DNA methylation and transcription

DNA methylation affects TF binding and transcription

Inroduction: It's commonly accepted that DNA methylation of a promoter repress transcription of this gene in normal tissues. Recently, a class of actively expressed genes having relatively methylated promoters has been discovered.

Our purposes:

• To explore the idea that DNA methylation affects TFBS, preventing some TF from binding to DNA, and therefore represses transcription.
  * To select TFs most likely sensitive to DNA methylation (first, in human, mb in other spicies later)
  

We plan to do:
1. Functional analysis
- Predict TFBS (TFBS clusters?) in promoters
- Estimate methylation level of each TFBS (may be, only core positions of TFBS)
- Calculate correlation between level of methylation and expression from given promoter for each TFBS
- Select lists of TFs with highest and lowest cc
2. Evolutionary analysis
- Predict TFBS (TFBS clusters?) in promoters
- For whole set of given TF's binding sites estimate probability of C>T SNP (in CG or in CNG) and of C>T interlineage substitution

We have data:
Primary cells:
peripheral blood mononuclear cells (genome-wide BS-seq + CAGE)
Tissues:
frontal cortex (genome-wide MeDIP-seq) - frontal lobe (CAGE)

We seek for data:
DNA methyaltion with single bp resolution (genome-wide or with coverage of not less when 1% of genome) in primary cells, tissues or cell lines represented in FANTOM5

Collaboration: Piotr (you are invited to add your plans of study on influence of TF on methylation)

TF binding affects DNA methylation

Collaborators are very welcome. If you have any ideas how to improve the research, please contact me directly or add your suggestion here.