| Literature DB >> 20593890 |
Bernardina T F van der Gun1, Maria Maluszynska-Hoffman, Antal Kiss, Alice J Arendzen, Marcel H J Ruiters, Pamela M J McLaughlin, Elmar Weinhold, Marianne G Rots.
Abstract
The epithelial cell adhesion molecule (EpCAM) is a membrane glycoprotein that has been identified as a marker of cancer-initiating cells. EpCAM is highly expressed on most carcinomas, and transient silencing of EpCAM expression leads to reduced oncogenic potential. To silence the EpCAM gene in a persistent manner via targeted DNA methylation, a low activity mutant (C141S) of the CpG-specific DNA methyltransferase M.SssI was coupled to a triple-helix-forming oligonucleotide (TFO-C141S) specifically designed for the EpCAM gene. Reporter plasmids encoding the green fluorescent protein under control of different EpCAM promoter fragments were treated with the TFO-C141S conjugate to determine the specificity of targeted DNA methylation in the context of a functional EpCAM promoter. Treatment of the plasmids with TFO-C141S resulted in efficient and specific methylation of the targeted CpG located directly downstream of the triple helix forming site (TFS). No background DNA methylation was observed neither in a 700 bp region of the EpCAM promoter nor in a 400 bp region of the reporter gene downstream of the TFS. Methylation of the target CpG did not have a detectable effect on promoter activity. This study shows that the combination of a specific TFO and a reduced activity methyltransferase variant can be used to target DNA methylation to predetermined sites with high specificity, allowing determination of crucial CpGs for promoter activity.Entities:
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Year: 2010 PMID: 20593890 PMCID: PMC2907751 DOI: 10.1021/bc1000388
Source DB: PubMed Journal: Bioconjug Chem ISSN: 1043-1802 Impact factor: 4.774
Figure 1Schematic overview of EpCAM promoter fragments in the GFP reporter plasmids. (A) Plasmid p39E encompasses the GFP gene under control of 3.4 kb of the EpCAM promoter. The Triple helix Forming Site (TFS) and sequences differing from the targeted TFS by only three or four mismatches (3MM or 4MM) are indicated. CpGs are depicted by vertical bars. The transcription start site (TSS) corresponds to position +1. The location of the amplicons analyzed for DNA methylation are indicated (not drawn to scale). (B) Sequence of one strand of bisulfite converted, fully methylated DNA of the TFS amplicon. All cytosines in CpG combination are assumed to be methylated and therefore not converted by bisulfite treatment. The CpGs are numbered and depicted in green. The TFS is shown in red, containing three Cs that have been converted to Ts. CpG number 7 is the targeted CpG.
Targeted DNA Methylation of p39E by TFO−C141S
| (A) Methylation Status of Bisulfite Amplicons for p39E Treated with TFO−C141S and the Methyl Donor SAM |
| (B) Methylation Status of Bisulfite Amplicons for p39E Treated with the Controls As Indicated |
Results of bisulfite sequencing.
Figure 2Effect of TFO−C141S treatment on GFP expression in EpCAM positive SKOV3 cells. (A) Relative GFP expression measured 48 h after transfection of pretreated p39E. Plasmid p39E was treated as indicated: p39E = treatment without TFO−C141S, treated with TFO only, with untargeted M.SssI or C141S, with the TFO−C141S conjugate or with 100-fold excess of TFO and TFO−C141S (=competition). The value obtained with p39E without TFO−C141S was taken as 100%. Shown is the average GFP expression (±SD) of one representative transfection performed in triplicate. (B) Relative GFP expression measured 48 h after transfection of pretreated deletion derivatives p7-2 and p4-1. For each derivative, the values obtained with samples treated without TFO−C141S were taken as 100%. Shown is the average GFP expression (±SEM) of the mean of three independent transfections performed in triplicate. (C) Relative GFP expression was measured 48 h after transfection of pretreated p39E or p39C. Treatments were as indicated: (+) or (−) indicates the presence or absence of the methyl donor (SAM). Shown is the average GFP expression (±SEM) of the mean of three independent transfections performed in triplicate.
Targeted DNA Methylation of p39E Deletion Derivatives by TFO−C141Sa
Methylation status of bisulfite amplicons for the deletion derivatives p39E treated with TFO−C141S and the methyl donor SAM. Shown are the results of bisulfite sequencing. n = number of clones analyzed. Below the lollipop: the percentage of clones of which the CpG was methylated. Open lollipop: 0% methylated CpG. Black lollipop: 100% methylated CpG.
Figure 3Effect of TFO-141S treatment on plasmid conformation. (A) Agarose gel electrophoresis of plasmids p39E and p11-1 treated with the TFO, WT M.SssI, C141S, or the TFO−C141S conjugate: lane 1, untreated; lane 2, without TFO−C141S; lane 3, TFO; lane 4, M.SssI; lane 5, C141S; lane 6, TFO−C141S; lane 7, TFO- C141S without SAM; lane 8, 100-fold excess of TFO and TFO−C141S; lane 9, marker; lane 10, without TFO−C141S; lane 11, C141S; lane 12, TFO−C141S. (B) Agarose gel electrophoresis of plasmid p39E treated with active and heat-inactivated C141S and TFO−C141S. The supercoiled plasmid was incubated at 30 °C for different time points as indicated above the lanes (hours). Then the samples were deproteinized before electrophoresis as described in Experimental Procedures. (C) Agarose gel electrophoresis of plasmid p39C and p39E treated with the TFO−C141S conjugate only or in the presence of 100-fold excess of TFO. Plasmids were incubated as in part B. Lane a is purified plasmid.