Understand the reasons why complex organisms need transcriptional regulation

Understand what the three eukaryotic RNA polymerases (eRNAPs) are responsible for producing

Understand and describe the positioning of the main regulatory elements in eukaryotic cells and know what binds to them (and when they bind to them)

• TATA box
• Initiator
• BRE
• DPE
• Enhancers

Be able to compare and contrast prokaryotic and eukaryotic promoter regions

List and understand the order of binding of the general transcription factors (and the specific regulatory elements they bind to if applicable)

Know and understand the role of the various proteins that are recruited to the CTD of RNA pol II

Understand how enhancers work with regards to their positioning and orientation, what types of proteins bind to them and how they interact with the promoter initiation complex

Understand in a general sense the two models of transcription termination

For the following mechanisms, understand/describe (to the detail discussed in lecture):

• The genomic features required for the mechanism to take place
• The steps of the mechanism
• The proteins involved at each step
• The outcome(s) of the mechanism

Mechanisms:

Transcription cycle

• Recognition and initiation
• DNA melting
• Promoter clearance Including the phosphorylation events of the CTD of RNA pol II

For mechanisms as well as the other proteins mentioned in the learning objectives, think about what would happen if you removed their functionality through mutagenesis.

Tools/assays to be familiar with and understand when and why they are used:

• Co-immunoprecipitation (Co-IP)
• Enhancer traps
• Linker scanning mutagenesis
• Gel mobility assay
• DNAse footprinting
• Inverse PCR (lecture 14 slide 43)