spt16

UniProt ID: O94267
Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Review Status: COMPLETE
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Gene Description

Essential large subunit of the FACT (Facilitates Chromatin Transcription) complex in S. pombe. Spt16 forms a heterodimer with Pob3 to act as a histone chaperone that transiently destabilizes nucleosomes during RNA polymerase II transcription elongation and restores nucleosomal structure in the wake of the polymerase. FACT can reorganize histone-DNA contacts without obligate eviction of an H2A-H2B dimer. The N-terminal domain contains a repurposed aminopeptidase P fold that directly binds histone H3-H4, while the C-terminal acidic tail engages H2A-H2B. Beyond transcription, FACT maintains chromatin integrity at centromeric heterochromatin independently of RNAi, facilitates heterochromatin spreading by suppressing histone turnover to enable the H3K9me2-to-me3 transition, prevents promiscuous CENP-A deposition at non-centromeric loci, and participates in replication-coupled parental histone segregation for epigenetic inheritance. FACT also maintains nucleosome occupancy at subtelomeric regions required for their compaction into knob structures.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006337 nucleosome disassembly
IBA
GO_REF:0000033 		ACCEPT
Summary: Supported by phylogenetic inference. FACT promotes transient nucleosome disassembly during transcription elongation, as demonstrated in S. pombe by the cooperation between Spt16/FACT and Fft3 to induce nucleosome disassembly at transcribing regions.
GO:0032784 regulation of DNA-templated transcription elongation
IBA
GO_REF:0000033 		ACCEPT
Summary: Correct. FACT is a well-established regulator of transcription elongation, facilitating Pol II passage through chromatin. Supported by multiple S. pombe studies showing Spt16 cooperates with Fft3 and is modulated by H2Bub during elongation.
Supporting Evidence:
PMID:28218250
Fun30Fft3 cooperates with FACT to induce nucleosome disassembly at transcribing regions, which accounts for a large fraction of RNAPII-mediated nucleosome disassembly.
PMID:31837996
...FACT and H2Bub globally repress antisense transcripts near the 5' end of genes and inside gene bodies, respectively...
GO:0035101 FACT complex
IBA
GO_REF:0000033 		ACCEPT
Summary: Redundant with IDA annotation from PMID:17614284 below. Correct annotation.
GO:0031491 nucleosome binding
IBA
GO_REF:0000033 		ACCEPT
Summary: Supported by structural evidence showing Spt16-N directly binds histone H3-H4 globular core domains and tails, and by the known H2A-H2B chaperone activity of the FACT complex.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005634 nucleus
IEA
GO_REF:0000044 		ACCEPT
Summary: Correct but redundant with IDA evidence from PMID:17614284. Nuclear localization is well established.
GO:0005694 chromosome
IEA
GO_REF:0000044 		ACCEPT
Summary: Reasonable inference from UniProt subcellular location. FACT associates with chromatin at transcribing regions, centromeres, and subtelomeres.
GO:0010468 regulation of gene expression
IEA
GO_REF:0000117 		KEEP AS NON CORE
Summary: Too general. More specific terms such as regulation of DNA-templated transcription elongation (GO:0032784) and chromatin organization (GO:0006325) are already annotated and better capture how FACT regulates gene expression.
Reason: Overly broad; specific child terms already annotated.
GO:0034728 nucleosome organization
IEA
GO_REF:0000117 		ACCEPT
Summary: Correct. FACT reorganizes nucleosomes during transcription and maintains nucleosome occupancy genome-wide. Redundant with NAS annotation from PMID:17614284.
GO:0035101 FACT complex
IEA
GO_REF:0000120 		ACCEPT
Summary: Redundant with IDA annotation from PMID:17614284. Correct.
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0006261 DNA-templated DNA replication
NAS
PMID:17614284
The chromatin-remodeling factor FACT contributes to centrome... 		KEEP AS NON CORE
Summary: Supported by NAS from PMID:17614284 which notes sensitivity of pob3 deletion to HU (hydroxyurea), implicating FACT in DNA replication. Additionally, PMID:38479839 directly demonstrates FACT role in parental histone transfer during replication. However, the direct replication role is better captured by the more specific term DNA replication-dependent chromatin assembly (GO:0006335).
Reason: Supported but less specific than GO:0006335 which is also annotated.
Supporting Evidence:
PMID:17614284
Cells lacking Pob3 are sensitive to HU, CPT, UV and (mildly) to 6-AU, suggesting DNA replication, DNA repair and transcription phenotypes
PMID:38479839
...the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance...
GO:0006335 DNA replication-dependent chromatin assembly
NAS
PMID:38479839
Coordination of histone chaperones for parental histone segr... 		ACCEPT
Summary: Well supported. PMID:38479839 directly demonstrates that FACT regulates parental histone H3-H4 transfer to both daughter strands during DNA replication and collaborates with Mcm2 and Dpb3/4 for epigenetic inheritance.
Supporting Evidence:
PMID:38479839
...the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance...
GO:0006338 chromatin remodeling
IMP
PMID:31837996
The Chaperone FACT and Histone H2B Ubiquitination Maintain S... 		ACCEPT
Summary: Supported. PMID:31837996 demonstrates via MNase-seq and H3 ChIP-seq that FACT mutants show defects in nucleosome positioning and phasing, especially at +1 and TSS-proximal nucleosomes, and loss of nucleosomes at subtelomeres. This constitutes chromatin remodeling activity.
Supporting Evidence:
PMID:31837996
...FACT maintains nucleosomes in subtelomeric regions, which is crucial for their compaction...
GO:0034728 nucleosome organization
NAS
PMID:17614284
The chromatin-remodeling factor FACT contributes to centrome... 		ACCEPT
Summary: Supported. PMID:17614284 establishes FACT as a chromatin remodeling factor in S. pombe, and nucleosome organization is a core function of FACT.
Supporting Evidence:
PMID:17614284
...our genetic and biochemical data implicate the chromatin remodeling complex FACT in forming functional centromeres...
GO:0000511 H2A-H2B histone complex chaperone activity
IC
GO_REF:0000111 		ACCEPT
Summary: Inferred from FACT complex membership. Consistent with direct experimental evidence in PMID:31837996 and PMID:34731638.
Supporting Evidence:
PMID:31837996
we performed nucleosome chaperoning assays with recombinant FACT and recombinant histone octamers
GO:0140673 transcription elongation-coupled chromatin remodeling
IC
GO_REF:0000111 		ACCEPT
Summary: Correct. Inferred from FACT complex membership. FACT's primary role is to reorganize nucleosomes during Pol II elongation, which is precisely this process.
Supporting Evidence:
PMID:28218250
Fun30Fft3 associates with RNAPII and collaborates with the histone chaperone, FACT, which facilitates RNAPII elongation through chromatin, to induce nucleosome disassembly at transcribing regions during RNAPII transcription.
GO:0006335 DNA replication-dependent chromatin assembly
IC
GO_REF:0000111 		ACCEPT
Summary: Inferred from FACT complex membership. Consistent with experimental evidence from PMID:38479839.
GO:0000511 H2A-H2B histone complex chaperone activity
EXP
PMID:31837996
The Chaperone FACT and Histone H2B Ubiquitination Maintain S... 		ACCEPT
Summary: Directly supported. PMID:31837996 demonstrates via in vitro nucleosome chaperoning assays that FACT deposits histones onto DNA, and the contributes_to qualifier is appropriate since this is a complex-level activity where Spt16 contributes as a subunit.
Supporting Evidence:
PMID:31837996
...we performed nucleosome chaperoning assays with recombinant FACT and recombinant histone octamers...
GO:0000511 H2A-H2B histone complex chaperone activity
EXP
PMID:34731638
The histone chaperone FACT facilitates heterochromatin sprea... 		ACCEPT
Summary: Supported. PMID:34731638 demonstrates FACT's histone chaperone function in the context of heterochromatin, showing FACT represses histone turnover which is critical for heterochromatin spreading.
Supporting Evidence:
PMID:34731638
...FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading...
GO:0140719 constitutive heterochromatin formation
IMP
PMID:34731638
The histone chaperone FACT facilitates heterochromatin sprea... 		ACCEPT
Summary: Well supported. PMID:34731638 demonstrates that FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes near heterochromatin boundaries. FACT promotes heterochromatin spreading by suppressing histone turnover.
Supporting Evidence:
PMID:34731638
...FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries...
GO:0000791 euchromatin
EXP
PMID:34731638
The histone chaperone FACT facilitates heterochromatin sprea... 		ACCEPT
Summary: Supported. FACT predominantly associates with gene bodies of actively transcribed genes in euchromatin, while affecting heterochromatin at boundaries.
Supporting Evidence:
PMID:34731638
...FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries...
GO:0140713 histone chaperone activity
IMP
PMID:23028377
Factors that promote H3 chromatin integrity during transcrip... 		ACCEPT
Summary: Well supported. PMID:23028377 demonstrates that FACT mutants impair maintenance of H3 chromatin on transcribed regions and promote widespread ectopic CENP-A(Cnp1) incorporation, directly showing histone chaperone function for maintaining H3 nucleosome integrity during transcription.
Supporting Evidence:
PMID:23028377
...Mutations in the histone chaperone FACT impair the maintenance of H3 chromatin on transcribed regions and promote widespread CENP-A(Cnp1) incorporation at non-centromeric sites...
GO:0006325 chromatin organization
EXP
PMID:23028377
Factors that promote H3 chromatin integrity during transcrip... 		KEEP AS NON CORE
Summary: Broadly correct. PMID:23028377 shows FACT maintains chromatin organization by preserving H3 chromatin integrity during transcription. This is a parent term of more specific annotations like nucleosome organization and chromatin remodeling that are also annotated.
Reason: Correct but broad; more specific child terms (nucleosome organization, chromatin remodeling) are also annotated.
Supporting Evidence:
PMID:23028377
...Mutations in the histone chaperone FACT impair the maintenance of H3 chromatin on transcribed regions and promote widespread CENP-A(Cnp1) incorporation at non-centromeric sites...
GO:0005634 nucleus
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		ACCEPT
Summary: High-throughput localization study confirming nuclear localization. Consistent with IDA from PMID:17614284.
Supporting Evidence:
PMID:16823372
...we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome...
GO:0005515 protein binding
IPI
PMID:17614284
The chromatin-remodeling factor FACT contributes to centrome... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:17614284
...Spt16 and Pob3 associate in vitro and...the interaction requires the Spt16-M domain...
GO:0005634 nucleus
IDA
PMID:17614284
The chromatin-remodeling factor FACT contributes to centrome... 		ACCEPT
Summary: Directly demonstrated by GFP-tagged Spt16 imaging showing nuclear localization.
Supporting Evidence:
PMID:17614284
...Pob3-GFP and Spt16-GFP are nuclear factors...
GO:0035101 FACT complex
IDA
PMID:17614284
The chromatin-remodeling factor FACT contributes to centrome... 		ACCEPT
Summary: Co-purification and interaction experiments identify Spt16 and Pob3 as the fission-yeast FACT complex.
Supporting Evidence:
PMID:17614284
...Mass spectrometry analysis identifies the two bands as Pob3 and Spt16...Spt16 and Pob3 associate in vitro and...the interaction requires the Spt16-M domain...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...
GO:0005515 protein binding
IPI
PMID:18579787
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding... 		KEEP AS NON CORE
Summary: The measured protein interaction is valid but does not specify the histone-chaperone function.
Reason: Retain the experimental interaction as non-core supporting context; the specific histone-chaperone and FACT-complex annotations capture the molecular function.
Supporting Evidence:
PMID:18579787
...the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails...

Core Functions

Histone chaperone within FACT that reorganizes nucleosomes and restores chromatin during RNA polymerase II transcription elongation. H2A-H2B handling is central, but full eviction of exactly one dimer is not an obligatory general mechanism.

Molecular Function:
H2A-H2B histone complex chaperone activity
Directly Involved In:
transcription elongation-coupled chromatin remodeling nucleosome organization
Cellular Locations:
euchromatin
In Complex:
FACT complex
Supporting Evidence:
  • PMID:28218250
    Fun30Fft3 associates with RNAPII and collaborates with the histone chaperone, FACT, which facilitates RNAPII elongation through chromatin, to induce nucleosome disassembly at transcribing regions during RNAPII transcription.
  • PMID:31837996
    ...FACT and H2Bub globally repress antisense transcripts near the 5' end of genes and inside gene bodies, respectively...
  • PMID:19683499
    Second, increased nuclease sensitivity can occur without displacement of dimers from the nucleosome.

Maintains chromatin integrity at heterochromatin domains by suppressing histone turnover, enabling the H3K9me2-to-me3 transition required for heterochromatin spreading from nucleation sites along chromosome arms.

Molecular Function:
histone chaperone activity
Directly Involved In:
constitutive heterochromatin formation
Cellular Locations:
nucleus
In Complex:
FACT complex
Supporting Evidence:
  • PMID:34731638
    ...FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading...
  • PMID:17614284
    Here we show that the histone chaperone and remodeling complex FACT is required for centromeric-heterochromatin integrity and accurate chromosome segregation

Chaperones parental histones H3-H4 during DNA replication, transferring them to both daughter strands in coordination with Mcm2 and Dpb3/4 to maintain histone density and enable epigenetic inheritance of chromatin states.

Molecular Function:
histone chaperone activity
Directly Involved In:
DNA replication-dependent chromatin assembly
Cellular Locations:
chromosome
In Complex:
FACT complex
Supporting Evidence:
  • PMID:38479839
    ...the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance...

References

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Suggested Questions for Experts

Q: Does Spt16 have functions independent of Pob3 in S. pombe beyond controlling 3' gene ends, given that spt16 is essential but pob3 is not?

Suggested experts: Ladurner AG, Braun S

Q: What is the precise mechanism by which FACT suppresses histone turnover at heterochromatic regions -- does it involve direct competition with Epe1 for nucleosome access?

Suggested experts: Murawska M, Al-Sady B

Q: How does FACT coordinate with the Mcm2 and Dpb3/4 histone chaperones during DNA replication fork passage to achieve balanced parental histone distribution?

Suggested experts: Jia S, Zhang Z

Suggested Experiments

Experiment: ChIP-seq of Spt16 in spt16 temperature-sensitive mutants at permissive and restrictive temperatures to map genome-wide FACT occupancy changes, particularly at heterochromatin boundaries and subtelomeres.

Hypothesis: FACT occupancy at heterochromatin boundaries correlates with H3K9me3 spreading capacity.

Experiment: eSPAN (enrichment and sequencing of protein-associated nascent DNA) analysis in spt16 conditional mutants to directly measure parental histone distribution asymmetry at replication forks.

Hypothesis: FACT impairment causes asymmetric parental histone distribution favoring the leading strand.

Experiment: Proximity ligation assay or cross-linking mass spectrometry to identify direct Spt16 interaction partners at heterochromatin versus euchromatin, testing whether Spt16 engages distinct co-factors in different chromatin contexts.

Hypothesis: Spt16 interacts with Clr4/Swi6 at heterochromatin but with elongation factors (Spt4/5/6) at euchromatin.

Deep Research

Bioreason Pro

(spt16-deep-research-bioreason-sft.md)

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Falcon

(spt16-deep-research-falcon.md)

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📚 Additional Documentation

Notes

(spt16-notes.md)

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Bioreason Sft Review

(bioreason-sft-review.md)

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Protnlm Function Review

(spt16-protnlm-function-review.md)

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📄 View Raw YAML

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