Evaluating DNA methylation and gene expression variability in the human term placenta

Avila, Luana; Yuen, Ryan K. C.; Diego‐Alvarez, Dan; Peñaherrera, Maria S.; Jiang, Ruiwei; Robinson, Wendy P.

doi:10.1016/j.placenta.2010.09.011

Cited by 79 publications

(82 citation statements)

References 39 publications

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“…Both analyses identified no significant systematic changes in methylation levels over time. Again, this is in accordance with previous studies examining potential DNA methylation changes in placenta tissue and whole blood in response to storage-time [17,21,33].…”

Section: Discussionsupporting

confidence: 93%

“…Inadequate handling and storage of blood samples can have detrimental effects on quality and quantity of extracted DNA [17,18]. Also, the integrity of RNA and protein can be affected by storage temperature [19][20][21]. Given that the dynamic nature of epigenetic regulation allows for an acute response to extracellular stimuli such as exercise, stress and nutrition factors [22][23][24], it is plausible that specific epigenetic changes can occur in blood cells ex vivo.…”

Section: High Quality Sequencing Data Generated From Time Points Up Tmentioning

confidence: 99%

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The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

et al. 2017

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Abstract:Background: Epigenetic epidemiology has proven an important research discipline in the delineation of diseases of complex etiology. The approach, in such studies, is often to use bio-banked clinical material, however, many such samples were collected for purposes other than epigenetic studies and, thus, potentially not processed and stored appropriately. The Danish National Birth Cohort (DNBC) includes more than 100,000 peripheral and umbilical cord blood samples shipped from maternity wards by ordinary mail in EDTA tubes. While this and other similar cohorts hold great promises for DNA methylation studies the potential systematic changes prompted by storage at ambient temperatures have never been assessed on a genome-wide level. Methods and Results: In this study, matched EDTA whole blood samples were stored up to three days at room temperature prior to DNA extraction and methylated DNA immunoprecipitation coupled with deep sequencing (MeDIP-seq). We established that the quality of the MeDIP-seq libraries was high and comparable across samples; and that the methylation profiles did not change systematically during the short-time storage at room temperature. Conclusion: The global DNA methylation profile is stable in whole blood samples stored for up to three days at room temperature in EDTA tubes making genome-wide methylation studies on such material feasible.

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Section: Discussionsupporting

confidence: 93%

Section: High Quality Sequencing Data Generated From Time Points Up Tmentioning

confidence: 99%

The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

et al. 2017

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“…For instance, glucocorticoids can cause an increase in SLC6A4 expression in human B-lymphoblastoid cells [162]. Furthermore, quantification of the readily degrading mRNA depends greatly on the sample processing time [163]. In contrast, methylation remains more constant over time.…”

Section: Discussionmentioning

confidence: 99%

Looking beyond the DNA sequence: the relevance of DNA methylation processes for the stress–diathesis model of depression

Booij

Wang

Lévesque

et al. 2013

Phil. Trans. R. Soc. B

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The functioning of the hypothalamic–pituitary–adrenal (HPA) axis and serotonergic (5-HT) system are known to be intertwined with mood. Alterations in these systems are often associated with depression. However, neither are sufficient to cause depression in and of themselves. It is now becoming increasingly clear that the environment plays a crucial role, particularly, the perinatal environment. In this review, we posit that early environmental stress triggers a series of epigenetic mechanisms that adapt the genome and programme the HPA axis and 5-HT system for survival in a harsh environment. We focus on DNA methylation as it is the most stable epigenetic mark. Given that DNA methylation patterns are in large part set within the perinatal period, long-term gene expression programming by DNA methylation is especially vulnerable to environmental insults during this period. We discuss specific examples of genes in the 5-HT system (serotonin transporter) and HPA axis (glucocorticoid receptor and arginine vasopressin enhancer) whose DNA methylation state is associated with early life experience and may potentially lead to depression vulnerability. We conclude with a discussion on the relevance of studying epigenetic mechanisms in peripheral tissue as a proxy for those occurring in the human brain and suggest avenues for future research.

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“…7 Previous findings have reported that DNA methylation marks are stable and accessible for measurement in placenta, 24 and that the GR gene is expressed in placenta. 25 Taken collectively, our data combined with this previous work suggests that DNA methylation of the GR gene promoter may be important in regulating GR gene expression, and this epigenetic alteration is linked to infant birthweight.…”

Section: Discussionmentioning

confidence: 99%

Birthweight is associated with DNA promoter methylation of the glucocorticoid receptor in human placenta

Filiberto

Maccani²,

Koestler³

et al. 2011

Epigenetics

149

108

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Evaluating DNA methylation and gene expression variability in the human term placenta

Cited by 79 publications

References 39 publications

The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

Looking beyond the DNA sequence: the relevance of DNA methylation processes for the stress–diathesis model of depression

Birthweight is associated with DNA promoter methylation of the glucocorticoid receptor in human placenta

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