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Rasoul Alikhani-Koopaei, Fatemeh Fouladkou, Felix J. Frey, Brigitte M. Frey
Published in Volume 114, Issue 8
J Clin Invest. 2004; 114(8):1146–1157 doi:10.1172/JCI21647
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Figure 5

EMSA with differentially methylated or unmethylated NF1 probes. (A and B) EMSA with fully methylated (Me-NF1) or unmethylated (U-NF1) NF1 probes of the human HSD11B2 promoter was performed on SW620 cell nuclear protein extracts after overexpression of HA-tagged murine NF1 isoforms NF1-A1.1, NF1-B2, NF1-C2, or NF1-X2 (A) and NF1-C2 or NF1-X2 (B). The position of methylation-specific complexes (Meth. Sp. compl.) and NF1-specific complexes (NF1 compl.) or nonspecific bands (N.S.) are indicated along the left margins. Supershifts were performed with HA-specific antibodies (Ab.HA). For competition studies, a 100-fold (×100) molar excess of a cold methylated (Me-), unmethylated (U-) or a consensus unmethylated (NF1-Cons. 100×) NF1 probe was used. The sequences and methylation sites of the probes are given in Table 1. (CE) EMSA with site-specific methylated probes. EMSA was performed on SW620 cell nuclear protein extracts after overexpression of the HA-tagged murine NF1-X2 isoform. Different DNA probes [Me-NF1(1CG), Me-NF1(2CG), Me-NF1, and U-NF1], including mutated probes [U-NF1(Tg) or Me-NF1(Tg)] and their corresponding cold competitors (×100), were used (see Table 1). Supershifts were performed with specific (Ab.HA, Ab.MBD1) or unrelated (Ab.MBD2 and Ab.Arnt) antibodies. Whereas C demonstrates that the position of CpG methylation and D, that the composition of core neighboring nucleotides affect the binding of NF1, E suggests that MBD1 interacts with NF1 at the NF1 binding site. Sp. compl.; specific complexes.