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Open AccessArticle

Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells

1
Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
2
Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
3
Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
*
Author to whom correspondence should be addressed.
Received: 13 August 2020 / Revised: 25 September 2020 / Accepted: 28 September 2020 / Published: 1 October 2020
(This article belongs to the Special Issue Epigenetics in Stem Cells and Their Derivatives)
Differential DNA methylation is characteristic of gene regulatory regions, such as enhancers, which mostly constitute low or intermediate CpG content in their DNA sequence. Consequently, quantification of changes in DNA methylation at these sites is challenging. Given that DNA methylation across most of the mammalian genome is maintained, the use of genome-wide bisulfite sequencing to measure fractional changes in DNA methylation at specific sites is an overexertion which is both expensive and cumbersome. Here, we developed a MethylRAD technique with an improved experimental plan and bioinformatic analysis tool to examine regional DNA methylation changes in embryonic stem cells (ESCs) during differentiation. The transcriptional silencing of pluripotency genes (PpGs) during ESC differentiation is accompanied by PpG enhancer (PpGe) silencing mediated by the demethylation of H3K4me1 by LSD1. Our MethylRAD data show that in the presence of LSD1 inhibitor, a significant fraction of LSD1-bound PpGe fails to gain DNA methylation. We further show that this effect is mostly observed in PpGes with low/intermediate CpG content. Underscoring the sensitivity and accuracy of MethylRAD sequencing, our study demonstrates that this method can detect small changes in DNA methylation in regulatory regions, including those with low/intermediate CpG content, thus asserting its use as a method of choice for diagnostic purposes. View Full-Text
Keywords: DNA methylation; embryonic stem cells; MethylRAD; enhancer; pluripotency genes; histone demethylase LSD1 DNA methylation; embryonic stem cells; MethylRAD; enhancer; pluripotency genes; histone demethylase LSD1
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MDPI and ACS Style

Saha, D.; Norvil, A.B.; Lanman, N.A.; Gowher, H. Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells. Epigenomes 2020, 4, 24. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4040024

AMA Style

Saha D, Norvil AB, Lanman NA, Gowher H. Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells. Epigenomes. 2020; 4(4):24. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4040024

Chicago/Turabian Style

Saha, Debapriya; Norvil, Allison B.; Lanman, Nadia A.; Gowher, Humaira. 2020. "Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells" Epigenomes 4, no. 4: 24. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4040024

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