module: dmel_rnapii_elongation_complexes
title: RNA polymerase II elongation complexes in Drosophila melanogaster
label: RNA polymerase II elongation complexes
module_type: PROTEIN_COMPLEX
description: >-
  After initiation, RNA polymerase II pauses shortly downstream of most
  Drosophila promoters, held by DSIF (Spt4-Spt5) and NELF. Release into
  productive elongation requires P-TEFb (Cdk9-CycT), which phosphorylates
  NELF, Spt5 and the polymerase C-terminal domain; P-TEFb is held inactive by
  Hexim within the 7SK snRNP and is also recruited within the super elongation
  complex (SEC), which carries the ELL elongation factor Su(Tpl). The related
  little elongation complex (LEC) promotes transcription of snRNA genes. During
  elongation, the PAF1 complex couples polymerase to co-transcriptional histone
  modification, FACT reorganizes nucleosomes in front of and behind the
  polymerase, and elongin stimulates the elongation rate.
summary: >-
  Pausing (DSIF, NELF), pause-release (P-TEFb, 7SK snRNP, SEC) and elongation
  (PAF1C, FACT, elongin, LEC) factors acting on RNA polymerase II.
concepts:
  - {id: GO:0008023, label: transcription elongation factor complex}
cellular_components:
  - {id: GO:0005634, label: nucleus}
parts:
  - id: dsif
    label: DSIF
    role: pausing and elongation factor
    group: DSIF
    complex_term: {id: GO:0032044, label: DSIF complex}
  - id: nelf
    label: Negative elongation factor
    role: promoter-proximal pausing
    group: NELF
    complex_term: {id: GO:0032021, label: NELF complex}
    processes:
      - {id: GO:0160239, label: transcription pausing by RNA polymerase II}
  - id: p_tefb
    label: P-TEFb
    role: pause-release kinase
    group: P-TEFB
    complex_term: {id: GO:0070691, label: P-TEFb complex}
    unit_functions:
      Cdk9: {id: GO:0008353, label: RNA polymerase II CTD heptapeptide repeat kinase activity}
  - id: snrnp_7sk
    label: 7SK snRNP
    role: P-TEFb sequestration
    description: >-
      7SK snRNA (snRNA:7SKa and snRNA:7SKb loci), the capping enzyme bin3, Larp7
      and Hexim, which binds and inhibits P-TEFb.
    group: 7SKRNP
    complex_term: {id: GO:0120259, label: 7SK snRNP}
  - id: sec
    label: Super elongation complex
    role: P-TEFb recruitment and elongation stimulation
    group: SEC
    complex_term: {id: GO:0032783, label: super elongation complex}
  - id: lec
    label: Little elongation complex
    role: snRNA gene transcription
    group: LEC
  - id: paf1c
    label: PAF1 complex
    role: elongation-coupled chromatin modification
    variant_sets:
      - id: paf1c_variants
        label: Somatic and testis-specific PAF1 complexes
        selection: ONE_OR_MORE
        variants:
          - {id: paf1c_somatic, label: PAF1 complex, group: PAF1C, complex_term: {id: GO:0016593, label: Cdc73/Paf1 complex}}
          - {id: paf1c_testis, label: Testis-specific PAF1 complex, group: PAF1C-T, complex_term: {id: GO:0016593, label: Cdc73/Paf1 complex}}
  - id: fact
    label: FACT
    role: nucleosome reorganization during elongation
    group: FACT
    complex_term: {id: GO:0035101, label: FACT complex}
  - id: elongin
    label: Elongin
    role: elongation rate stimulation
    group: ELO
    complex_term: {id: GO:0070449, label: elongin complex}
connections:
  - {source: snrnp_7sk, target: p_tefb, connection_type: NEGATIVELY_REGULATES, description: Hexim in the 7SK snRNP binds and inhibits P-TEFb.}
  - {source: p_tefb, target: nelf, connection_type: NEGATIVELY_REGULATES, description: P-TEFb phosphorylation of NELF releases paused polymerase.}
notes: >-
  Boundary. The module groups the FlyBase elongation-factor complexes; RNA
  polymerase II is in dmel_nuclear_rna_polymerases. Eaf and Su(Tpl) are members
  of both SEC and LEC, and ear of both SEC and TFIIF, as in FlyBase. P-TEFb is a
  component of SEC in mammals but FlyBase lists it as a separate group, which is
  followed here. The testis-specific PAF1C is modelled as a variant of PAF1C
  because its subunits are testis paralogs of the somatic subunits; Ski8
  (homolog of the PAF1C subunit WDR61/SKIC8) is listed by FlyBase in the testis
  variant. The 7SK snRNA genes have no protein product and are grounded to
  FlyBase gene ids.