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Trying to represent transcription

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

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Trying to represent transcription

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

  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. 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

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

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

  11. 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)

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

  13. Binding to transcription regulatory regions

  14. Using the has_part relationshipfor transcription factor activities

  15. RNA polymerase III promoters

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

  17. Functions as part of processes

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