Affinage

SUPT6H

Transcription elongation factor SPT6 · UniProt Q7KZ85

Round 2 corrected
Length
1726 aa
Mass
199.1 kDa
Annotated
2026-04-28
50 papers in source corpus 12 papers cited in narrative 12 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SUPT6H is a histone H3 chaperone and transcription elongation factor that couples RNA polymerase II (RNAPII) processivity and termination to co-transcriptional chromatin maintenance, mRNA processing, and export. It binds the Ser2-phosphorylated RNAPII CTD through its SH2 domain and recruits the Iws1–HYPB/Setd2 complex to establish H3K36me3 across transcribed gene bodies, thereby suppressing aberrant lncRNA transcription, R-loop accumulation, and replication stress (PMID:17234882, PMID:19141475, PMID:30449723). Acute degradation studies demonstrate that SUPT6H is directly required for RNAPII processivity on protein-coding genes and for proper transcriptional termination, whereas cryptic intragenic transcription arises secondarily from accumulated epigenetic perturbation (PMID:34233157). Homozygous Supt6h loss is embryonic lethal in mice, and conditional ablation in parvalbumin-expressing interneurons causes neuronal loss, seizures, and behavioral abnormalities, linking SUPT6H haploinsufficiency to neurodevelopmental disease (PMID:41864309).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1996 Medium

    Cloning of human SUPT6H as the orthologue of yeast SPT6 established that its nuclear, acidic, SH2-domain-containing architecture is conserved across metazoans, suggesting a chromatin-regulatory transcription function.

    Evidence cDNA cloning, sequence analysis, and Northern blotting of human and mouse transcripts

    PMID:8786132

    Open questions at the time
    • No functional data beyond sequence homology
    • SH2 domain function uncharacterized
    • No chromatin interaction demonstrated
  2. 2007 High

    Identification of the SH2 domain as a phosphoserine-dependent reader of the Ser2-phosphorylated RNAPII CTD resolved how SUPT6H is recruited to elongating polymerase and revealed a co-transcriptional role in mRNA processing and export distinct from elongation rate control.

    Evidence Co-immunoprecipitation, SH2 point mutagenesis (R1358K), in vitro elongation assays, and RNA analysis of HIV-1 and c-myc transcripts

    PMID:17234882

    Open questions at the time
    • How SH2-CTD binding is coordinated with other CTD readers was unknown
    • In vivo genome-wide consequences not tested
  3. 2008 High

    Demonstration that SUPT6H recruits Iws1 and HYPB/Setd2 to form a CTD-anchored megacomplex responsible for H3K36me3 across transcribed regions connected SUPT6H to co-transcriptional histone methylation and mRNA export.

    Evidence Recombinant CTD binding assays, siRNA knockdowns, ChIP, RNA FISH, and Co-IP

    PMID:19141475

    Open questions at the time
    • Structural basis of SUPT6H–Iws1 interaction not resolved at atomic level
    • Contribution of other H3K36 methyltransferases in the absence of SUPT6H unknown
  4. 2014 Medium

    Linking SUPT6H to regulation of H2B monoubiquitination and suppression of H3K27me3 at lineage-specific genes expanded its function beyond elongation to epigenetic control of cellular differentiation and estrogen-responsive transcription.

    Evidence siRNA knockdown, ChIP, Co-IP with RNF40, and gene expression profiling in breast cancer cells

    PMID:24441044

    Open questions at the time
    • Whether SUPT6H directly modulates PRC2/H3K27me3 deposition or acts indirectly through H2Bub1 was unclear
    • Single cell-type study
  5. 2018 High

    A 3.1 Å cryo-EM structure of the activated Pol II elongation complex with SPT6, DSIF, and PAF revealed that SPT6 contacts the phosphorylated CTD linker and opens the DSIF RNA clamp, providing the first structural framework for how SPT6 promotes elongation competence.

    Evidence Cryo-EM of in vitro reconstituted Sus scrofa Pol II with human DSIF, PAF, and SPT6; biochemical assembly assays

    PMID:30135578

    Open questions at the time
    • Structure captured a single conformational state; dynamics of SPT6 engagement during elongation unknown
    • Human Pol II–SPT6 structure not yet solved
  6. 2018 High

    Genome-wide depletion studies showed that SUPT6H maintains H3K36me3 at protein-coding genes and suppresses it at lncRNA loci; loss of this partitioning impairs Integrator-mediated lncRNA termination, causing R-loop formation and replication stress.

    Evidence siRNA knockdown, ChIP-seq, RNA-seq, R-loop immunofluorescence, and DNA damage/senescence assays in human cells

    PMID:30449723

    Open questions at the time
    • Whether R-loop-induced senescence is the primary physiological consequence of SUPT6H loss in vivo was untested
    • Direct mechanism of Integrator recruitment by H3K36me3 not resolved
  7. 2021 High

    Acute protein degradation of SPT6 temporally dissected its functions, establishing that RNAPII processivity and termination are immediate, direct consequences of SPT6 loss, whereas cryptic intragenic transcription is a delayed, epigenetically driven secondary effect.

    Evidence Auxin-inducible degron in human cells, TT-seq, mNET-seq, ChIP-seq, and mathematical modeling

    PMID:34233157

    Open questions at the time
    • Whether processivity and termination functions are mechanistically separable remains unresolved
    • Histone chaperone activity not directly measured in this system
  8. 2022 Medium

    CDK12 was shown to stabilize SPT6 occupancy at epidermal differentiation gene bodies, providing an upstream kinase-dependent mechanism that links CTD phosphorylation to SPT6 retention on tissue-specific genes.

    Evidence CDK12 siRNA knockdown, ChIP for SPT6, and gene expression analysis in regenerated human epidermis

    PMID:35325240

    Open questions at the time
    • Whether CDK12 phosphorylates SPT6 directly or acts solely through CTD Ser2 phosphorylation is unknown
    • Single tissue context
  9. 2026 High

    In vivo conditional knockout and human variant analysis established that SUPT6H is essential for embryonic viability and for maintenance of parvalbumin-expressing GABAergic interneurons, linking haploinsufficiency to neurodevelopmental phenotypes including seizures.

    Evidence Conditional Cre-lox knockout in PV interneurons, behavioral testing, immunofluorescence, and molecular modeling of 18 sporadic SNVs from human developmental disorders

    PMID:41864309

    Open questions at the time
    • Transcriptomic and epigenomic changes in PV interneurons upon Supt6h loss not profiled
    • Whether SUPT6H variants cause disease through H3K36me3 loss, termination defects, or other mechanisms is unresolved
    • No rescue experiments with wild-type SUPT6H in the mouse model

Open questions

Synthesis pass · forward-looking unresolved questions
  • The relative contributions of SUPT6H's histone chaperone versus CTD-binding activities to its in vivo functions remain mechanistically unresolved, and a high-resolution structure of human SPT6 in the context of its Iws1–Setd2 recruitment module is lacking.
  • No separation-of-function allele dissecting chaperone from CTD-reader activity in mammalian cells
  • Atomic structure of SUPT6H–Iws1–Setd2 ternary complex unavailable
  • Cell-type-specific roles beyond interneurons and epidermis unexplored

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 5 GO:0042393 histone binding 3 GO:0005198 structural molecule activity 2
Localization
GO:0005634 nucleus 6 GO:0005694 chromosome 4
Pathway
R-HSA-74160 Gene expression (Transcription) 6 R-HSA-4839726 Chromatin organization 4 R-HSA-8953854 Metabolism of RNA 3
Partners
CDK12IWS1POLR2ARNF40SETD2SSRP1SUPT5H
Complex memberships
RNAPII activated elongation complex (with DSIF/PAF)SPT6–Iws1–HYPB/Setd2 megacomplex

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1996 SUPT6H (human) and Supt6h (mouse) were isolated and sequenced as homologues of yeast SPT6 and C. elegans emb-5. The derived 1603-aa human protein contains a highly acidic 5'-region, a degenerate SH2 domain, and a leucine zipper, consistent with a nuclear protein that regulates transcription through establishment or maintenance of chromatin structure. The gene maps to chromosome 17q11.2 and is constitutively expressed as a 7.0-kb transcript. cDNA cloning, sequence analysis, Northern blotting, somatic cell hybrid analysis, in situ hybridization Genomics Medium 8786132
2007 Mammalian SPT6 (SUPT6H) binds Ser2-phosphorylated RNA polymerase II (RNAPIIo) through its primitive SH2 domain, which recognizes phosphoserine. An R1358K point mutation in the SH2 domain blocked binding to RNAPIIo without affecting transcription elongation rates in vitro, but caused splicing defects and nuclear retention of HIV-1 and c-myc RNAs in cells, indicating a cotranscriptional role in mRNA processing and export. Co-immunoprecipitation, in vitro transcription elongation assay, SH2 point mutagenesis, RNA analysis, ectopic domain expression Genes & development High 17234882
2007 SUPT6H was identified as part of the human RNA polymerase II transcription machinery interaction network by systematic affinity purification-mass spectrometry, placing it in a high-confidence protein interaction network with other elongation and RNA processing factors. Affinity purification coupled to mass spectrometry (AP-MS) of tagged transcription complex components Molecular cell Medium 17643375
2008 SUPT6H (Spt6) binds selectively to uninterrupted consensus repeats in the N-terminal half of the RNAPII CTD and recruits Iws1 (hIws1), which in turn recruits the HYPB/Setd2 histone H3K36 methyltransferase, forming a megacomplex required for H3K36me3 across transcribed regions and for mRNA export. Recombinant protein binding assay, knockdown (siRNA), ChIP, RNA FISH, Co-IP Genes & development High 19141475
2012 Endogenous AID-containing protein complexes from chromatin of diversifying B cells contain SUPT6H alongside RNA polymerase II elongation and chromatin modification complex members (including SUPT5H and FACT), indicating SUPT6H is part of the elongation machinery that provides AID access to immunoglobulin loci during immune diversification. Endogenous protein complex isolation from chromatin, mass spectrometry, depletion experiments The Journal of experimental medicine Medium 23008333
2014 SUPT6H is required for estrogen-regulated transcription and maintenance of chromatin structure in breast cancer cells, in part through interaction with RNF40 and regulation of histone H2B monoubiquitination (H2Bub1). SUPT6H is also required for cellular differentiation and suppression of repressive H3K27me3 on lineage-specific genes. siRNA knockdown, ChIP, co-immunoprecipitation, gene expression analysis in breast cancer cells Oncogene Medium 24441044
2018 Cryo-EM structure of the activated Pol II elongation complex (Sus scrofa Pol II with human DSIF, PAF, and SPT6) at 3.1 Å resolution showed that SPT6 binds to the phosphorylated CTD linker of Pol II and opens the RNA clamp formed by DSIF. Formation of the complex required P-TEFb kinase activity and both PAF and SPT6 as elongation factors. Cryo-EM structure determination, in vitro reconstitution of activated elongation complex, biochemical assembly assay Nature High 30135578
2018 Depletion of SUPT6H (SPT6) in human cells redistributes H3K36me3 histone marks from active protein-coding to lncRNA genes, impairs recruitment of the Integrator complex to chromatin causing lncRNA transcriptional termination defects, leading to extended polyadenylated lncRNAs, increased R-loop formation, DNA replication stress, and cellular senescence. siRNA knockdown, ChIP-seq, RNA-seq, R-loop immunofluorescence, DNA damage assays, senescence assays Molecular cell High 30449723
2021 Targeted acute protein degradation (auxin-inducible degron) of SPT6 in human cells revealed that SPT6 is a crucial factor for RNAPII processivity (productive transcription of protein-coding genes) and for RNAPII termination; acute depletion induced readthrough transcription at thousands of genes. Cryptic intragenic transcription required prolonged depletion and was attributable to accumulated epigenetic perturbations rather than an immediate role of SPT6. Targeted protein degradation (auxin-inducible degron), TT-seq, mNET-seq, ChIP-seq, mathematical modeling Molecular cell High 34233157
2022 CDK12 promotes transcription elongation of epidermal differentiation genes by stabilizing binding of the elongation factor SPT6 (SUPT6H) to target genes and promoting Ser2 phosphorylation on the RNAPII CTD; CDK12 depletion reduced SPT6 occupancy at differentiation gene loci. siRNA knockdown of CDK12, ChIP, gene expression analysis in regenerated human epidermis Stem cells Medium 35325240
2022 SUPT6H was identified as a direct target of miR-423-5p in human cardiomyocytes using luciferase reporter assay. SUPT6H knockdown aggravated Angiotensin II-induced cardiomyocyte hypertrophy and oxidative stress, whereas miR-423-5p inhibition (which increases SUPT6H expression) was protective, establishing SUPT6H as a downstream effector in the miR-423-5p/cardiomyocyte hypertrophy axis. Luciferase reporter assay, siRNA knockdown, miRNA inhibitor transfection, cell hypertrophy assays, oxidative stress measurement The Tohoku journal of experimental medicine Medium 36517015
2026 Analysis of 18 sporadic SUPT6H single-nucleotide variants associated with human developmental disorders showed by molecular modeling that they are likely deleterious (loss-of-function). In vivo, homozygous or heterozygous Supt6 null mice are embryonic lethal. Conditional knockout of Supt6 in parvalbumin-expressing GABAergic interneurons caused motor defects and behavioral seizures (homozygous) or neuropsychiatric-relevant behavioral phenotypes (heterozygous), with significant reduction of parvalbumin-expressing neurons in both genotypes. Molecular modeling of SNVs, conditional knockout mouse generation (Cre-lox in PV interneurons), behavioral testing, immunofluorescence for parvalbumin neurons Biochimica et biophysica acta. Molecular basis of disease High 41864309

Source papers

Stage 0 corpus · 50 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2009 Defining the human deubiquitinating enzyme interaction landscape. Cell 1282 19615732
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2012 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell 973 22681889
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2005 A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 568 16273093
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
2007 Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Molecular cell 367 17643375
2018 Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 341 30135578
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2017 Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proceedings of the National Academy of Sciences of the United States of America 282 28611215
2007 The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes & development 213 17234882
2008 The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes & development 200 19141475
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2020 Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Molecular cell 159 32416067
2012 Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Molecular & cellular proteomics : MCP 145 22586326
2018 Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence. Molecular cell 144 30449723
2017 RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. BMC biology 135 29117863
2014 The central role of EED in the orchestration of polycomb group complexes. Nature communications 131 24457600
2000 NF1 microdeletion syndrome: refined FISH characterization of sporadic and familial deletions with locus-specific probes. American journal of human genetics 83 10631140
2021 Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Molecular cell 60 34233157
2012 A role for the RNA pol II-associated PAF complex in AID-induced immune diversification. The Journal of experimental medicine 56 23008333
2014 SUPT6H controls estrogen receptor activity and cellular differentiation by multiple epigenomic mechanisms. Oncogene 46 24441044
2022 S100A10 and its binding partners in depression and antidepressant actions. Frontiers in molecular neuroscience 27 36046712
2020 The plasma peptides of sepsis. Clinical proteomics 26 32636717
1996 Identification and analysis of the human and murine putative chromatin structure regulator SUPT6H and Supt6h. Genomics 25 8786132
2019 Whole Exome Sequencing of Ulcerative Colitis-associated Colorectal Cancer Based on Novel Somatic Mutations Identified in Chinese Patients. Inflammatory bowel diseases 21 30794281
2009 Identification of novel SHPS-1-associated proteins and their roles in regulation of insulin-like growth factor-dependent responses in vascular smooth muscle cells. Molecular & cellular proteomics : MCP 20 19299420
1996 Isolation, sequencing, and mapping of the human homologue of the yeast transcription factor, SPT5. Genomics 19 8975720
2015 Exome sequencing of bilateral testicular germ cell tumors suggests independent development lineages. Neoplasia (New York, N.Y.) 15 25748235
2023 Transcriptomic and immunophenotypic characterization of two cases of adamantinoma-like Ewing sarcoma of the thyroid gland. Histopathology 4 37195579
2026 A Novel Platinum-Resistance-related Gene Signature in Ovarian Cancer: Identification and Patient-derived Organoids Verification. Current cancer drug targets 3 39901543
2023 Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines. Frontiers in immunology 3 36818472
2022 CDK12 Is Necessary to Promote Epidermal Differentiation Through Transcription Elongation. Stem cells (Dayton, Ohio) 3 35325240
2022 MiR-423-5p Inhibition Exerts Protective Effects on Angiotensin II-Induced Cardiomyocyte Hypertrophy. The Tohoku journal of experimental medicine 2 36517015
2020 Germline Sequencing Identifies Rare Variants in Finnish Subjects with Familial Germ Cell Tumors. The application of clinical genetics 2 32636668
2026 Genetic alterations in SUPT6H are associated with neurodevelopmental disorders. Biochimica et biophysica acta. Molecular basis of disease 0 41864309
2026 Common Genes Between Hyperlipidemia and Aortic Dissection and Their Regulatory Mechanisms. Clinical therapeutics 0 41866271
2025 A graph neural network approach for hierarchical mapping of breast cancer protein communities. BMC bioinformatics 0 39838298