user:Yohhans

1. Mechanism of Transcription
2. Transcription
3. Structure of RNA
4. RNA Synthesis
5. Three stages in transcription
6. RNA polymerase
7. E. coli RNA polymerase
8. Sigma factors
9. Lac operon
10. Control of elongation in E. coli
11. Eukaryotic RNA polymerases
12. Three Eukaryotic RNA polymerases are multi-protein complexes that share many common subunits
13. Promoter
14. TATA box
15. Initiator sequences (INR)
16. CpG island promoter
17. General transcription factors
18. Transcription initiation
19. Regulation of transcription elongation

1. Part 1
2. Part 2
3. Part 3
4. Part 4

Misc. intro stuff

1. Central problem is to figure out how genes are selected for expression during growth, differentiation, or in response to the environment
2. Need to determine how a gene is specified by cis-DNA
3. cis-elements are promoters, enhancers, silencers and insulators

First we are going to look at core promoter elements. The core promoter is a region that is upstream of the transcription start site (TSS +1), and it contains several elements that facilitate the binding of regulatory elements. These elements form the pre-initiation complex (PIC).

Core promoters are divided into two different classes: TSS is focused over a narrow region, or it is dispersed over a broad region (50-100bp). Some core promoter elements include BRE (GC rich region that is the TFIIB recognition site. CpG dinucleotide is very important here: [GC][GC][GA]CGCC, the TATA box (TATA[AT]A[AT][AG]), and the Inr. A promoter element downstream of the TSS is called a downstream core promoter element.

Despite the TATA box being the

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