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

Problems with transcription in GO

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?

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 RNAP Basal 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… 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)

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 *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. 2006 May-Jun;41(3):105-78. (PMID:16858867)

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? Bacterial (E. coli sigma70) RNA polymerase II

Binding to transcription regulatory regions

Using the has_part relationship for transcription factor activities

RNA polymerase III promoters

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

Functions as part of processes