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Table 3 Expected sign of SCC M/E depending on TF binding preferences and function

From: Effects of cytosine methylation on transcription factor binding sites

TF binding preferences
TF function Unmethylated DNA Methylated DNA Both
Activator (1) negative SCC M/E (2) positive SCC M/E insignificant SCC M/E
Repressor (3) positive SCC M/E (4) negative SCC M/E insignificant SCC M/E
Both insignificant SCC M/E insignificant SCC M/E  
  1. There are four possible scenarios of interaction of DNA methylation and TF functions:
  2. (1) TF can bind unmethylated DNA and cannot bind methylated DNA. TF acts as a transcription activator. The methylation profile of cytosines within TFBS should be negatively correlated with TSS expression.
  3. (2) TF can bind methylated DNA and cannot bind unmethylated DNA. TF acts as a transcription activator. The methylation profile of cytosines within TFBS should be positively correlated with TSS expression.
  4. (3) TF can bind unmethylated DNA and cannot bind methylated DNA. TF acts as a transcription repressor. The methylation profile of cytosines within TFBS should be positively correlated with TSS expression.
  5. (4) TF can bind methylated DNA and cannot bind unmethylated DNA. TF acts as transcription repressor. The methylation profile of cytosines within TFBS should be negatively correlated with TSS expression.