[mock] Gene regulation

[shouldsee]

LoL

1. On which protein is the first ChIP-Seq is performed?

2. In ChIP-Seq, what factors contribute to a spurious peak? What experimental/computational procedures can you take to reduce such noises?

3. How is a TF-binding motif represented computationally? How can you use this representation to interrogate observed sequence reads?

4. What are the necessary and essential conditions for a gene to be transcribed?

5. List experiment techniques to interrogate

   • RNAPII activity
   • Ribosome activity
   • DNA methylation
   • Chromatin Accessibility
   • Histone modification
   • TF binding-site
   • ncRNA effect site

[shouldsee]

Answers

1. STAT1, a transcription factor stimulating immune cells.

2. • Experimental: Use a control. Probing chromatin accessibility
   • Computational: Peak-calling using dynamic Poisson modelling (MACS). Account for degeneracy of a ~20mer over the genome and adjust read concentration. Cross-validate with other genomic tracks.