POB3 Notes

2026-09-28 IBA and literature re-review

IBA

GOA contains one IBA row for POB3: GO:0035101 FACT complex, with
PANTHER:PTN002492356 in the WITH/FROM column. The cached PAINT export for
PTHR45849 FACT COMPLEX SUBUNIT SSRP1 places the FACT-complex IBD on
PTN002492356, a eukaryotic node seeded by direct FACT-complex annotations from
S. cerevisiae POB3, fission yeast pob3, Drosophila Ssrp, Arabidopsis SSRP1,
and vertebrate SSRP1 descendants. The budding-yeast target is present among the
IBA donors because it helped seed the ancestral node; that is expected PAINT
behavior, not circularity. I kept the row as ACCEPT and marked the propagation
review NO_FAILURE_CORE.

Cached literature

• Brewster et al. characterized Cdc68/Spt16 and Pob3 as the abundant CP complex
  and localized the function to the Spt16-Pob3 dimer PMID:9705338.
• Wittmeyer et al. showed that purified Spt16 and Pob3 form a stable, abundant
  heterodimer that is nuclear/chromatin-associated and linked to DNA polymerase
  alpha/primase PMID:10413469; the preceding Pol alpha affinity study already
  identified both Spt16 and Pob3 as Pol1-binding proteins PMID:9199353.
• Schlesinger and Formosa isolated pob3 mutants and showed defects in both
  transcription and replication, including hydroxyurea sensitivity and delayed S
  phase progression PMID:10924459.
• Formosa et al. showed that Nhp6-bound nucleosomes recruit Spt16-Pob3 to form
  SPN-nucleosomes with altered mobility and DNase I sensitivity; the same paper
  explicitly notes that yeast Pob3 lacks the HMG1 DNA-binding motif present in
  metazoan SSRP1 PMID:11432837.
• Ruone/Rhoades/Formosa and later Rhoades/Ruone/Formosa established the
  two-step Nhp6 then Spt16-Pob3 nucleosome-reorganization mechanism in vitro
  [PMID:12952948, PMID:15082784], and Xin et al. refined the model by showing
  that yFACT increases nucleosomal DNA accessibility without obligatory
  H2A-H2B dimer displacement PMID:19683499.
• VanDemark et al. mapped overlapping essential roles for the Spt16 N-terminal
  domain and Pob3 middle domain and connected yFACT to multiple histone contacts
  PMID:18089575. Hoffmann and Neumann later mapped Pob3's acidic C terminus as
  the major in vivo H2A-H2B contact surface, found the C-terminal NLS, and
  linked the CTD deletion to hydroxyurea sensitivity PMID:26414936.
• The Pol II transcription annotations are grounded in the older elongation and
  initiation papers [PMID:14585989, PMID:15987999]. Martin et al. showed in 2018
  that FACT occupancy on S. cerevisiae chromatin is transcription-dependent and
  preferentially tracks RNAP-disrupted nucleosomes PMID:30237209; Pathak et
  al. connected FACT recruitment to histone H3 acetylation genome-wide
  PMID:29695490.
• Shukla et al. extended Spt16/FACT biology to Pol III-transcribed loci, showing
  Spt16 enrichment near the 3' end of all Pol III genes and stress-responsive,
  gene-specific effects on downstream nucleosome positioning and Pol III output
  PMID:33277439.

Newer papers searched

Recent yeast FACT papers add useful mechanistic context but do not require new
GO assertions for POB3 beyond FACT complex membership, histone/nucleosome
binding, and participation in chromatin-based transcription and replication.
Byrd et al. tested fourteen PMA1 3'-end deletion alleles and found that one
modestly increased Spt16 occupancy while also retaining some Pol II and altering
nucleosome occupancy at the same 3' region PMID:39103906. Barman et al. used
Pob3/Spt16 TAP-MS in soluble and insoluble fractions to expand the FACT
interaction network and to show that San1-dependent regulation of Spt16 changes
associations with epigenetic, transcription, and repair factors PMID:39855624.

Curation decisions

• Retained the IBA GO:0035101 FACT complex as a sound conserved complex
  inference from PANTHER:PTN002492356.
• Switched the UniProt-keyword GO:0006351 DNA-templated transcription row to
  ACCEPT, because the broad process is a core FACT role and is already used in
  the transcription core function.
• Changed all ten GO:0005515 protein binding IPI rows to REMOVE. The AP-MS
  and targeted interaction evidence is real, but the bare parent term is
  uninformative; the review already captures the biologically interpretable
  interactions as FACT complex membership, nucleosome binding, histone binding,
  replication, and transcription/chromatin organization.