Affinage

USP16

Ubiquitin carboxyl-terminal hydrolase 16 · UniProt Q9Y5T5

Round 2 corrected
Length
823 aa
Mass
93.6 kDa
Annotated
2026-04-28
66 papers in source corpus 31 papers cited in narrative 31 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

USP16 (Ubp-M) is a cysteine-class deubiquitinase that removes monoubiquitin from histone H2AK119 to antagonize PRC1-mediated transcriptional silencing, thereby regulating stem cell self-renewal, hematopoietic differentiation, oocyte-to-zygote transition, and cell cycle progression (PMID:10077596, PMID:24025767, PMID:26699484, PMID:35640597). Its ZnF-UBP/BUZ domain senses free ubiquitin C-termini and relieves catalytic product inhibition, while CDK1-mediated S552 phosphorylation and O-GlcNAcylation at T203/S214 coordinately regulate nuclear–cytoplasmic shuttling and substrate selectivity; cryo-EM reveals a nucleosome-binding mode independent of the H2A-H2B acidic patch, mechanistically distinct from PR-DUB (PMID:17512543, PMID:24013421, PMID:38462164, PMID:38918638). Beyond histones, USP16 deubiquitinates diverse non-histone substrates—Plk1 at kinetochores, calcineurin A (K29-linked chains) to enable NFAT signaling, IKKβ at K238 to promote NF-κB activation, JAK1, KEAP1, Drp1, NLRP3, and RPS27a on cytoplasmic pre-40S ribosomes—and additionally possesses ISG15 and Fubi cross-reactive protease activity required for ribosome maturation (PMID:26323689, PMID:31135381, PMID:33523871, PMID:32129764, PMID:38055744, PMID:37443395). Triplication of USP16 in Down syndrome (trisomy 21) models causally reduces stem cell self-renewal and accelerates senescence through derepression of Cdkn2a, a phenotype rescued by reducing USP16 copy number (PMID:24025767).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1999 High

    Identification of USP16 as a mitotically regulated H2A deubiquitinase established the first direct link between ubiquitin removal from histones and cell cycle control.

    Evidence In vitro deubiquitination of H2A by recombinant Ubp-M; phosphorylation by mitotic extracts; GFP-fusion imaging showing cytoplasmic localization and mitotic chromosome association of catalytic mutants with cell cycle arrest phenotype

    PMID:10077596

    Open questions at the time
    • Phosphorylation site and responsible kinase not yet identified
    • In vivo chromatin substrates uncharacterized
    • Mechanism of cytoplasmic retention unknown
  2. 2007 High

    Structural determination of the ZnF-UBP/BUZ domain revealed how USP16 specifically senses free ubiquitin C-termini, explaining its selectivity for unconjugated ubiquitin and providing a framework for understanding substrate engagement.

    Evidence NMR solution structure; ubiquitin-binding mapping; fluorescence polarization showing abolition of binding upon G76 carboxylate modification

    PMID:17512543

    Open questions at the time
    • How BUZ domain integrates with catalytic domain during substrate processing unknown
    • No full-length structure available
    • Histone H3-H4 tetramer binding significance not clarified until 2010
  3. 2013 High

    Two parallel advances established USP16's physiological significance: triplication in a Down syndrome mouse model causally reduced stem cell self-renewal via H2AK119ub-Cdkn2a derepression, while CDK1 phosphorylation at S552 was shown to control nuclear entry by disrupting CRM1 interaction.

    Evidence Ts65Dn trisomic mice with rescue by Usp16 allele reduction; CDK1/cyclin B in vitro kinase assay with MS-identified S552; CRM1 co-IP; flow cytometry cell cycle analysis

    PMID:24013421 PMID:24025767

    Open questions at the time
    • Whether S552 phosphorylation affects substrate specificity in vivo unknown
    • Downstream chromatin targets beyond Cdkn2a not mapped genome-wide
    • Precise timing of nuclear entry relative to chromatin deubiquitination unclear
  4. 2014 High

    Discovery that HERC2 recruits USP16 and that USP16 deubiquitinates both H2AK119 and H2AK15 broadened its chromatin substrate range and connected it to DNA damage response signaling.

    Evidence Reciprocal co-IP with domain mapping; in vitro deubiquitination of H2AK119ub and H2AK15ub; siRNA with ubiquitin foci quantification after DNA damage

    PMID:25305019

    Open questions at the time
    • How USP16 is released from HERC2 during damage response unclear
    • Relative contribution to H2AK15 versus H2AK119 in vivo unresolved
    • Whether HERC2 modulates USP16 catalytic activity directly unknown
  5. 2015 High

    Conditional knockout and identification of a non-histone substrate established USP16 as both essential for hematopoiesis (via PRC1-counterbalancing H2AK119ub regulation of Cdkn1a) and a regulator of mitotic fidelity (via Plk1 deubiquitination at kinetochores).

    Evidence Bone marrow conditional KO with ChIP-seq, RNA-seq, and Cdkn1a rescue; Plk1 co-IP and ubiquitination assay with kinetochore localization imaging and chromosome alignment phenotype

    PMID:26323689 PMID:26699484

    Open questions at the time
    • Full repertoire of PRC1-counterbalanced target genes not defined
    • How USP16 is recruited to kinetochores unknown
    • Whether Plk1 deubiquitination requires the BUZ domain untested
  6. 2019 High

    Identification of calcineurin A as a K29-linked polyubiquitin substrate revealed USP16's role in calcium-NFAT signaling and T cell function, extending its biology well beyond chromatin.

    Evidence K327 site and K29 linkage mapping; T cell-specific conditional KO with reduced EAE and IBD severity; NFAT reporter assays

    PMID:31135381

    Open questions at the time
    • How calcium signal activates USP16 toward calcineurin A mechanistically unclear
    • Whether K29-linked deubiquitination is a general USP16 activity unknown
    • Calcineurin A deubiquitination not reconstituted with purified components
  7. 2020 High

    Three concurrent advances resolved USP16's spatial regulation, its role in ribosome biogenesis, and the protective logic of cytoplasmic sequestration: CRM1-dependent export keeps USP16 out of the nucleus to protect DSB repair; on late cytoplasmic pre-40S particles, USP16 deubiquitinates RPS27a for final 18S rRNA maturation.

    Evidence NES/NLS mutant analysis with leptomycin B and DSB repair assays; MS of RIOK1-trapped pre-ribosomal complexes; USP16 deletion with rRNA processing northern blots

    PMID:32005696 PMID:32129764

    Open questions at the time
    • How USP16 is recruited to pre-40S particles unclear
    • Whether ribosome biogenesis function requires BUZ domain unknown
    • Relationship between cytoplasmic sequestration and ribosomal function not tested
  8. 2021 High

    Identification of IKKβ (K238) and JAK1 as USP16 substrates with in vivo validation positioned USP16 as a multi-pathway immune signaling regulator, while c-Myc stabilization connected it to oncogenic proliferation.

    Evidence IKKβ K238 site by MS with myeloid-conditional KO reducing IBD; JAK1 co-IP with Usp16 KO attenuating K-ras-driven lung tumorigenesis; c-Myc co-IP with xenograft rescue

    PMID:33523871 PMID:33546726 PMID:34294846

    Open questions at the time
    • Selectivity determinants for IKKβ versus other IKK complex members unknown
    • In vitro reconstitution of JAK1 deubiquitination not shown
    • Whether c-Myc deubiquitination is direct or requires adaptor proteins unclear
  9. 2022 High

    USP16 was established as the major H2AK119ub deubiquitinase in oocytes required for zygotic genome activation, and its dosage-dependent regulation of Cdkn2a/BMP signaling was linked to Alzheimer's disease neuropathology.

    Evidence Oocyte-specific conditional KO with genome-wide ChIP-seq showing H2AK119ub at TSSs; AD mouse model with USP16 reduction rescuing cognitive deficits and astrogliosis

    PMID:35311644 PMID:35640597

    Open questions at the time
    • Identity of specific zygotic genes requiring USP16-dependent deubiquitination for activation not fully resolved
    • Whether BMP pathway regulation involves direct deubiquitination of a BMP component unclear
    • Whether oocyte and somatic H2AK119ub functions share identical mechanisms unknown
  10. 2023 High

    Discovery of ISG15 and Fubi cross-reactivity, KEAP1 deubiquitination, and Drp1 stabilization dramatically expanded USP16's substrate repertoire to include ubiquitin-like proteins and mitochondrial/inflammasome regulators.

    Evidence ISG15 activity-based profiling with in vitro cleavage reconstitution; Fubi chemoproteomics with cleavage assays; KEAP1 reciprocal co-IP with hepatic IRI model; Drp1 co-IP/GST pulldown with gouty arthritis model

    PMID:37443395 PMID:37488647 PMID:37777507 PMID:38055744

    Open questions at the time
    • Structural basis for ISG15/Fubi recognition by USP16 catalytic domain unknown
    • Whether KEAP1 deubiquitination is direct or scaffold-mediated not fully resolved
    • Relative physiological importance of Fubi versus ubiquitin processing undetermined
  11. 2024 High

    Cryo-EM structure of USP16 on an H2AK119Ub nucleosome revealed an acidic-patch-independent binding mode fundamentally distinct from PR-DUB, and O-GlcNAcylation was shown to tune catalytic activity and nuclear-cytoplasmic partitioning in opposition to CDK1 phosphorylation.

    Evidence Cryo-EM structure at resolution sufficient to resolve nucleosome contacts; site-specific O-GlcNAc mutants with in vitro deubiquitination assays and chromosome segregation imaging

    PMID:38462164 PMID:38918638

    Open questions at the time
    • How O-GlcNAcylation structurally alters catalytic domain conformation unknown
    • Whether acidic-patch independence applies to all nucleosomal substrates untested
    • Contribution of conformational heterogeneity to substrate selectivity not quantified
  12. 2025 Medium

    Recent studies extended USP16 to mitochondrial localization alongside PRC1, S-nitrosylation-mediated activity regulation (C731) with KDM1A as a new substrate, and a kinetic mechanism whereby the ZnF-UBP domain relieves product inhibition in cis.

    Evidence Mitochondrial fractionation and PLA; SNO site identification at C731 with CME model; in vitro kinetic analysis of ZnF-UBP domain mutants and trans-activation experiments (preprint)

    PMID:41086206 PMID:41339351 PMID:bio_10.1101_2025.09.28.679104

    Open questions at the time
    • Specific mitochondrial substrates of USP16 not identified
    • S-nitrosylation regulation awaits independent confirmation and structural characterization
    • Product inhibition relief mechanism demonstrated in preprint only, awaiting peer review

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include: the full structural basis for USP16's remarkable multi-substrate selectivity across ubiquitin, ISG15, and Fubi; how post-translational modifications (phosphorylation, O-GlcNAcylation, S-nitrosylation) are integrated to direct USP16 toward specific substrates in specific compartments; and whether USP16's mitochondrial localization reflects an autonomous deubiquitination program.
  • No integrative structural model of full-length USP16 with post-translational modifications
  • Substrate selection logic across compartments not understood
  • Mitochondrial enzymatic activity not reconstituted

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 14 GO:0016787 hydrolase activity 7 GO:0042393 histone binding 6
Localization
GO:0005694 chromosome 4 GO:0005634 nucleus 3 GO:0005829 cytosol 3 GO:0005840 ribosome 2 GO:0005739 mitochondrion 1
Pathway
R-HSA-162582 Signal Transduction 5 R-HSA-4839726 Chromatin organization 5 R-HSA-1640170 Cell Cycle 4 R-HSA-1266738 Developmental Biology 3 R-HSA-168256 Immune System 3 R-HSA-392499 Metabolism of proteins 2 R-HSA-5357801 Programmed Cell Death 2 R-HSA-73894 DNA Repair 2
Partners
CRM1HERC2IKBKBKEAP1MYCPLK1PPP3CARPS27A
Complex memberships
late cytoplasmic pre-40S ribosomal subunit

Evidence

Reading pass · 31 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 USP16 (Ubp-M) is phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition; purified recombinant Ubp-M deubiquitinates histone H2A in vitro; the wild-type protein localizes to the cytoplasm, while catalytically inactive mutants (lacking the active-site cysteine) associate with mitotic chromosomes and cause cell cycle arrest and apoptosis upon transfection. In vitro deubiquitination assay with recombinant protein; in vitro phosphorylation with mitotic extracts and purified cdc2/cyclin B; GFP-fusion live-cell imaging; transfection of mutant constructs with viability readout Proceedings of the National Academy of Sciences of the United States of America High 10077596
2007 The BUZ domain of Ubp-M (USP16) adopts a structure with three zinc-binding sites forming a pair of cross-braced ring fingers within a third zinc finger; this domain specifically recognizes the free C-terminal tail of ubiquitin (GlyGly-COOH), and any modification of the G76 carboxylate abolishes binding, defining a 'free ubiquitin sensor' function. NMR solution structure determination; ubiquitin-binding mapping by NMR; fluorescence polarization binding assays with C-terminal ubiquitin peptides Journal of molecular biology High 17512543
2010 The BUZ domain of Ubp-M (USP16) exhibits sequence-specific recognition of C-terminal GlyGly-containing peptides; it binds the histone H3–H4 tetramer complex in vitro pull-down, and its sequence specificity differs from that of the HDAC6 BUZ domain. One-bead-one-compound peptide library screening; alanine scanning; fluorescence polarization binding assays; in vitro pull-down with histone complexes Biochemistry High 21090589
2013 Triplication of Usp16 in Ts65Dn (Down syndrome model) mice reduces self-renewal of hematopoietic stem cells, mammary epithelial cells, neural progenitors, and fibroblasts; Usp16 removes ubiquitin from histone H2A lysine 119 (H2AK119); elevated Usp16 is associated with decreased ubiquitination of Cdkn2a and accelerated senescence; reduction of Usp16 by one allele or siRNA rescues these defects. Mouse genetic model (Ts65Dn trisomic); siRNA knockdown; colony and self-renewal assays; histone H2A deubiquitination assays; senescence assays; human tissue overexpression/knockdown experiments Nature High 24025767
2013 CDK1 (cyclin-dependent kinase 1)/cyclin B phosphorylates USP16 (Ubp-M) at serine 552; this phosphorylation is required for G2/M cell cycle progression and reduces interaction with the nuclear export protein CRM1, thereby facilitating USP16 nuclear localization during mitosis; S552 phosphorylation does not affect deubiquitination activity or substrate specificity. Mass spectrometry identification of phosphorylation site; in vitro kinase assay with purified CDK1/cyclin B; in vivo phosphorylation assays; co-immunoprecipitation with CRM1; cell cycle analysis by flow cytometry Cell cycle High 24013421
2014 USP16 interacts with HERC2 through its coiled-coil domain (HERC2 binds via its C-terminal HECT domain); HERC2 knockdown affects ubiquitinated H2A levels through USP16; USP16 levels increase in response to DNA damage in a HERC2-dependent manner; increased USP16 negatively regulates DNA damage-induced ubiquitin foci formation and downstream factor recruitment; USP16 deubiquitinates both H2AK119 and H2AK15 ubiquitination in vitro. Co-immunoprecipitation; domain-mapping experiments; in vitro deubiquitination assay; siRNA knockdown; immunofluorescence for ubiquitin foci; DNA damage response assays The Journal of biological chemistry High 25305019
2015 Conditional deletion of Usp16 in mouse bone marrow increases global H2AK119 ubiquitination and causes lethality with dramatic reduction of mature hematopoietic and progenitor cells; ChIP-seq showed Usp16 bound hematopoietic regulator genes; Usp16 and PRC1 counterbalance each other for H2A ubiquitination; Usp16 deletion alters cell cycle via upregulation of Cdkn1a (p21), and Cdkn1a knockdown rescues the differentiation defect. Conditional knockout mouse; ChIP-seq; RNA-seq; flow cytometry; PRC1 subunit knockdown rescue experiment; cell cycle analysis Proceedings of the National Academy of Sciences of the United States of America High 26699484
2015 USP16 deubiquitinates Plk1 (Polo-like kinase 1), enhancing its interaction with kinetochore protein BubR1 and retaining Plk1 at kinetochores during early mitosis; USP16 knockdown increases Plk1 ubiquitination and decreases kinetochore-localized Plk1, causing chromosome misalignment. Co-immunoprecipitation; ubiquitination assays; siRNA knockdown; immunofluorescence for kinetochore localization; chromosome alignment assays The Journal of cell biology High 26323689
2018 Usp16 modulates the Wnt signaling pathway in mammary epithelia, fibroblasts and MEFs; reduced Usp16 increases tissue responsiveness to Wnt (upregulation of Axin2), expands the basal mammary compartment, and increases regeneration; this regulation is mediated at least partly through Cdkn2a activation and affects Rspo-mediated phosphorylation of LRP6; in Down syndrome model (Ts65Dn), extra Usp16 copy dampens Wnt activation, and genetic Wnt upregulation rescues proliferation defects. Mouse genetic models (Usp16 reduction, Ts65Dn); mammary epithelial regeneration assays; Wnt target gene expression; LRP6 phosphorylation western blot; in vitro and in vivo epithelial repopulation assays Scientific reports Medium 30504774
2019 Calcineurin A (CNA) is constitutively ubiquitinated on K327 with K29-linked polyubiquitin chains, impairing NFAT recruitment; USP16 removes this ubiquitin in response to intracellular calcium stimulation, enabling NFAT-targeted gene transcription; USP16 deficiency prevents calcium-triggered CNA deubiquitination, causing defective T cell maintenance and proliferation; T cell-specific USP16 knockout mice show reduced autoimmune encephalitis and IBD severity. Co-immunoprecipitation; ubiquitination assays identifying K327 site and K29 linkage; T cell-specific knockout mice; NFAT transcription reporter assays; in vivo disease models (EAE, IBD) The Journal of clinical investigation High 31135381
2020 USP16 is predominantly cytoplasmic during all interphase cell cycle phases due to a nuclear export signal (NES) that drives CRM1-dependent export; a non-canonical nuclear localization signal (NLS) has minimal role in nuclear entry; USP16 is only transiently retained in the nucleus after mitosis; forced nuclear localization of USP16 abolishes DNA double-strand break (DSB) repair, indicating that cytoplasmic exclusion protects nuclear DSB repair from unrestrained USP16 DUB activity. Fluorescence live-cell imaging; NES/NLS mutant analysis; leptomycin B treatment (CRM1 inhibition); DNA damage assays with enforced nuclear USP16; cell fractionation Journal of cell science High 32005696
2020 USP16 is a component of late cytoplasmic pre-40S ribosomal subunits; it deubiquitinates an internal lysine of ribosomal protein RPS27a/eS31; USP16 deletion causes defects in final 18S rRNA processing and retarded recycling of late-acting ribosome biogenesis factors, revealing a role in the ultimate step of 40S subunit maturation; RPS27a ubiquitination depends on active translation. Mass spectrometry of pre-ribosomal complexes trapped on RIOK1; USP16 deletion; northern blot for rRNA processing; factor recycling assays; ubiquitination analysis of RPS27a eLife High 32129764
2021 USP16 deubiquitinates and stabilizes c-Myc protein; USP16 interacts with c-Myc by co-immunoprecipitation and co-localization; USP16 depletion suppresses proliferation of castration-resistant prostate cancer cells in vitro and in vivo; c-Myc overexpression rescues USP16 depletion phenotype. Co-immunoprecipitation; ubiquitination assays; shRNA knockdown; xenograft mouse model; c-Myc rescue experiment Journal of experimental & clinical cancer research Medium 33546726
2021 USP16 deubiquitinates IKKβ on K238, and this deubiquitination selectively promotes IKKβ-mediated phosphorylation of p105 (NF-κB1) without directly affecting p65 or IκBα phosphorylation; myeloid-conditional USP16 knockout mice exhibit reduced IBD severity. Mass spectrometry identification of IKKβ ubiquitination site; co-immunoprecipitation; ubiquitination assays; myeloid-specific conditional KO mouse; IBD disease model; substrate-specific phosphorylation analysis Science advances High 33523871
2021 USP16 interacts with and deubiquitinates JAK1, thereby promoting JAK1 signaling and lung tumor growth in K-RAS-driven tumorigenesis; Usp16 deletion in mice significantly attenuates K-rasG12D-induced lung tumorigenesis; USP16 upregulation upon RAS activation also prevents ROS-induced p38 activation. Co-immunoprecipitation; ubiquitination assays; Usp16 conditional KO in K-rasG12D mouse lung tumor model; ROS and p38 signaling analysis Oncogene Medium 34294846
2022 USP16 is the major deubiquitinase for H2AK119ub1 in mouse oocytes; conditional knockout of Usp16 in oocytes does not impair survival, growth, or meiotic maturation, but causes defects in zygotic genome activation and developmental competence after fertilization, associated with high levels of maternal H2AK119ub on zygotic genomes; ChIP-seq revealed H2AK119ub1 is enriched at TSSs of maternal genes in fully grown oocytes and declines during meiotic resumption in a USP16-dependent manner. Oocyte-specific conditional knockout; ChIP-seq for H2AK119ub1 genome-wide; embryo development assays; immunofluorescence Nucleic acids research High 35640597
2022 Reduction of USP16 in a mouse Alzheimer's disease model prevents neural precursor cell (NPC) self-renewal defects, cognitive deficits, and astrogliosis in vivo; this operates through decreased Cdkn2a expression and mitigation of aberrant BMP signaling pathway activation, identifying BMP pathway regulation as a novel USP16 function. Mouse AD model; genetic reduction of USP16; NPC self-renewal assays; in vivo cognitive testing; astrogliosis quantification; gene expression analysis for Cdkn2a and BMP pathway eLife Medium 35311644
2023 USP16 interacts with and deubiquitinates KEAP1; FGF18 treatment reduces USP16 levels, leading to increased KEAP1 ubiquitination and Nrf2 activation; Nrf2 directly binds the USP16 promoter forming a negative feedback loop; this USP16/KEAP1/Nrf2 axis mediates FGF18 protection against hepatic ischemia-reperfusion injury. Co-immunoprecipitation; ubiquitination assays; ChIP for Nrf2 binding to USP16 promoter; USP16 knockdown/overexpression; hepatic IRI mouse model; HSC-specific FGF18 deletion Nature communications High 37777507
2023 USP16 is an ISG15 cross-reactive protease identified by ISG15 activity-based profiling; recombinant USP16 cleaves pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, and deISGylates substrates from cell lysates; USP16 depletion increases interferon-induced ISGylation; USP16-dependent ISG15 substrates include metabolic enzymes (malate dehydrogenase, SOD1, fructose-bisphosphate aldolase A, glutamic-oxaloacetic transaminase 1). ISG15 activity-based profiling; in vitro cleavage assays with recombinant USP16 and ISG15 substrates; USP16 depletion with ISGylation analysis; interactome profiling of ISG15 substrates Proceedings of the National Academy of Sciences of the United States of America High 38055744
2023 USP16 has dual ubiquitin/Fubi cleavage activity; chemoproteomics using a chemical tool kit identified USP16 alongside USP36 as Fubi proteases; USP16 plays a synergistic role in Fubi-S30 maturation, which is required for translationally competent ribosomes. Chemoproteomics with Fubi activity-based probes; in vitro Fubi cleavage assays; Fubi C-terminal hydrolase measurements; functional maturation assays Nature chemical biology High 37443395
2023 USP16 deubiquitinates and stabilizes Drp1 through direct interaction; USP16 is upregulated in MSU-stimulated macrophages and promotes gouty arthritis via Drp1-dependent mitochondrial fission and NF-κB/NLRP3 inflammasome activation. Co-immunoprecipitation; GST pull-down; ubiquitination assays; transmission electron microscopy of mitochondria; NLRP3 inflammasome activation assays; gouty arthritis mouse model Arthritis research & therapy Medium 37488647
2024 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome reveals a mode of H2AK119Ub deubiquitination fundamentally distinct from that of PR-DUB: USP16 recognizes the nucleosome independently of the H2A-H2B acidic patch, and shows conformational heterogeneity in the ubiquitin motif and H2A C-terminal tail. Cryo-EM structure determination of USP16-H2AK119Ub nucleosome complex Nature structural & molecular biology High 38918638
2024 USP16 is O-GlcNAcylated on Thr203 and Ser214; mutation of Thr203 (adjacent to catalytic Cys204) reduces deubiquitination activity toward H2AK119ub in vitro and in cells, while Ser214 mutation has the opposite effect; O-GlcNAcylation antagonizes CDK1-mediated S552 phosphorylation and promotes USP16 nuclear export; O-GlcNAcylation is required for deubiquitination of Plk1 and subsequent proper chromosome segregation and cytokinesis. Site-specific O-GlcNAc mutant analysis; in vitro H2A deubiquitination assays; phosphorylation-specific antibody; nuclear export assays; Plk1 ubiquitination assays; chromosome segregation and cytokinesis imaging The Journal of biological chemistry High 38462164
2025 PRC1 and USP16 are both localized in mitochondria (in addition to the nucleus); mitochondria-specific depletion of PRC1 subunit RING2 alters ubiquitination of mitochondrial proteins including H2Aub; disruption of PRC1 causes alterations in mitochondrial proteome, mitochondrial integrity, and impaired respiratory function. Immunofluorescence; proximity ligation assays; cell fractionation; biochemical analyses of isolated/affinity-purified mitochondria; auxin-inducible mitochondria-specific RING2 depletion; proteomics; mitochondrial respiration assays Proceedings of the National Academy of Sciences of the United States of America Medium 41086206
2025 USP16 S-nitrosylation at C731 by iNOS impairs its deubiquitinase activity toward KDM1A; during coronary microembolization, reduced USP16 activity leads to K355 ubiquitination and degradation of KDM1A, which normally removes H3K9me1/2 from GCLM and GLS promoters to maintain glutathione homeostasis. Site-specific S-nitrosylation identification; ubiquitination assays for KDM1A K355; ChIP for KDM1A at GCLM/GLS promoters; USP16 knockdown/overexpression; CME mouse model Nature communications Medium 41339351
2025 The ZnF-UBP domain of USP16 can bind ubiquitin substrates but also serves as a crucial regulator of enzyme kinetics by relieving product inhibition: after Ub cleavage, slow release of Ub from the catalytic domain causes product inhibition, which the ZnF-UBP domain overcomes in cis by capturing the released ubiquitin product; supplying the ZnF-UBP domain in trans activates USP16 and other USP enzymes. In vitro kinetic analysis of USP16 and ZnF-UBP domain mutants; trans-activation experiments with isolated ZnF-UBP domain; comparison across 8 of 14 ZnF-UBP-containing USPs bioRxivpreprint High bio_10.1101_2025.09.28.679104
2026 USP16 deubiquitinates and stabilizes NLRP3 in keratinocytes by removing K48-linked ubiquitination, thereby enhancing inflammasome activity; keratinocyte-specific USP16 knockdown ameliorates psoriatic phenotypes including epidermal hyperplasia; NLRP3 activator or overexpression counteracts the therapeutic effects of USP16 reduction. Co-immunoprecipitation; ubiquitination assays; RNA-seq; keratinocyte-specific knockdown; psoriasis mouse model; rescue experiments with NLRP3 activator JCI insight Medium 41591834
2026 USP16 deubiquitinates and stabilizes E2F1 through direct interaction; stabilized E2F1 transcriptionally activates Notch1; this USP16/E2F1/Notch1 axis drives M2 macrophage polarization in colorectal cancer. Co-immunoprecipitation; ubiquitination assays; E2F1 and Notch1 rescue/knockdown experiments; macrophage polarization assays; conditioned medium tumor proliferation/invasion assays Cytotechnology Medium 41873345
2026 LPS-induced RUNX2 transcriptionally activates USP16 expression; USP16 then deubiquitinates mitoferrin-2 (MFRN2) at K97, removing K27-linked ubiquitin chains and stabilizing MFRN2, which leads to mitochondrial iron dyshomeostasis and epithelial ferroptosis in sepsis-induced acute lung injury. ChIP for RUNX2 binding to USP16 promoter; ubiquitination assays for MFRN2 K97; USP16 overexpression/knockdown; ferroptosis assays; ALI mouse model Cell reports Medium 41894390
2020 USP16 deubiquitinates and stabilizes LDL receptor (LDLR), preventing ubiquitylation-dependent LDLR degradation and thereby promoting LDL uptake. Co-immunoprecipitation; ubiquitination assays; LDL uptake assays; USP16 overexpression/knockdown International heart journal Low 32999190
2022 MNX1-AS1 lncRNA recruits USP16 to suppress IGF2BP3 degradation (deubiquitination), stabilizing IGF2BP3 and sustaining Hippo pathway inactivation in gallbladder cancer. Co-immunoprecipitation of USP16 with IGF2BP3; ubiquitination assays; lncRNA-protein interaction assays; Hippo pathway reporter Cancer letters Low 35953000

Source papers

Stage 0 corpus · 66 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
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
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
1996 Generation and analysis of 280,000 human expressed sequence tags. Genome research 376 8889549
2010 Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nature structural & molecular biology 274 20622874
2014 Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. The EMBO journal 259 25527291
2013 A strategy for modulation of enzymes in the ubiquitin system. Science (New York, N.Y.) 250 23287719
2016 An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature communications 211 27173435
2011 The differential modulation of USP activity by internal regulatory domains, interactors and eight ubiquitin chain types. Chemistry & biology 176 22195557
2014 USP21 negatively regulates antiviral response by acting as a RIG-I deubiquitinase. The Journal of experimental medicine 157 24493797
2011 Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21. EMBO reports 154 21399617
2017 Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Molecular cell 151 28943312
2021 USP48 Is Upregulated by Mettl14 to Attenuate Hepatocellular Carcinoma via Regulating SIRT6 Stabilization. Cancer research 124 33903120
2004 A protein interaction framework for human mRNA degradation. Genome research 123 15231747
2010 Transcriptional activation of polycomb-repressed genes by ZRF1. Nature 119 21179169
2012 Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions. Molecular biology of the cell 105 22298430
2013 Usp16 contributes to somatic stem-cell defects in Down's syndrome. Nature 104 24025767
2009 Ubiquitin-specific peptidase 21 inhibits tumor necrosis factor alpha-induced nuclear factor kappaB activation via binding to and deubiquitinating receptor-interacting protein 1. The Journal of biological chemistry 102 19910467
2000 Identification of a novel isopeptidase with dual specificity for ubiquitin- and NEDD8-conjugated proteins. The Journal of biological chemistry 98 10799498
2021 The deubiquitinase OTUD1 inhibits colonic inflammation by suppressing RIPK1-mediated NF-κB signaling. Cellular & molecular immunology 93 34876703
2017 p38 inhibition provides anti-DNA virus immunity by regulation of USP21 phosphorylation and STING activation. The Journal of experimental medicine 92 28254948
1999 A mutant deubiquitinating enzyme (Ubp-M) associates with mitotic chromosomes and blocks cell division. Proceedings of the National Academy of Sciences of the United States of America 84 10077596
2019 USP21 deubiquitinase promotes pancreas cancer cell stemness via Wnt pathway activation. Genes & development 83 31488580
2019 FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell reports 82 30865895
2020 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell reports 79 32814053
2013 Identification of the E3 deubiquitinase ubiquitin-specific peptidase 21 (USP21) as a positive regulator of the transcription factor GATA3. The Journal of biological chemistry 79 23395819
2015 The histone H2A deubiquitinase Usp16 regulates hematopoiesis and hematopoietic stem cell function. Proceedings of the National Academy of Sciences of the United States of America 66 26699484
2014 The histone H2A deubiquitinase USP16 interacts with HERC2 and fine-tunes cellular response to DNA damage. The Journal of biological chemistry 60 25305019
2021 USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc. Journal of experimental & clinical cancer research : CR 58 33546726
2023 FGF18 alleviates hepatic ischemia-reperfusion injury via the USP16-mediated KEAP1/Nrf2 signaling pathway in male mice. Nature communications 56 37777507
2007 Solution structure of the Ubp-M BUZ domain, a highly specific protein module that recognizes the C-terminal tail of free ubiquitin. Journal of molecular biology 49 17512543
2019 USP16-mediated deubiquitination of calcineurin A controls peripheral T cell maintenance. The Journal of clinical investigation 45 31135381
2015 Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis. The Journal of cell biology 43 26323689
2017 Long Non-Coding RNA Linc-USP16 Functions As a Tumour Suppressor in Hepatocellular Carcinoma by Regulating PTEN Expression. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 39 29179215
2020 USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit. eLife 34 32129764
2022 LncRNA MNX1-AS1 sustains inactivation of Hippo pathway through a positive feedback loop with USP16/IGF2BP3 axis in gallbladder cancer. Cancer letters 32 35953000
2016 USP16 Downregulation by Carboxyl-terminal Truncated HBx Promotes the Growth of Hepatocellular Carcinoma Cells. Scientific reports 31 27633997
2022 USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation. Nucleic acids research 30 35640597
2021 Substrate-specific recognition of IKKs mediated by USP16 facilitates autoimmune inflammation. Science advances 29 33523871
2010 HDAC6 and Ubp-M BUZ domains recognize specific C-terminal sequences of proteins. Biochemistry 26 21090589
2023 USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism. Proceedings of the National Academy of Sciences of the United States of America 21 38055744
2023 Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36. Nature chemical biology 20 37443395
2024 Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Nature structural & molecular biology 19 38918638
2023 Deubiquitinase USP16 induces gouty arthritis via Drp1-dependent mitochondrial fission and NLRP3 inflammasome activation. Arthritis research & therapy 17 37488647
2020 A potent nuclear export mechanism imposes USP16 cytoplasmic localization during interphase. Journal of cell science 15 32005696
2013 Ubp-M serine 552 phosphorylation by cyclin-dependent kinase 1 regulates cell cycle progression. Cell cycle (Georgetown, Tex.) 14 24013421
2022 Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model. eLife 11 35311644
2021 The deubiquitinase USP16 functions as an oncogenic factor in K-RAS-driven lung tumorigenesis. Oncogene 10 34294846
2024 O-GlcNAcylation stimulates the deubiquitination activity of USP16 and regulates cell cycle progression. The Journal of biological chemistry 9 38462164
2018 Usp16 modulates Wnt signaling in primary tissues through Cdkn2a regulation. Scientific reports 9 30504774
2013 Usp16: key controller of stem cells in Down syndrome. The EMBO journal 9 24076652
2020 USP16 Regulates the Stability and Function of LDL receptor by Deubiquitination. International heart journal 8 32999190
2020 Copy number variation of the USP16 gene and its association with milk traits in Chinese Holstein cattle. Animal biotechnology 3 32646283
2021 CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1. Frontiers in cell and developmental biology 2 34136489
2025 Polycomb Repressive Complex 1 and USP16 localize to the mitochondrion and influence its function. Proceedings of the National Academy of Sciences of the United States of America 1 41086206
2026 USP16 drives psoriasis progression by deubiquitinating and stabilizing NLRP3 in keratinocytes. JCI insight 0 41591834
2026 Development of a Dual Chemical Probe for the USP16 and HDAC6 Zinc-Finger Ubiquitin-Binding Domain. Journal of medicinal chemistry 0 41718545
2026 USP16 promotes M2 polarization of macrophages in colorectal cancer by activating the Notch pathway via inducing the deubiquitination of E2F1. Cytotechnology 0 41873345
2026 RUNX2 and USP16 stabilize MFRN2 to maintain pulmonary epithelial barrier integrity in sepsis-induced acute lung injury. Cell reports 0 41894390
2025 USP16 S-nitrosylation aggravates coronary microembolization-induced myocardial injury via repressing KDM1A-mediated glutathione homeostasis. Nature communications 0 41339351