Global analysis of DNA methylation and transcription of human repetitive sequences.

Horard, Béatrice; Eymery, Angéline; Fourel, Geneviève; Vassetzky, Nikita S.; Puechberty, Jacques; Roizes, Gérard; Lebrigand, Kévin; Barbry, Pascal; Laugraud, Aurélie; Gautier, Christian; Simon, Elsa Ben; Devaux, Frédéric; Magdinier, Frédérique; Vourc’h, Claire; Gilson, Éric

doi:10.4161/epi.4.5.9284

Cited by 29 publications

(27 citation statements)

References 70 publications

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“…Finally, genome-wide studies tend to ignore repetitive regions due to technical difficulties, and the few studies that focused specifically on mapping DNA methylation in repetitive regions did so at relatively low coverage50–52. The current dataset was well-suited to analyze DNA methylation in repetitive regions because the joint results obtained by three different experimental methods helped us to control for technical artifacts that can burden the analysis of repetitive DNA.…”

Section: Discussionmentioning

confidence: 98%

Quantitative comparison of genome-wide DNA methylation mapping technologies

et al. 2010

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DNA methylation is a key component of mammalian gene regulation and the most classical example of an epigenetic mark. DNA methylation patterns are mitotically heritable and stable over time, but they undergo considerable changes in response to cell differentiation, diseases and environmental influences. Several methods have been developed for DNA methylation profiling on a genomic scale. Here, we benchmark four of these methods on two sample pairs, comparing their accuracy and power to detect DNA methylation differences. The results show that all evaluated methods (MeDIP-seq: methylated DNA immunoprecipitation, MethylCap-seq: methylated DNA capture by affinity purification, RRBS: reduced representation bisulfite sequencing, and the Infinium HumanMethylation27 assay) produce accurate DNA methylation data. However, these methods differ in their ability to detect differentially methylated regions between pairs of samples. We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies.

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Section: Discussionmentioning

confidence: 98%

Quantitative comparison of genome-wide DNA methylation mapping technologies

et al. 2010

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“…DNA was treated with PureLink RNase A from Invitrogen (Carlsbad, CA, USA) and precipitated with a classic phenol chloroform protocol as described previously [49,50]. 4 µg to 6 µg of DNA was used for MeDIP [49,50]. An in vitro methylated DNA from Drosophila melanogaster was used as a positive control for the MeDIP.…”

Section: Methodsmentioning

confidence: 99%

Epigenetic interplay between mouse endogenous retroviruses and host genes

et al. 2012

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BackgroundTransposable elements are often the targets of repressive epigenetic modifications such as DNA methylation that, in theory, have the potential to spread toward nearby genes and induce epigenetic silencing. To better understand the role of DNA methylation in the relationship between transposable elements and genes, we assessed the methylation state of mouse endogenous retroviruses (ERVs) located near genes.ResultsWe found that ERVs of the ETn/MusD family show decreased DNA methylation when near transcription start sites in tissues where the nearby gene is expressed. ERVs belonging to the IAP family, however, are generally heavily methylated, regardless of the genomic environment and the tissue studied. Furthermore, we found full-length ETn and IAP copies that display differential DNA methylation between their two long terminal repeats (LTRs), suggesting that the environment surrounding gene promoters can prevent methylation of the nearby LTR. Spreading from methylated ERV copies to nearby genes was rarely observed, with the regions between the ERVs and genes apparently acting as a boundary, enriched in H3K4me3 and CTCF, which possibly protects the unmethylated gene promoter. Furthermore, the flanking regions of unmethylated ERV copies harbor H3K4me3, consistent with spreading of euchromatin from the host gene toward ERV insertions.ConclusionsWe have shown that spreading of DNA methylation from ERV copies toward active gene promoters is rare. We provide evidence that genes can be protected from ERV-induced heterochromatin spreading by either blocking the invasion of repressive marks or by spreading euchromatin toward the ERV copy.

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“…The quality of the DNA was controlled by gel analysis and spectrometry. For MeDIP experiments sonicated DNA was denatured and immunoprecipitated with an anti 5-methyl-cytosine antibody (Megabase Research Products) (14). Control immunoprecipitation was performed with anti IgG antibody (Sigma).…”

Section: Methodsmentioning

confidence: 99%

A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells

Eymery

Horard

Atifi-Borel

et al. 2009

Nucleic Acids Research

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Although there is now evidence that the expression of centromeric (CT) and pericentric (PCT) sequences are key players in major genomic functions, their transcriptional status in human cells is still poorly known. The main reason for this lack of data is the complexity and high level of polymorphism of these repeated sequences, which hampers straightforward analyses by available transcriptomic approaches. Here a transcriptomic macro-array dedicated to the analysis of CT and PCT expression is developed and validated in heat-shocked (HS) HeLa cells. For the first time, the expression status of CT and PCT sequences is analyzed in a series of normal and cancer human cells and tissues demonstrating that they are repressed in all normal tissues except in the testis, where PCT transcripts are found. Moreover, PCT sequences are specifically expressed in HS cells in a Heat-Shock Factor 1 (HSF1)-dependent fashion, and we show here that another independent pathway, involving DNA hypo-methylation, can also trigger their expression. Interestingly, CT and PCT were found illegitimately expressed in somatic cancer samples, whereas PCT were repressed in testis cancer, suggesting that the expression of CT and PCT sequences may represent a good indicator of epigenetic deregulations occurring in response to environmental changes or in cell transformation.

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Global analysis of DNA methylation and transcription of human repetitive sequences.

Cited by 29 publications

References 70 publications

Quantitative comparison of genome-wide DNA methylation mapping technologies

Quantitative comparison of genome-wide DNA methylation mapping technologies

Epigenetic interplay between mouse endogenous retroviruses and host genes

A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells

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