Bioinformatic Analysis of DNA Methylation in Neural Progenitor Cell Models of Alcohol Abuse.

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Authors: Oni, Eileen N; Hart, Ronald P
Year: 2016
Journal: Current pharmacology reports
PMID: 27774408
DOI: 10.1007/s40495-016-0065-y
PMCID: PMC5070667

#	Section	Preview
0	Introduction – why is DNA methylation important in alcohol abuse?	During differentiation, DNA undergoes epigenetic remodeling to specify cell fate and regulate key…
1	Introduction – why is DNA methylation important in alcohol abuse?	cost to the entire United States believed to be $4 billion annually (American Academy of Pediatrics…
2	Introduction – why is DNA methylation important in alcohol abuse?	Several recent publications sought to understand the epigenetic effects of alcohol, specifically,…
3	Methods for DNA methylation analysis	Techniques for assessing genome-wide DNA methylation have been evolving rapidly over the past few…
4	Methods for DNA methylation analysis	unenriched DNA using contrasting probe dye colors. This is a cost-effective way to sample nearly…
5	Methods for DNA methylation analysis	targeted bisulfite sequencing is available. For example, Agilent uses a large number of…
6	Analysis of DNA methylation in models of fetal alcohol exposure — Whole embryo exposure	An early whole-genome study of ethanol exposure utilized whole-embryo cultures of mouse (Liu et al.…
7	Analysis of DNA methylation in models of fetal alcohol exposure — Whole embryo exposure	and compared with unprocessed DNA samples using Nimblegen arrays focusing on CpG islands and…
8	Analysis of DNA methylation in models of fetal alcohol exposure — Whole embryo exposure	A finer analysis of the probe-level data focused on sequences with two consecutive probes defined as…
9	Analysis of DNA methylation in models of fetal alcohol exposure — Whole embryo exposure	This study provided a valuable contribution by carefully classifying a major developmental phenotype…
10	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	The chronic consumption of alcohol, especially during key growth stages such as pregnancy or…
11	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	Hicks and colleagues (2010) hypothesized that ethanol induces epigenetic alterations of cell cycle…
12	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	To identify molecular pathways responsible for the cell cycle effects of ethanol exposure in the…
13	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	To analyze genome wide DNA methylation of NSC cultures following ethanol treatment, CpG methylation…
14	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	To understand the physiological relevance of these transcript alterations in vivo, the expression of…
15	Analysis of DNA methylation in models of fetal alcohol exposure — Neural stem cells and cell cycle control	While in many ways this study used a logically similar approach as that used by Liu (2009), the…
16	Analysis of DNA methylation in models of fetal alcohol exposure — Ethanol regulation of methylation in DRG NSC	Another study (Zhou et al. 2011) aimed to model the epigenetic effects of FAS in NSC. Previous work…
17	Analysis of DNA methylation in models of fetal alcohol exposure — Ethanol regulation of methylation in DRG NSC	Rat DRG NSCs were plated in the absence of bFGF to promote differentiation, and then split into…
18	Analysis of DNA methylation in models of fetal alcohol exposure — Ethanol regulation of methylation in DRG NSC	To identify DMRs, DNA samples from untreated differentiated cells or undifferentiated cells, with or…
19	Analysis of DNA methylation in models of fetal alcohol exposure — Ethanol regulation of methylation in DRG NSC	First, average level analysis considered the mean of all probes near each transcription start site…

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