'patchwork' of gene inactivation along the chromosome, with approximately 15% of genes escaping. Such genes are therefore potentially subject to sex-specific imbalance between males and females. Aside from XIST, the non-coding RNA on the X chromosome destined to be inactivated, very little is known about the extent of loci that may be selectively silenced on the active X chromosome (Xa). Using longitudinal array-based DNA methylation profiling of two human tissues, we have identified specific and widespread active X-specific DNA methylation showing stability over time and across tissues of disparate origin. Our panel of X-chromosome loci subject to methylation on Xa reflects a potentially novel mechanism for controlling female-specific X inactivation and sex-specific dimorphisms in humans. Further work is needed to investigate these phenomena.

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Exposing the DNA methylome iceberg

Cited by 63 publications

References 75 publications

Evaluation of the Infinium Methylation 450K technology

Evaluation of the Infinium Methylation 450K technology

Human Th1 and Th17 Cells Exhibit Epigenetic Stability at Signature Cytokine and Transcription Factor Loci

Human active X-specific DNA methylation events showing stability across time and tissues

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