Lecture 17: Transcription Factor Motif and ChIP-seq

What is ATAC-seq used for?

To identify open chromatin regions, indicating active regulatory elements.

How does ATAC-seq relate to gene expression?

It reflects epigenetic control — accessible DNA regions often regulate transcription. 

What does RNA-seq measure?

Gene expression (RNA transcripts)

What does ATAC-seq measure?

Chromatin accessibility (open regulatory DNA).

Why is both RNA-seq measure & ATAC-seq measure used?

RNA-seq shows output (gene activity), ATAC-seq shows regulation (control regions).

What is notable about hemoglobin gene clusters? 

Genes are regulated in clusters, often controlled by shared regulatory elements 

What does TBP stand for? 

TATA-binding protein. 

What is the TATA box?

A promoter DNA sequence that binds to initiate transcription

What are transcription factors?

Proteins that binds to specific DNA sequences to regulate transcription

What are TF binding motifs? 

Short, specific DNA sequences recognized by TFs. 

What does ChIP-seq stand for?

Chromatin Immunoprecipitation Sequencing

What is the purpose of the ChIP-seq?

To identify where specific proteins (i.e., TFs) binds to DNA genome-wide.

What does ChIP-seq reveal? 

Functional regulatory elements such as promoters, enhancers, or binding sites.