DNA methylation mapping by tag-modified bisulfite genomic sequencing

Han, Weiguo; Cauchi, Stéphane; Herman, James G.; Spivack, Simon D.

doi:10.1016/j.ab.2006.05.010

Cited by 36 publications

(39 citation statements)

References 40 publications

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“…The GSTP1 promoter has been shown to be hypermethylated in a variety of cancers, so one possible additional explanation for differences in mRNA expression could be that genetic polymorphisms result in variation in baseline promoter methylation status and, thus, mRNA expression. However, work by Han and colleagues indicates that, in the absence of disease, GSTP1 promoter methylation is conserved across tissue types and among individual subjects (49). Therefore, other variables, such as differences in transacting factors, posttranscriptional modification, and altered mRNA stability or transcription factor binding due to SNPs outside of the resequenced region, may be responsible for the remaining interindividual variation in mRNA expression.…”

Section: Discussionmentioning

confidence: 99%

GlutathioneS-Transferase P1: Gene Sequence Variation and Functional Genomic Studies

Moyer

Salavaggione²,

Wu³

et al. 2008

Cancer Research

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Glutathione S-transferase P1 (GSTP1) is of importance for cancer research because of its role in detoxifying carcinogens, activating antineoplastic prodrugs, metabolizing chemotherapeutic agents, and its involvement in cell cycle and apoptosis regulation. Two common GSTP1 genetic polymorphisms have been studied extensively. However, the full range of GSTP1 genetic variation has not been systematically characterized in the absence of disease pathology. We set out to identify common GSTP1 polymorphisms in four ethnic groups, followed by functional genomic studies. All exons, splice junctions, and the 5 ¶-flanking region of GSTP1 were resequenced using 60 DNA samples each from four ethnic groups. The 35 single-nucleotide polymorphisms (SNP) identified included six nonsynonymous SNPs and 17 previously unreported polymorphisms. GSTP1 variant allozymes were then expressed in COS-1 cells, and five displayed significantly altered levels of enzyme activity. One decreased to 22% of the wild-type (WT) activity. Four variant allozymes had K m values that differed significantly from that of the WT, and five showed altered levels of immunoreactive protein compared with WT, with a significant correlation (r = 0.79, P < 0.007) between levels of immunoreactive protein and enzyme activity in these samples. In the Mexican American population, five linked SNPs were significantly associated with GSTP1 mRNA expression, one of which was found by electrophoretic mobility shift assay to alter protein binding. These studies have identified functionally significant genetic variation, in addition to the two frequently studied GSTP1 nonsynonymous SNPs, that may influence GSTP1's contribution to carcinogen and drug metabolism, and possibly disease pathogenesis and/ or drug response. [Cancer Res 2008;68(12):4791-801]

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Section: Discussionmentioning

confidence: 99%

GlutathioneS-Transferase P1: Gene Sequence Variation and Functional Genomic Studies

Moyer

Salavaggione²,

Wu³

et al. 2008

Cancer Research

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“…This allows one to look at 20-30 CpGs within an amplicon. Addition of M13 sequence and a G or C rich tag containing at least 50% cytosines (forward primer) or guanines (reverse primer) to the nested PCR primers for direct sequencing improved the bisulfite sequence quality, 26,38 by increasing the binding specificity during the Sanger sequencing reaction.…”

Section: ©2 0 1 1 L a N D E S B I O S C I E N C E D O N O T D I S Tmentioning

confidence: 99%

Limiting dilution bisulfite (pyro)sequencing reveals parent-specific methylation patterns in single early mouse embryos and bovine oocytes

et al. 2011

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“…Subsequently, gene-specific single PCRs with nested primers were used to amplify single DNA molecules. The sequencing performance of the CG-poor DNA was enhanced by tagging the inner primers with a stuffer sequence (Han et al 2006) and further improved by additionally tagging the stuffer with an M13-tag. All primers used in multiplex and gene-specific PCR are summarized in Table 8.…”

Section: Repeat Analysesmentioning

confidence: 99%

DNA methylation and mRNA expression profiles in bovine oocytes derived from prepubertal and adult donors

Diederich¹,

Hansmann²,

Heinzmann³

et al. 2012

Reproduction

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The developmental capacity of oocytes from prepubertal cattle is reduced compared with their adult counterparts, and epigenetic mechanisms are thought to be involved herein. Here, we analyzed DNA methylation in three developmentally important, nonimprinted genes (SLC2A1, PRDX1, ZAR1) and two satellite sequences, i.e. 'bovine testis satellite I' (BTS) and 'Bos taurus alpha satellite I' (BTaS). In parallel, mRNA expression of the genes was determined by quantitative real-time PCR. Oocytes were retrieved from prepubertal calves and adult cows twice per week over a 3-week period by ultrasound-guided follicular aspiration after treatment with FSH and/or IGF1. Both immature and in vitro matured prepubertal and adult oocytes showed a distinct hypomethylation profile of the three genes without differences between the two types of donors. The methylation status of the BTS sequence changed according to the age and treatment while the methylation status of BTaS sequence remained largely unchanged across the different age and treatment groups. Relative transcript abundance of the selected genes was significantly different in immature and in vitro matured oocytes; only minor changes related to origin and treatment were observed. In conclusion, methylation levels of the investigated satellite sequences were high (O50%) in all groups and showed significant variation depending on the age, treatment, or in vitro maturation. To what extent this is involved in the acquisition of developmental competence of bovine oocytes needs further study.

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DNA methylation mapping by tag-modified bisulfite genomic sequencing

Cited by 36 publications

References 40 publications

GlutathioneS-Transferase P1: Gene Sequence Variation and Functional Genomic Studies

GlutathioneS-Transferase P1: Gene Sequence Variation and Functional Genomic Studies

Limiting dilution bisulfite (pyro)sequencing reveals parent-specific methylation patterns in single early mouse embryos and bovine oocytes

DNA methylation and mRNA expression profiles in bovine oocytes derived from prepubertal and adult donors

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