module: dmel_rnapii_general_transcription_factors
title: RNA polymerase II general transcription factors in Drosophila melanogaster
label: RNA polymerase II general transcription factors
module_type: PROTEIN_COMPLEX
description: >-
  The general transcription factors TFIID, TFIIA, TFIIB, TFIIE, TFIIF and TFIIH
  assemble with RNA polymerase II on core promoters to form the preinitiation
  complex. TFIID, built from the TATA-box binding protein (TBP) and
  TBP-associated factors (TAFs), recognizes core promoter elements; TFIIA
  stabilizes TBP binding to DNA. TFIIF escorts polymerase into the complex and
  TFIIE recruits TFIIH. TFIIH contains the XPB (hay) translocase that opens
  promoter DNA, the XPD helicase, and the CDK-activating kinase (Cdk7, CycH,
  Mat1), which phosphorylates the polymerase C-terminal domain during
  initiation; TFIIH also acts in nucleotide excision repair. In Drosophila
  testis, paralogous testis-specific TAFs (tTAFs) and a germline TFIIA small
  subunit variant drive the spermatocyte transcription program.
summary: >-
  TFIID, TFIIA, TFIIE, TFIIF and TFIIH, which assemble the RNA polymerase II
  preinitiation complex at core promoters.
concepts:
  - {id: GO:0097550, label: transcription preinitiation complex}
cellular_components:
  - {id: GO:0005634, label: nucleus}
parts:
  - id: tfiid
    label: TFIID
    role: core promoter recognition
    description: >-
      TBP and TBP-associated factors. FlyBase also lists Gas41 (YEATS domain)
      and cabeza (caz, FET family) in this group as TFIID-associated proteins.
    group: TFIID
    complex_term: {id: GO:0005669, label: transcription factor TFIID complex}
    function: {id: GO:0016251, label: RNA polymerase II general transcription initiation factor activity}
    processes:
      - {id: GO:0006367, label: transcription initiation at RNA polymerase II promoter}
  - id: tfiia
    label: TFIIA
    role: TBP-DNA stabilization
    variant_sets:
      - id: tfiia_variants
        label: TFIIA small-subunit variants
        selection: ONE_OR_MORE
        variants:
          - {id: tfiia_s, label: TFIIA with TfIIA-S, group: TFIIA-S, complex_term: {id: GO:0005672, label: transcription factor TFIIA complex}}
          - {id: tfiia_s2, label: Germline TFIIA with TfIIA-S-2, group: TFIIA-S2, complex_term: {id: GO:0005672, label: transcription factor TFIIA complex}}
  - id: tfiie
    label: TFIIE
    role: TFIIH recruitment
    group: TFIIE
    complex_term: {id: GO:0005673, label: transcription factor TFIIE complex}
    function: {id: GO:0016251, label: RNA polymerase II general transcription initiation factor activity}
  - id: tfiif
    label: TFIIF
    role: polymerase recruitment to the preinitiation complex
    description: >-
      TfIIFalpha and TfIIFbeta; FlyBase also includes ear, the YEATS-domain
      ENL/AF9 relative, whose yeast counterpart Taf14 is a TFIIF subunit.
    group: TFIIF
    complex_term: {id: GO:0005674, label: transcription factor TFIIF complex}
    function: {id: GO:0016251, label: RNA polymerase II general transcription initiation factor activity}
  - id: tfiih
    label: TFIIH
    role: promoter opening and CTD phosphorylation
    complex_term: {id: GO:0005675, label: transcription factor TFIIH holo complex}
    parts:
      - id: tfiih_core
        label: TFIIH core
        role: DNA translocase and helicase core
        group: TFIIH-C
        complex_term: {id: GO:0000439, label: transcription factor TFIIH core complex}
        unit_functions:
          Xpd: {id: GO:0043139, label: 5'-3' DNA helicase activity}
      - id: cak
        label: CDK-activating kinase
        role: RNA polymerase II CTD kinase
        group: CAK
        complex_term: {id: GO:0070985, label: transcription factor TFIIK complex}
        unit_functions:
          Cdk7: {id: GO:0008353, label: RNA polymerase II CTD heptapeptide repeat kinase activity}
  - id: testis_tafs
    label: Testis-specific TBP-associated factors
    role: testis-specific TFIID-related factors
    description: >-
      tTAFs (can, mia, nht, sa, Taf12L) are paralogs of TFIID TAFs expressed in
      primary spermatocytes, where they are needed for transcription of
      spermatid differentiation genes and meiotic cell-cycle genes.
    group: T-TAF
    complex: false
notes: >-
  Boundary. TFIIB (TfIIB) has no FlyBase group of its own in this set and is not
  added. FlyBase's CAK-XPD group (Cdk7, CycH, Mat1, Xpd) is fully covered by the
  CAK part plus Xpd in the TFIIH core part, so it is not modelled as a separate
  node. Gas41 and caz are FlyBase TFIID group members kept as listed;
  they are not canonical TAFs. The tTAFs are emitted one annoton per gene because
  the composition of testis TFIID-like complexes is not settled. RNA polymerase
  II itself is in dmel_nuclear_rna_polymerases.