DNA-Methylation Analysis by the Bisulfite-Assisted Genomic Sequencing Method

Hájková, Petra; El‐Maarri, Osman; Engemann, Sabine; Oswald, Joachim; Olek, Alexander; Walter, Jörn

doi:10.1385/1-59259-182-5:143

Cited by 71 publications

(65 citation statements)

References 11 publications

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“…Lymphoma samples B1, B13, and B16 show considerable overlap in methylated CpG sequences within exon 2, and all three tumors have undetectable PUMA mRNA transcripts. To determine whether BL tumors with low or no PUMA expression were associated with increased DNA methylation, we analyzed the methylation status of the first three CpG regions of PUMA by using a sodium bisulfite modification and a PCR-based approach (17). Interestingly, three of the six primary BL tumors that lack detectable PUMA expression (samples B1, B13, and B16) exhibited significant DNA methylation within exon 2 (Fig.…”

Section: Puma Deficiency Accelerates E-myc Lymphomagenesismentioning

confidence: 99%

Selection against PUMA Gene Expression in Myc-Driven B-Cell Lymphomagenesis

Garrison

Jeffers²,

Yang

et al. 2008

Molecular and Cellular Biology

133

113

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The p53 tumor suppressor pathway limits oncogenesis by inducing cell cycle arrest or apoptosis. A key p53 target gene is PUMA, which encodes a BH3-only proapoptotic protein. Here we demonstrate that Puma deletion in the E-Myc mouse model of Burkitt lymphoma accelerates lymphomagenesis and that ϳ75% of E-Myc lymphomas naturally select against Puma protein expression. Furthermore, approximately 40% of primary human Burkitt lymphomas fail to express detectable levels of PUMA and in some tumors this is associated with DNA methylation. Burkitt lymphoma cell lines phenocopy the primary tumors with respect to DNA methylation and diminished PUMA expression, which can be reactivated following inhibition of DNA methyltransferases. These findings establish that PUMA is silenced in human malignancies, and they suggest PUMA as a target for the development of novel chemotherapeutics.

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Section: Puma Deficiency Accelerates E-myc Lymphomagenesismentioning

confidence: 99%

Selection against PUMA Gene Expression in Myc-Driven B-Cell Lymphomagenesis

Garrison

Jeffers²,

Yang

et al. 2008

Molecular and Cellular Biology

133

113

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“…Furthermore bisulfite sequencing analysis (see example in figure 6) can identify the DNA methylation status along the DNA single strand, and can also detect the DNA methylation pattern of DNA double strands since the converted DNA strands are no longer self-complementary and the amplification products can be measured individually (27,28). Bisulfite-based DNA methylation analyse are more quantitative, sensible, efficient, and allows for a wide spectrum of sample analyses, compared with other DNA methylation approaches, some of them based on the sensitivity of restriction enzymes that can specifically recognize methylated cytosines within their cleavage recognition sites (28)(29)(30)(31)(32)(33) …”

Section: Dna Methylationmentioning

confidence: 99%

Study of the Epigenetic Signals in the Human Genome

Ferreira

Afreixo

Moura

et al. 2017

11th International Conference on Practical Applications of Computational Biology &Amp; Bioinformatics

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“…DNA methylation analysis by sequencing DNA methylation status was determined using sodium bisulfite treatment (Hajkova et al 2002). Bisulfite treatment was performed with ≤2 μg of 32 samples of genomic DNA from different tissues using Epitect Plus Bisulfite Conversion Kit (Qiagen, Valencia, CA, USA) and EZ DNA MethylationGold Kit (Zymo Research, Irvine, CA, USA) following manufacturer's guidelines.…”

Section: Pcr and Genotypingmentioning

confidence: 99%

“…To confirm allele-specific methylation, the reverse strand was analyzed separately with allele-specific sequencing primers amplifying two fragments (511 and 418 bp) to encompass the promoter region (Hajkova et al 2002).…”

Section: Pcr and Genotypingmentioning

confidence: 99%

In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene

Gonzalez¹,

Salces-Ortiz²,

Calvo

et al. 2016

Cell Stress and Chaperones

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Gene promoters are essential regions of DNA where the transcriptional molecular machinery to produce RNA molecules is recruited. In this process, DNA epigenetic modifications can acquire a fundamental role in the regulation of gene expression. Recently, in a previous work of our group, functional features and DNA methylation involved in the ovine HSP90AA1 gene expression regulation have been observed. In this work, we report a combination of methylation analysis by bisulfite sequencing in several tissues and at different developmental stages together with in silico bioinformatic analysis of putative regulating factors in order to identify regulative mechanisms both at the promoter and gene body. Our results show a "hybrid structure" (TATA box + CpG island) of the ovine HSP90AA1 gene promoter both in somatic and nondifferentiated germ tissues, revealing the ability of the HSP90AA1 gene to be regulated both in an inducible and constitutive fashion. In addition, in silico analysis showed that several putative alternative spliced regulatory motifs, exonic splicing enhancers (ESEs), and G-quadruplex secondary structures were somehow related to the DNA methylation pattern found. The results obtained here could help explain the differences in cell-type transcripts, tissue expression rate, and transcription silencing mechanisms found in this gene.

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DNA-Methylation Analysis by the Bisulfite-Assisted Genomic Sequencing Method

Cited by 71 publications

References 11 publications

Selection against PUMA Gene Expression in Myc-Driven B-Cell Lymphomagenesis

Selection against PUMA Gene Expression in Myc-Driven B-Cell Lymphomagenesis

Study of the Epigenetic Signals in the Human Genome

In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene

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