Voynich Transcription - A Glyph-Based Transcription of the Voynich Manuscript
Trying to represent transcription The functions, the process, and the connections between the two.
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Transcript of Trying to represent transcription The functions, the process, and the connections between the two.
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