TFIID

"TFIID is an ~1 megadalton (1000 kDa) complex consisting of TBP and TAF1–13" → about 71 kDa per protein (700 aa)

• Recent insights into the structure of TFIID, its assembly, and its binding to core promoters
  • Role in transcription initiation
    • Recognizes core promoter sequences — binds to all promoters and loads TBP, regardless of TATA box → recruits PIC via TBP (TFIIH, RNAP, Mediator complexes)
      • Binding to core promoter → release of TBP from Lobe A; inhibitory interactions blocking functional surfaces are overcome
      • Last step of TBP-promoter binding sterically causes release from TAF11 on Lobe A → opens binding to TFIIB → recruits Pol II, likely bound to TFIIH
      • Dynamics likely regulated by co-factors, gene-specific activators and repressors
    • Regulates expression by contact with gene-specific cofactors, ADs, RDs, chromatin mods
  • Structure
    • Difficult to study: hard to recombinantly express, limited endogenous sources, flexible + fragile complex
    • Cryo-EM → horseshoe shape with three lobes (A, B, C); B and C are relatively rigid but A moves from touching lobe C (canonical) to B (rearranged)
      • Only rearranged state can bind DNA (studied using super core promoter (SCP) DNA)
      • TAF1-TAF7 module interacts with downstream core promoter sequences
      • TAF1: disordered region interacts with Inr; zinc knuckle domain may also interact with DNA
      • Lobe A → nucleosome core particle-like octamer of histone fold domains (4th pair differs when interacting with B vs C) — used for scaffolding instead of DNA wrapping like actual histones (lost positive charge)
  • TFIID assembly
    • Model: four subcomplexes of TAFs form in cytoplasm, each with an NLS → goes to nucleus and finishes assembly
    • How is asymmetry established?
  • Human versus yeast
    • Some structural differences
    • Uncertain whether mechanism of TBP loading is conserved
    • Best known differences in IDRs, which bind co-activators + chromatin
      • In humans: N-term of TAF4 is most well-characterized AD; vs N-term of TAF12 in yeast
      • In humans: TAF3 PHD binds H3K4me3, TAF1 double-bromo domain binds H4Kac; neither exist in yeast
    • Plant TAFs more closely resemble yeast TAFs, suggesting metazoan TFIID is more specialized
• Structure of human TFIID and mechanism of TBP loading onto promoter DNA
• Structural insights into preinitiation complex assembly on core promoters
• Structural dynamics and DNA interaction of human TFIID
• TATA-less promoters — how is TFIID recruited?
  • Sharp versus broad TSS selection

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Mediator

• Roger Kornberg (Mediator, transcriptional squelching)

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Other mechanisms of activation

• p300
• PFAC and whatever
• Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes (link needed)