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List of subjects:

1. TF binding site mapping genome-wide

2. TF sequence element prediction

3. biochemical determination of binding sequence (e.g. SELEX)

4. Activity assays for TFs

(Samar El Sherbiny)

TF binding site mapping genome-wide

The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We have different techniques able to identify this TFBS: 

a. ChIP-seq

ChIP-seq is a technique that combines two aspects: chromatine immunoprecipitation with sequencing. It's a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific antibody. The bound DNA is then coprecipitated, purified, and sequenced. 

Advantages:

• We can analyze the entire genome;
• It reveals gene regulatory networks in combination with RNA sequencing and methylation analysis;
• It offers compatibility with various input DNA samples.

ChIP-seq workflow: