1. Trying to represent transcription
The functions, the process, and the connections between the two

2. Problems with transcription in GO

3. Problems with transcription in GO
Def: Plays a role in regulating transcription;
may bind a promoter or enhancer DNA sequence
or interact with a DNA-binding transcription factor.
- Why does RNA pol II transcription factor activity NOT have any relationship to DNA binding?
- What exactly is “general” vs “nonspecific” vs “specific” transcription?
- What is a transcription regulator activity in terms of function, rather than process?
- Why does transcription factor activity NOT have any relationship to promoter binding?

4. Major goals for overhaul
Define transcription factor activities in terms of HOW they act,
e.g. promoter binding, RNA polymerase binding, etc.
- Remove terms from Molecular Function that are defined in terms of the process,
rather than in terms of HOW they act

5. Bacterial (E. coli) Transcription: core RNAP vs holo RNAP
Ishihama FEMS Microbiol Rev. 34(5): (PMID: )

6. Bacterial (E. coli) Transcription: basal transcription
Promoter - binding site for holo RNAP
Basal transcription - requires only holo RNAP

7. Bacterial (E. coli) Transcription: activated transcription
Ishihama FEMS Microbiol Rev. 34(5): (PMID: )
Activated transcription - requires a transcription factor in addition to holo RNAP
Transcription factor classes defined by which RNAP subunit contacted,
as well as by whether or not DNA is contacted

8. Transcription in eukaryotes: somewhat more complex…
Multisubunit nuclear RNA polymerases
RNA polymerase I – large rRNA transcript (more in Trypanosomes)
RNA polymerase II – mRNAs, most snRNAs, many snoRNAs, more…
RNA polymerase III – 5S rRNA, tRNAs, snRNA U6 (usually), more…
80% 5%
15%
RNA polymerase IV (plants) – siRNAs
RNA polymerase V (plants) – noncoding transcripts at target loci
Mitochondrial RNA polymerase(s)
RNAP (phage T3/T7 like) – mito rRNAs, many mito tRNAs, a few proteins
RNAP (in plants; bacterial-type)
Plastid (chloroplast) RNA polymerases
RNAP (bacterial-type x2)
RNAP (phage T3/T7 like)

9. RNA pol II transcription: core (basal) promoter elements
Thomas MC & Chiang CM. Crit Rev Biochem Mol Biol May-Jun;41(3): (PMID: )

10. RNA pol II transcription: Preinitiation Complex (PIC) assembly
*General
=> basal
Do bind DNA
Do not bind DNA
General* transcription – only needs general transcription factors
Thomas MC & Chiang CM. Crit Rev Biochem Mol Biol May-Jun;41(3): (PMID: )

11. RNA pol II transcription: PIC assembly - more than 1 way…
Sikorski TW & Buratowski S. Curr Opin Cell Biol Jun;21(3): (PMID: )

12. What is a promoter?
Bacterial (E. coli sigma70)
RNA polymerase II

13. Binding to transcription regulatory regions

14. Using the has_part relationship for transcription factor activities

16. RNA polymerase III promoters

17. RNAP III transcription factors
TFIIIC
Schramm L, Hernandez N. Genes Dev Oct 15;16(20): (PMID: )

18. Functions as part of processes