Affinage

SUPT5H

Transcription elongation factor SPT5 · UniProt O00267

Length
1087 aa
Mass
121.0 kDa
Annotated
2026-04-28
100 papers in source corpus 40 papers cited in narrative 39 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SUPT5H encodes the large subunit of the DSIF complex (with SPT4), a universally conserved RNA Polymerase II elongation factor that orchestrates promoter-proximal pausing, productive elongation, cotranscriptional RNA processing, chromatin maintenance, and transcription termination. DSIF is recruited to Pol II shortly after initiation, where its KOW domains contact nascent RNA and upstream DNA to establish the paused state, while its KOW2-3 domain recruits NELF; CDK9-mediated phosphorylation of the SPT5 linker (Ser666), CTR1, and CTR2 domains then coordinately drives pause release, tunes elongation speed, and regulates termination, with PNUTS-PP1 dephosphorylation downstream of poly(A) sites decelerating Pol II for Xrn2-dependent torpedo termination (PMID:9450929, PMID:34534457, PMID:40250441, PMID:31677974, PMID:39746995). The SPT5 C-terminal repeat domain serves as a phosphorylation-regulated docking platform that recruits mRNA capping enzyme, PAF complex (via phospho-CTR–Rtf1 Plus3 domain interaction), spliceosomal snRNPs, and 3′-end cleavage factors, coupling elongation to all major cotranscriptional processing events (PMID:11893740, PMID:24939935, PMID:24101474, PMID:22290438, PMID:31289129). SPT5 additionally protects promoter-proximal Pol II from CUL3-ARMC5–dependent ubiquitination and proteasomal degradation, preserves nucleosomal histones during transcription through its N-terminal acidic histone-binding tail, facilitates AID targeting for immunoglobulin class-switch recombination at stalled Pol II sites, and supports enhancer–promoter looping required for super-enhancer function (PMID:34480849, PMID:39854452, PMID:35102600, PMID:20887897, PMID:32251373).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 1998 High

    Identification of DSIF as an SPT5–SPT4 complex that both pauses and stimulates Pol II resolved the paradox of how a single elongation factor could exert both positive and negative effects on transcription.

    Evidence Biochemical purification from HeLa extracts with in vitro transcription, plus co-IP and genetic suppression in yeast

    PMID:9450929 PMID:9450930

    Open questions at the time
    • Mechanism of switching between pausing and stimulation unknown
    • No structural information on Pol II–DSIF interface
  2. 2000 High

    Domain mapping of SPT5 revealed that the CTR1 repeat is a P-TEFb/CDK9 substrate critical for both repression and activation, establishing phosphorylation as the regulatory switch for DSIF function.

    Evidence Domain deletion, in vitro transcription, and CDK9 phosphorylation assays; Drosophila polytene chromosome localization at paused and active loci

    PMID:10757782 PMID:11040217

    Open questions at the time
    • Phosphorylation sites not mapped at single-residue resolution
    • How phospho-CTR recruits downstream effectors unknown
  3. 2002 High

    The SPT5 CTR was shown to directly recruit mRNA capping enzymes, revealing the first cotranscriptional processing function of DSIF and establishing the CTR as a multi-purpose effector platform analogous to the Pol II CTD.

    Evidence In vitro binding of S. pombe capping enzymes to Spt5 CTD nonamer repeats, two-hybrid, and domain mapping; HIV transcription immunodepletion assays

    PMID:11809800 PMID:11893740

    Open questions at the time
    • Whether CTR phosphorylation modulates capping enzyme binding not yet tested
    • No structural basis for CTR–capping enzyme interaction
  4. 2003 High

    Discovery that PRMT1/PRMT5 methylate SPT5 arginine residues to modulate Pol II interaction, and that Spt5 co-purifies with elongation/processing factors (TFIIF, capping enzyme, FACT), expanded the view of SPT5 as an integration hub for elongation and processing.

    Evidence In vitro methylation with mutagenesis, co-immunopurification/mass spectrometry, genetic interaction with capping enzyme, pre-mRNA splicing assays in yeast

    PMID:12556496 PMID:12718890

    Open questions at the time
    • Specific arginine sites and their individual contributions unresolved
    • Mechanistic link between methylation and elongation rate unclear
  5. 2008 High

    The crystal structure of Spt4–Spt5(NGN) defined the acid-dipole interface that nucleates DSIF and suggested how Spt4 stabilizes the KOW domain architecture required for Pol II engagement.

    Evidence X-ray crystallography of yeast Spt4–Spt5(NGN), validated by mutagenesis and archaeal reconstitution

    PMID:19000817

    Open questions at the time
    • Full-length Spt5 structure on Pol II not available
    • How KOW domains are arranged relative to Pol II exit channels unknown
  6. 2009 High

    BUR kinase phosphorylation of the Spt5 CTR was shown to be required for PAF complex recruitment and downstream histone modifications (H2Bub, H3K4me3, H3K36me3), establishing a direct signaling cascade from Spt5 phosphorylation to chromatin state.

    Evidence Chemical-genetic (analog-sensitive) kinase inhibition, in vitro phosphorylation, ChIP for PAF and histone marks, Spt5 CTR deletion

    PMID:19365074 PMID:19581288

    Open questions at the time
    • Whether CDK9 or BUR kinase is the primary CTR kinase in metazoans debated
    • How phospho-CTR is read by PAF subunits not structurally resolved
  7. 2010 High

    SPT5 was identified as the factor that targets AID to stalled Pol II sites for immunoglobulin class-switch recombination and somatic hypermutation, linking transcription elongation control to adaptive immunity.

    Evidence shRNA screen, co-immunoprecipitation of AID–Spt5, ChIP-seq colocalization in B cells

    PMID:20887897

    Open questions at the time
    • Structural basis of AID–Spt5 interaction unknown
    • Whether Spt5 phosphorylation state controls AID targeting not tested
  8. 2013 High

    Crystal structures of phospho-Spt5 CTR bound to Rtf1 Plus3 domain provided the structural code for PAF complex recruitment, showing phosphothreonine recognition drives the interaction and explaining the kinase-dependent chromatin modification cascade.

    Evidence X-ray crystallography, in vitro binding with phospho-peptides, in vivo ChIP of Rtf1/Paf1C

    PMID:23775116 PMID:24101474

    Open questions at the time
    • Whether CTR1 and CTR2 repeats bind Rtf1 with different affinities unclear
    • Competition between CTR-binding partners not characterized
  9. 2014 High

    Site-specific crosslinking and crystallography mapped the multi-domain architecture of Spt5 on Pol II: KOW4-5 locks the clamp in closed conformation, the CTD recruits capping GTase via an OB-fold docking site regulated by Thr1 phosphorylation, establishing a binary 'Spt5 CTD code' for capping enzyme.

    Evidence Unnatural amino acid photocrosslinking, X-ray crystallography of GTase–Spt5 CTD, mutagenesis, yeast genetics

    PMID:24813444 PMID:24939935

    Open questions at the time
    • How CTR phosphorylation by different kinases is temporally ordered not resolved
    • Whether clamp closure by KOW4-5 is reversible during elongation unknown
  10. 2017 High

    Functional dissection in Drosophila assigned specific roles to individual KOW domains: KOW5 contacts nascent RNA for pause positioning, KOW2-3 recruits NELF, and KOW1 engages upstream DNA for DSIF–Pol II association, completing the domain-to-function map for pausing.

    Evidence Drosophila nuclear extract reconstitution, RNA crosslinking, domain deletions with in vivo validation

    PMID:28213523

    Open questions at the time
    • Whether human KOW domains have identical division of labor not directly tested
    • Structural basis of KOW2-3–NELF interaction unknown
  11. 2019 High

    Multiple studies converged to show that Spt5 dephosphorylation by PNUTS-PP1 downstream of poly(A) sites decelerates Pol II for Xrn2-mediated termination, while Spt5 depletion reveals its role in maintaining Pol II processivity past promoter-proximal barriers and suppressing antisense transcription.

    Evidence PNUTS-PP1 point mutation with GRO-seq/ChIP-seq; conditional Spt5 depletion in MEFs (NET-seq) and S. pombe (NET-seq, RNA-seq); MYC–SPT5 interaction by MS and ChIP

    PMID:28366642 PMID:29514850 PMID:30928206 PMID:31677974

    Open questions at the time
    • Whether dephosphorylation of linker vs CTR contributes differentially to deceleration unknown
    • How MYC–SPT5 handoff to Pol II is structurally coordinated unresolved
  12. 2021 High

    Acute SPT5 depletion revealed that DSIF protects promoter-proximal Pol II from CUL3-dependent ubiquitination and proteasomal degradation, and that SPT5 linker phosphorylation at Ser666 is the key trigger for pause release antagonized by Integrator-PP2A.

    Evidence Auxin/dTAG-mediated acute depletion, ChIP-seq, PRO-seq, phosphomutant analysis, genetic epistasis with CUL3/VCP/CDK9

    PMID:34480849 PMID:34534457

    Open questions at the time
    • How CUL3-ARMC5 recognizes Pol II lacking SPT5 at structural level unknown
    • Whether Integrator-PP2A directly dephosphorylates Ser666 or acts indirectly unclear
  13. 2022 High

    The Spt5 N-terminal acidic tail was identified as a histone-binding motif essential for viability that prevents loss of nucleosomal histones during active transcription, revealing a chromatin maintenance function separate from elongation control.

    Evidence Yeast genetics (viability), in vitro histone binding, histone ChIP in transcribed regions

    PMID:35102600

    Open questions at the time
    • Whether the histone-binding tail cooperates with FACT or functions independently not resolved
    • Structural basis of histone capture by Spt5N unknown
  14. 2025 High

    Systematic phosphomutant analysis established that CDK9 phosphorylation of SPT5 linker, CTR1, and CTR2 coordinately and additively controls pause release, elongation speed, splicing, and termination; ARMC5 was identified as the CUL3 adaptor targeting Pol II lacking SPT5; and Spt5 was shown to directly stimulate Xrn2 torpedo nuclease activity.

    Evidence Phosphomimetic/null mutations with PRO-seq and TT-seq; proteomic identification of ARMC5 with ChIP-seq; in vitro Xrn2 activity reconstitution with Spt5; Pcf11–Spt5 condensate imaging in Drosophila

    PMID:39746995 PMID:39854452 PMID:40015272 PMID:40250441

    Open questions at the time
    • How the three phosphorylation domains are temporally ordered during the transcription cycle in living cells not resolved
    • Whether Spt5 stimulation of Xrn2 requires direct physical contact or is indirect unknown
    • Full cryo-EM structure of mammalian Pol II–DSIF with all processing factors not yet available

Open questions

Synthesis pass · forward-looking unresolved questions
  • A complete temporal map of SPT5 phosphorylation/dephosphorylation events across the transcription cycle, the structural basis of SPT5 interactions with all cotranscriptional processing machineries simultaneously, and whether SPT5 condensate formation is mechanistically required in vivo remain unresolved.
  • No time-resolved single-molecule measurement of SPT5 phosphoform transitions during a single transcription cycle
  • No high-resolution structure of mammalian DSIF simultaneously engaging capping enzyme, PAF, spliceosome, and cleavage factors
  • Functional significance of SPT5 phase separation/condensates not validated by separation-of-function mutations in endogenous loci

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0003723 RNA binding 2 GO:0008092 cytoskeletal protein binding 1 GO:0042393 histone binding 1
Localization
GO:0005654 nucleoplasm 4 GO:0005694 chromosome 2
Pathway
R-HSA-74160 Gene expression (Transcription) 6 R-HSA-8953854 Metabolism of RNA 6 R-HSA-4839726 Chromatin organization 3 R-HSA-168256 Immune System 2
Partners
AICDAARMC5CDK9MYCPOLR2ARTF1SUPT4H1XRN2
Complex memberships
DSIF (SPT4–SPT5)

Evidence

Reading pass · 39 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 DSIF (DRB sensitivity-inducing factor), composed of human SPT5 (p160, SUPT5H) and SPT4 (p14), was purified from HeLa nuclear extracts and shown to cause pausing of RNA polymerase II in conjunction with DRB, and to stimulate elongation at limiting NTP concentrations, establishing SUPT5H as a transcription elongation factor that regulates Pol II processivity. Biochemical purification from HeLa nuclear extracts, in vitro transcription assays, cDNA cloning, recombinant protein complementation Genes & development High 9450929
1998 Spt5 (yeast ortholog of SUPT5H) is physically associated with RNA Pol II in vivo, forms a tight complex with Spt4 (without Spt6), and genetic suppression of spt5 conditional mutations by RNA Pol II subunit mutations establishes Spt4-Spt5 as a transcription elongation regulator acting directly on the polymerase. Co-immunoprecipitation, genetic suppressor analysis, double-mutant analysis in S. cerevisiae Genes & development High 9450930
1997 Human SUPT5H protein is reversibly phosphorylated during mitosis, as demonstrated by purification from HeLa cells and analysis of its phosphorylation state through the cell cycle. Protein purification from HeLa cells, cell cycle phosphorylation analysis FEBS letters Medium 9199507
2000 Domains of SPT5 required for transcriptional regulation were mapped: SPT4-binding domain, RNA Pol II-binding domain, and the C-terminal repeat domain CTR1, which is a substrate for P-TEFb (CDK9/cyclin T1) phosphorylation and is critical for DRB-mediated repression and Tat-dependent activation in vitro. Domain deletion/truncation analysis, in vitro transcription assays, phosphorylation assays with CDK9 Molecular and cellular biology High 10757782
2000 Drosophila Spt5 colocalizes with phosphorylated, actively elongating RNA Pol II on polytene chromosomes and is present at uninduced heat shock gene promoters; upon heat shock, Spt5 associates with both 5' and 3' ends of heat shock genes, supporting roles in promoter-proximal pausing and transcription elongation in vivo. Immunofluorescence on polytene chromosomes, chromatin immunoprecipitation Genes & development High 11040216 11040217
2002 SPT5 is recruited to the HIV-1 transcription complex shortly after initiation, and is hyperphosphorylated by CDK9 in parallel with Pol II CTD during Tat activation; immunodepletion shows SPT5 is not required for Tat-dependent kinase activation but prevents premature RNA dissociation at terminator sequences and reduces pausing at arrest sites during late elongation. Three-stage in vitro transcription assay, immunodepletion, chase experiments Molecular and cellular biology High 11809800
2003 SPT5 is specifically methylated by PRMT1 and PRMT5 on arginine residues; this methylation regulates SPT5 interaction with RNA Pol II and affects promoter association and transcriptional elongation properties. Biochemical co-immunoprecipitation, in vitro methylation assay, specific arginine mutant analysis, promoter ChIP Molecular cell High 12718890
2003 Yeast Spt5 co-immunopurifies with general elongation factors TFIIF and TFIIS, Spt6, FACT, mRNA capping enzyme and cap methyltransferase; spt4/spt5 mutations show genetic interactions with capping enzyme gene mutations and cause accumulation of unspliced pre-mRNA, revealing dual roles in pre-mRNA processing and elongation. Co-immunopurification/mass spectrometry, genetic interaction analysis, pre-mRNA splicing assays Molecular and cellular biology High 12556496
2002 Fission yeast capping enzymes (RNA triphosphatase Pct1 and guanylyltransferase Pce1) bind independently to the C-terminal repeat domain of Spt5 in vitro and in vivo (two-hybrid); as few as four Spt5 CTD nonamer repeats suffice for Pct1 binding; Spt5 is essential in S. pombe and interacts with Spt4 via a central domain distinct from the CTD. In vitro binding assays, two-hybrid, deletion analysis The Journal of biological chemistry High 11893740
2008 Crystal structure of S. cerevisiae Spt4 bound to the NGN domain of Spt5 reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction; mutations disrupting this interface disrupt the complex; archaeal Spt4 and Spt5 homologs also form a complex; the structure suggests Spt4 stabilizes the functional conformation of Spt5 KOW domains. X-ray crystallography, mutagenesis, complex reconstitution Structure High 19000817
2009 Yeast BUR kinase (Bur1-Bur2) phosphorylates the Spt5 C-terminal repeat domain (CTR) both in vivo and in isolated elongation complexes in vitro; deletion of Spt5 CTD or mutation of Bur1-targeted serines reduces PAF complex recruitment to elongating Pol II and decreases histone H3K4 trimethylation; Bur1 also contributes to Pol II CTD Ser-2 phosphorylation. Chemical genetics (analog-sensitive kinase), in vitro phosphorylation, ChIP, histone modification assays Molecular and cellular biology High 19365074 19581288
2009 The Spt5 CTR is required for PAF complex recruitment to transcribed regions, histone H2B K123 monoubiquitination, and H3 K4 and K36 trimethylation; BUR kinase phosphorylates the Spt5 CTR in vitro, linking Spt5 CTR phosphorylation to chromatin modification during elongation. In vitro kinase assay, genetic deletion of Spt5 CTR, ChIP, histone modification analysis Proceedings of the National Academy of Sciences High 19365074
2010 AID (activation-induced cytidine deaminase) interacts directly with Spt5, and Spt5 is required for class switch recombination; Spt5 facilitates the association between AID and stalled Pol II, and AID recruitment to Ig and non-Ig target loci; ChIP-seq shows Spt5 colocalizes with AID and stalled Pol II, and Spt5 accumulation at stalled Pol II sites predicts AID-induced mutation. shRNA screen, co-immunoprecipitation, ChIP-seq Cell High 20887897
2010 The Spt5 CTR interacts with yeast 3' RNA cleavage factor I (CFI) in vitro, and ChIP shows the Spt5 CTR is required for normal CFI recruitment to 3' ends of genes, linking Spt5 to 3' RNA processing. In vitro binding assay, chromatin immunoprecipitation, genome-wide ChIP profiling Molecular and cellular biology High 22290438
2013 Crystal structure of human Rtf1 Plus3 domain in complex with a phosphorylated Spt5 CTR repeat reveals that Spt5 binding involves phosphothreonine recognition and hydrophobic interfaces; mutations in these interfaces diminish Spt5 binding in vitro and Rtf1/Paf1C chromatin localization in vivo. X-ray crystallography, in vitro binding assays, in vivo ChIP Proceedings of the National Academy of Sciences High 24101474
2013 A conserved domain of Rtf1 (Spt5-interacting domain) is necessary and sufficient for direct physical interaction with Spt5 CTR; mutations in this domain or deletion of Spt5 CTR disrupt the Rtf1-Spt5 interaction and release Paf1C from chromatin; in vitro experiments confirm the interaction is direct. Yeast two-hybrid, in vitro binding, co-immunoprecipitation, ChIP Molecular and cellular biology High 23775116
2014 Spt5 interacts with RNA Pol II through its KOW4-5 domains (contacting Rpb4/7) and also with Rpb1 and Rpb2 at the clamp, protrusion, and wall domains via site-specific photocrosslinking; KOW4-5 interactions lock the clamp in closed conformation, promoting elongation and repressing transcription-coupled repair (TCR). Unnatural amino acid site-specific photocrosslinking, domain deletion, elongation and TCR assays Nucleic acids research High 24813444
2014 Crystal structure of fission yeast RNA guanylyltransferase (GTase) bound to the Spt5 CTD reveals a separate docking site in the OB-fold domain that captures the Trp4 residue of the Spt5 nonapeptide repeat; GTase binds Spt5 and Pol2 CTDs at distinct sites; Thr1 phosphorylation of the Spt5 CTD inhibits GTase binding, while Ser5-PO4 on Pol2 CTD is required — establishing a binary 'Spt5 CTD code' read by capping enzyme. X-ray crystallography, in vitro binding assays, mutagenesis, yeast genetic complementation Genes & development High 24939935
2015 Crystal structures of Spt5 KOW1-Linker1 (K1L1) and KOW2-KOW3 domains from S. cerevisiae reveal that K1L1 has a positively charged patch (PCP) that binds nucleic acids in vitro and is required for in vivo function; Spt4 and K1L1 have functionally overlapping interactions with nucleic acids upstream of the transcription bubble. X-ray crystallography, biochemical nucleic acid binding assays, yeast growth assays Molecular and cellular biology High 26217010
2019 PNUTS-PP1 phosphatase dephosphorylates Spt5, and this dephosphorylation downstream of poly(A) sites causes RNA Pol II deceleration from >2 kb/min to <1 kb/min; both PNUTS-PP1 and Spt5 dephosphorylation are required for transcription termination, supporting a 'sitting duck torpedo' mechanism where Pol II deceleration makes it a viable target for Xrn2. PNUTS-PP1 point mutation (W401A), genome-wide GRO-seq, ChIP-seq, Spt5 phosphorylation analysis Molecular cell High 31677974
2019 MYC directly binds SPT5, recruits SPT5 to promoters, and enables CDK7-dependent transfer of SPT5 onto Pol II; MYC is required for fast and processive transcription elongation; high MYC levels sequester SPT5 into non-functional complexes, decreasing expression of growth-suppressive genes. Mass spectrometry of MYC and Pol II complexes, co-immunoprecipitation, ChIP, nascent RNA sequencing Molecular cell High 30928206
2021 SPT5 depletion causes ubiquitination and proteasomal degradation of core RNA Pol II subunit RPB1 specifically at promoter-proximal regions; this degradation requires the E3 ligase Cullin 3, the unfoldase VCP/p97, and a novel form of CDK9 kinase complex; the mechanism is evolutionarily conserved from yeast to human cells. Acute protein depletion (auxin-inducible degron), western blot, co-immunoprecipitation, genetic epistasis with Cullin 3/VCP/CDK9 Molecular cell High 34480849
2021 Rapid SPT5 depletion causes pronounced reduction of paused Pol II at promoters and enhancers; phosphorylation of SPT5 linker at serine 666 potentiates pause release and is antagonized by Integrator-PP2A (INTAC); phosphorylation of the SPT5 CTR links to 3' end termination; SPT5 is required for global transcription activation. Rapid degradation system (dTAG), ChIP-seq, PRO-seq, phospho-mutant analysis Molecular cell High 34534457
2022 Spt5 N-terminal acidic tail (Spt5N) contains a histone-binding motif that is required for viability in yeast; Spt5N is positioned between the downstream nucleosome and upstream DNA emerging from Pol II; loss of this motif causes loss of nucleosomal histones within actively transcribed regions, establishing that Spt5 couples processive transcription to histone capture and re-deposition. Yeast genetics (viability assay), biochemical histone binding assay, histone ChIP in actively transcribed regions The EMBO journal High 35102600
2022 The ZWC complex (ZC3H4, WDR82, CK2) localizes to transcription start sites via interaction with S5-phosphorylated Pol II CTD and phosphorylates the N-terminal acidic domain of SPT5; this SPT5 phosphorylation suppresses divergent antisense transcription during early elongation. Co-immunoprecipitation, ChIP-seq, phosphorylation assays, depletion studies Nucleic acids research High 35325203
2025 Tripartite phosphorylation of SPT5 by CDK9 in the linker, CTR1, and CTR2 domains coordinately controls pause release, elongation speed, and termination; linker phosphorylation promotes pause release while CTR1 loss slows elongation, and CTR2 mutation partially reverses this slowing; all three together have additive effects on splicing, termination, and mRNA levels. Phosphomimetic and phospho-null mutations, PRO-seq, TT-seq, splicing analysis, cell proliferation assays in HCT116 cells Molecular cell High 40250441
2025 ARMC5 is identified as a CUL3 adaptor required for VCP/p97-dependent degradation of SPT5-depleted, promoter-proximal Pol II; interaction between ARMC5 and Pol II requires CDK9 activity, supporting a phospho-dependent degradation model; ARMC5 targets promoter-proximal Pol II in a BTB domain-dependent manner. Proteomic screening, co-immunoprecipitation, genome-wide ChIP-seq, CDK9 inhibition Science advances High 39854452
2017 Spt5 KOW4 and KOW5 domains are essential for promoter-proximal pausing in Drosophila; KOW5 directly contacts nascent RNA (shown by RNA crosslinking), and deletion disrupts this interaction and shifts pause location; the KOW2-3 domain mediates NELF recruitment to the elongation complex; KOW1 interaction with upstream DNA helix is required for DSIF association with the Pol II elongation complex. Drosophila nuclear extract reconstitution, RNA crosslinking, domain deletion/mutation analysis, in vivo genetics The Journal of biological chemistry High 28213523
2020 Spt5-mediated enhancer transcription is required for super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus; Spt5 depletion causes loss of enhancer-promoter looping without affecting H3K27ac, chromatin accessibility, or Mediator/cohesin occupancy; CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Spt5 depletion in mouse B cells, Hi-C/4C (chromatin conformation), CRISPRa rescue, PRO-seq, ChIP-seq Nature genetics High 32251373
2019 Spt5 depletion in mouse embryonic fibroblasts does not cause global elongation rate defects but causes a fraction of Pol II molecules to be dislodged during elongation within a narrow window 15–20 kb from the promoter, coinciding with the stage where Pol II attains maximum elongation speed; long genes show greater dependency on Spt5 for optimal elongation efficiency. Spt5 depletion in MEFs, NET-seq/GRO-seq, Pol II ChIP-seq The EMBO journal High 29514850
2019 Spt5 depletion in fission yeast causes reduced RNAPII and relative accumulation over the first ~500 bp of genes, with widespread antisense transcription initiating within this barrier region, revealing Spt5 is required for transcription past a promoter-proximal barrier and to suppress antisense transcription. Conditional Spt5 depletion in S. pombe, NET-seq, RNAPII ChIP-seq, RNA-seq Molecular cell High 28366642
2019 Spt5 directly co-immunoprecipitates with core spliceosomal proteins and all spliceosomal snRNAs; Spt5 depletion impairs cotranscriptional U5 snRNP accumulation at intron-containing genes and reduces cotranscriptional spliceosome assembly, revealing a role in coupling splicing to transcription elongation. Auxin-inducible Spt5 depletion, co-immunoprecipitation, ChIP, RNA-seq RNA Medium 31289129
2016 O-GlcNAcase (OGA) physically associates with SPT5 and TIF1β in a purified complex that has elongation activity in vitro; OGA activity is required for elongation in crude nuclear extract; ChIP-seq shows OGA maps to TSS/5' gene ends overlapping with Pol II and SPT5. In vitro transcription assays, co-immunoprecipitation, ChIP-seq The Journal of biological chemistry Medium 27601472
2025 Xrn2 (torpedo nuclease) forms a stable complex with elongating Pol II; Spt5 stimulates Xrn2 activity to ensure efficient nascent RNA degradation leading to Pol II dislodgement; Spt5 also coordinates pre-mRNA splicing and 3'-end processing, and attenuates expression of non-coding transcripts. Co-immunoprecipitation of Pol II-Xrn2 complex, in vitro Xrn2 activity assays with/without Spt5, ChIP-seq, RNA-seq Nature communications High 39746995
2025 LEDGF/p75 is enriched at paused promoters and prevents phosphorylation of the SPT5 PRD/CTR1 domain by the super elongation complex (SEC); deletion of LEDGF IBD increases SEC occupancy and SPT5 PRD phosphorylation at promoters, promoting pause release; CTR1 and CTR2 of SPT5 play pivotal roles in Pol II pausing and elongation, respectively. ChIP-seq, co-immunoprecipitation, phosphorylation analysis, domain deletion Science advances Medium 39823345
2023 The super elongation complex (SEC) induces SPT5 phase transition into elongation droplets during transcriptional pause release; SPT5 per se forms clusters, and its disordered domain is required for pause release and gene activation; SEC depletion increases SPT5 pausing clusters; disease-associated SEC mutations impair elongation droplet phase properties. Imaging of SPT5 condensates/droplets, SEC depletion, domain deletion, fluorescence microscopy EMBO reports Medium 36629390
1999 Tat-SF1 associates with human SPT5 (hSPT5) and RAP30 (TFIIF subunit) in nuclear extracts; small fractions of hSPT5 and Pol II are associated with Tat-SF1; overexpression of Tat-SF1 and hSPT5 specifically stimulates Tat-dependent transcription in vivo. Co-immunoprecipitation, overexpression assays in vivo Molecular and cellular biology Medium 10454543
2009 SPT4 protects Spt5 from degradation and stabilizes Spt5 interaction with Pol II; the C-terminal repeat (CTR) domain of Spt5 (dispensable for viability and not involved in Spt4/Pol II interactions) suppresses Rad26-independent transcription-coupled repair (TCR); Bur kinase phosphorylates the Spt5 CTR and inactivation of Bur kinase partially alleviates TCR. Genetic deletion analysis, in vivo Pol II ChIP, kinase inactivation The Journal of biological chemistry Medium 20042611
2025 Pcf11 forms condensates with unphosphorylated Spt5 (promoted by PP1/PNUTS phosphatase during termination) to stall RNA Pol II; Pcf11/Spt5 condensates control termination by decelerating polymerase elongation; this mechanism is exploited by piRNAs to silence transposons. Drosophila RNAi screen, tethering assays, condensate imaging, phosphatase manipulation Molecular cell Medium 40015272

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes & development 625 9450929
1998 Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes & development 393 9450930
2010 Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Cell 297 20887897
2003 Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Molecular and cellular biology 241 12556496
2000 High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes & development 236 11040217
2003 Methylation of SPT5 regulates its interaction with RNA polymerase II and transcriptional elongation properties. Molecular cell 199 12718890
2000 Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes & development 195 11040216
2000 Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Molecular and cellular biology 188 10757782
2019 Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism. Molecular cell 171 31677974
2009 Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Molecular and cellular biology 152 19581288
1991 SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat. Molecular and cellular biology 147 1840633
2002 Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5. The Journal of biological chemistry 130 11893740
2009 Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proceedings of the National Academy of Sciences of the United States of America 124 19365074
2009 RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO reports 116 19343051
2012 The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation. Biochimica et biophysica acta 115 22982195
2002 Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Molecular and cellular biology 102 11809800
2019 MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation. Molecular cell 99 30928206
2002 The elongation factors Pandora/Spt6 and Foggy/Spt5 promote transcription in the zebrafish embryo. Development (Cambridge, England) 95 11923199
2013 Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proceedings of the National Academy of Sciences of the United States of America 91 24101474
2021 SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape. Molecular cell 82 34534457
2021 SPT5 stabilization of promoter-proximal RNA polymerase II. Molecular cell 81 34480849
2017 Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Molecular cell 80 28366642
2001 Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics 78 11606527
2012 Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex. The EMBO journal 70 22796944
1998 Role of the human homolog of the yeast transcription factor SPT5 in HIV-1 Tat-activation. Journal of molecular biology 65 9514752
2009 Histone H3K4 and K36 methylation, Chd1 and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription. Genetics 61 19948887
2008 Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation. Structure (London, England : 1993) 61 19000817
2020 Mechanisms of Transcription Elongation Factor DSIF (Spt4-Spt5). Journal of molecular biology 60 32987031
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2012 The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I. Molecular and cellular biology 58 22290438
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2017 Phosphorylation of SPT5 by CDKD;2 Is Required for VIP5 Recruitment and Normal Flowering in Arabidopsis thaliana. The Plant cell 31 28188267
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2017 CDK9 and SPT5 proteins are specifically required for expression of herpes simplex virus 1 replication-dependent late genes. The Journal of biological chemistry 12 28743741
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2020 SUPT5H Post-Transcriptional Silencing Modulates PIN1 Expression, Inhibits Tumorigenicity, and Induces Apoptosis of Human Breast Cancer Cells. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 10 32961044
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