Trying to represent transcription

The functions, the process, and the connections between the two

Problems with transcription in GO

Problems with transcription in GO

- Why does RNA pol II transcription factor activity NOT have any relationship to DNA binding?

- What exactly is “general” vs “nonspecific” vs “specific” transcription?

- Why does transcription factor activity NOT have any relationship to promoter binding?

- What is a transcription regulator activity in terms of function, rather than process?

Def: Plays a role in regulating transcription;may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.

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

Bacterial (E. coli) Transcription:core RNAP vs holo RNAP

Ishihama. 2010. FEMS Microbiol Rev. 34(5):611-27 (PMID:20629756)

Bacterial (E. coli) Transcription:basal transcription

Promoter - binding site for holo RNAPBasal transcription - requires only holo RNAP

Bacterial (E. coli) Transcription:activated transcription

Ishihama. 2010. FEMS Microbiol Rev. 34(5):611-27 (PMID:20629756)

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

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…

•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

Plastid (chloroplast) RNA polymerases•RNAP (bacterial-type x2) •RNAP (phage T3/T7 like)

•RNAP (in plants; bacterial-type)

80% 5%15%

RNA pol II transcription:core (basal) promoter elements

Thomas MC & Chiang CM. Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78. (PMID:16858867)

RNA pol II transcription:Preinitiation Complex (PIC) assembly

Thomas MC & Chiang CM. Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78. (PMID:16858867)

Do not bind DNADo bind DNA

General* transcription – only needs general transcription factors

*General => basal

RNA pol II transcription:PIC assembly - more than 1 way…

Sikorski TW & Buratowski S. Curr Opin Cell Biol. 2009 Jun;21(3):344-51. (PMID:19411170)

What is a promoter?

RNA polymerase II

Bacterial (E. coli sigma70)

Binding to transcription regulatory regions

Using the has_part relationshipfor transcription factor activities

RNA polymerase III promoters

RNAP III transcription factors

Schramm L, Hernandez N. Genes Dev. 2002 Oct 15;16(20):2593-620. (PMID:12381659)

TFIIIC

Functions as part of processes