Post on 05-Jan-2016
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