Direct bisulfite sequencing of CNRIP1, FBN1, INA , and SNCA confirmed methylation status as assessed by methylation-specific polymerase chain reaction (MSP). A) CNRIP1. B) FBN1. C) INA. D) SNCA. For all panels, the upper part is a schematic presentation of the CpG sites (vertical bars) amplified by the bisulfite sequencing primers (110 to 470, NM_015463; -85 to 325, NM_000138; -110 to 71, NM_032727; and -169 to 91, NM_000345, respectively). The transcription start site is represented by +1 and the arrows indicate the location of the MSP and qMSP primers. For the lower part of the panels, black circles represent methylated CpGs (the presence of more than 80% cytosine); white circles represent unmethylated CpGs (0 to 20% cytosine); and gray circles represent partially methylated sites (20-80% cytosine). The column of U, M, and U/M at the right side of this lower part lists the methylation status of the respective cell lines as assessed by us using MSP analyses. The transcription start point of CNRIP1 is here according to hg17 NM_015463. When the gene was annotated the transcription start point was moved 340 bases upstream of the indicated position. Abbreviations: MSP, methylation-specific polymerase chain reaction; s, sense; as, antisense; p, probe; U, unmethylated; M, methylated; U/M, presence of both unmethylated and methylated band.