Affinage

USP16

Ubiquitin carboxyl-terminal hydrolase 16 · UniProt Q9Y5T5

Length
823 aa
Mass
93.6 kDa
Annotated
2026-06-10
37 papers in source corpus 31 papers cited in narrative 31 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

USP16 (originally Ubp-M) is a deubiquitinating enzyme whose best-defined function is the removal of monoubiquitin from histone H2A at lysine 119 (H2AK119ub), thereby directly antagonizing PRC1-mediated chromatin silencing to control gene expression, stem cell self-renewal, and developmental reprogramming (PMID:24025767, PMID:26699484). By counterbalancing PRC1 at H2AK119ub, USP16 derepresses targets including Cdkn2a/Cdkn1a, and its dosage governs self-renewal of hematopoietic, mammary, neural, and fibroblast progenitors, with triplication accelerating senescence and genetic reduction rescuing self-renewal and BMP/Wnt signaling defects (PMID:24025767, PMID:35311644, PMID:30504774). In oocytes USP16 is the major H2AK119ub eraser, and its removal of maternal H2AK119ub during maturation is required for zygotic genome activation (PMID:35640597). A cryo-EM structure of the USP16–H2AK119ub nucleosome complex shows substrate recognition independent of the H2A–H2B acidic patch, distinguishing it from PR-DUB (PMID:38918638). Catalysis depends on the USP domain (active-site Cys204) assisted by a ZnF-UBP/BUZ domain that binds the free ubiquitin C-terminal Gly-Gly motif and relieves product inhibition during turnover [PMID:17512543, PMID:21090589, PMID:bio_10.1101_2025.09.28.679104]. USP16 activity and localization are tightly regulated through the cell cycle: CDK1/cyclin B phosphorylates Ser552 to limit CRM1-dependent nuclear export and permit transient post-mitotic nuclear retention, while O-GlcNAcylation at Thr203/Ser214 modulates catalytic output and promotes nuclear export, and an active NES otherwise keeps the enzyme cytoplasmic to restrain unregulated H2A deubiquitination during DNA double-strand break repair (PMID:24013421, PMID:32005696, PMID:38462164). Beyond histones, USP16 deubiquitinates and stabilizes a broad set of non-histone substrates—Plk1 at kinetochores, calcineurin A in NFAT/T-cell signaling, IKKβ, JAK1, KEAP1, Drp1, NLRP3, TOM40, and ribosomal protein RPS27a/eS31—linking it to mitosis, immune and inflammatory signaling, mitochondrial homeostasis, and 40S ribosome maturation (PMID:26323689, PMID:31135381, PMID:32129764, PMID:33523871, PMID:37777507, PMID:42236685, PMID:41591834). Its ZnF-UBP domain additionally confers dual ubiquitin/Fubi cleavage activity, deISGylating substrates and contributing to Fubi-S30 maturation for translationally competent ribosomes (PMID:38055744, PMID:37443395).

Mechanistic history

Synthesis pass · year-by-year structured walk · 22 steps
  1. 1999 High

    Establishing USP16 as a histone H2A deubiquitinase under cell-cycle control answered whether a DUB directly reverses histone ubiquitination and is itself mitotically regulated.

    Evidence In vitro deubiquitination, in vitro kinase assay with cdc2/cyclin B, GFP live-cell imaging and catalytic-mutant transfection

    PMID:10077596

    Open questions at the time
    • Did not identify the specific H2A lysine targeted
    • Mechanism linking catalytic-mutant chromatin retention to apoptosis unresolved
  2. 2007 High

    Solving the BUZ/ZnF-UBP domain structure defined how USP16 recognizes free ubiquitin C-termini, establishing a substrate/product recognition module distinct from the catalytic domain.

    Evidence NMR solution structure and ubiquitin-peptide binding affinity measurements

    PMID:17512543

    Open questions at the time
    • Functional consequence of free-ubiquitin binding for catalysis not yet established
    • No structure of full-length enzyme or catalytic domain
  3. 2010 Medium

    Defining BUZ-domain sequence specificity and H3–H4 tetramer binding refined how the recognition module discriminates substrates relative to other BUZ-domain proteins.

    Evidence Peptide library screen, alanine scanning, fluorescence polarization and in vitro pull-down

    PMID:21090589

    Open questions at the time
    • In vitro binding only; cellular relevance of H3–H4 interaction untested
    • Single lab without orthogonal structural confirmation of histone binding
  4. 2013 High

    Identifying H2AK119 as the chromatin substrate and demonstrating PRC1 antagonism placed USP16 at the center of stem-cell self-renewal control and Down-syndrome dosage phenotypes.

    Evidence Ts65Dn trisomy mouse model, siRNA knockdown, self-renewal and senescence assays with histone ubiquitination analysis

    PMID:24025767

    Open questions at the time
    • Whether all phenotypes are H2AK119ub-dependent versus non-histone substrate effects not fully separated
    • Direct genome-wide chromatin occupancy not yet mapped
  5. 2013 High

    Mapping CDK1-dependent Ser552 phosphorylation explained how mitotic kinase signaling gates USP16 nuclear access and G2/M progression without altering its catalytic activity.

    Evidence In vitro kinase assay, mass spectrometry, CRM1 Co-IP, cell-cycle and localization analysis

    PMID:24013421

    Open questions at the time
    • Phosphatase reversing Ser552 not identified
    • Nuclear substrates relevant to G2/M progression not defined here
  6. 2014 High

    Linking USP16 to HERC2 and to both H2AK119 and H2AK15 deubiquitination connected the enzyme to negative regulation of DNA-damage ubiquitin signaling.

    Evidence Reciprocal Co-IP with domain mapping, in vitro deubiquitination, siRNA knockdown and DNA-damage foci assays

    PMID:25305019

    Open questions at the time
    • How HERC2 stabilizes USP16 mechanistically unclear
    • E3 ligase depositing H2AK15ub in this context not defined
  7. 2015 High

    Discovery of Plk1 as a kinetochore substrate established USP16's first non-histone target and a direct role in chromosome alignment during mitosis.

    Evidence siRNA knockdown, Co-IP, ubiquitination and kinetochore-localization imaging, chromosome-alignment assays

    PMID:26323689

    Open questions at the time
    • Ubiquitin linkage type on Plk1 not defined
    • E3 ligase counteracted by USP16 unidentified
  8. 2015 High

    Conditional Usp16 deletion in bone marrow established in vivo that USP16 and PRC1 reciprocally set global H2AK119ub levels controlling hematopoietic lineage commitment.

    Evidence Conditional knockout, ChIP-seq, RNA-seq, PRC1 and Cdkn1a knockdown epistasis, flow cytometry

    PMID:26699484

    Open questions at the time
    • Lethality mechanism beyond hematopoietic loss not resolved
    • Contribution of non-histone substrates to phenotype not separated
  9. 2018 Medium

    Connecting USP16 dosage to Wnt responsiveness via Cdkn2a and LRP6 phosphorylation extended its self-renewal role to tissue regeneration capacity.

    Evidence Allele reduction in Ts65Dn mice, mammary regeneration, Axin2 Wnt reporter, LRP6 phosphorylation and siRNA knockdown

    PMID:30504774

    Open questions at the time
    • Whether USP16 acts on a direct Wnt-pathway substrate or only via Cdkn2a unresolved
    • Single lab
  10. 2019 High

    Identifying calcineurin A K327 deubiquitination revealed USP16 as a calcium-responsive regulator of NFAT signaling and T-cell maintenance with autoimmune-disease relevance.

    Evidence Co-IP, K29-linkage-specific ubiquitination assays, T-cell-specific KO, NFAT reporter, EAE and IBD models

    PMID:31135381

    Open questions at the time
    • E3 ligase generating K29 chains on CNA not identified
    • Structural basis of linkage specificity unknown
  11. 2020 High

    Defining a dominant NES established that USP16 is predominantly cytoplasmic and must be excluded from the nucleus to avoid unrestrained DUB activity that impairs DSB repair.

    Evidence Live-cell imaging, NES/NLS mutagenesis, forced-nuclear constructs and DSB repair assays

    PMID:32005696

    Open questions at the time
    • Reconciliation with HERC2-dependent damage role not fully resolved
    • Nuclear cofactors restraining activity unidentified
  12. 2020 High

    Finding USP16 in late pre-40S particles and acting on RPS27a/eS31 revealed an unexpected role in cytoplasmic ribosome maturation.

    Evidence MS of RIOK1-trapped pre-ribosomes, USP16 deletion, pre-rRNA processing and biogenesis-factor recycling assays

    PMID:32129764

    Open questions at the time
    • E3 ligase ubiquitinating eS31 during translation not defined
    • Coupling between deubiquitination and 18S processing mechanistically unclear
  13. 2021 Medium

    A cluster of studies established USP16 as a deubiquitinase stabilizing oncogenic and signaling substrates (c-Myc, IKKβ, JAK1), broadening its role to cancer and inflammatory signaling.

    Evidence Co-IP, ubiquitination/deubiquitination and substrate-phosphorylation assays, conditional/myeloid KO mice, rescue and xenograft/tumor models

    PMID:33523871 PMID:33546726 PMID:34294846

    Open questions at the time
    • Most lack in vitro reconstitution of direct catalysis
    • Ubiquitin linkage specificity on several substrates undefined
  14. 2022 High

    Identifying USP16 as the major oocyte H2AK119ub eraser linked its chromatin activity to zygotic genome activation and developmental competence.

    Evidence Oocyte conditional KO, genome-wide H2AK119ub ChIP-seq, RNA-seq and embryo development assays

    PMID:35640597

    Open questions at the time
    • How USP16-dependent erasure is timed during maturation unclear
    • Downstream zygotic targets not fully resolved
  15. 2022 Medium

    Genetic USP16 reduction rescuing NPC self-renewal and cognition in an Alzheimer's model reinforced the Cdkn2a/BMP axis as a therapeutic node.

    Evidence Heterozygous knockout, NPC self-renewal assays, cognitive testing, Cdkn2a/BMP pathway analysis

    PMID:35311644

    Open questions at the time
    • Direct USP16 substrate in BMP regulation not identified
    • Single lab
  16. 2023 High

    Multiple studies extended USP16 substrate range to KEAP1, Drp1 and downstream NLRP3, embedding it in redox (Nrf2), mitochondrial fission and inflammasome regulation.

    Evidence Co-IP, GST pull-down, deubiquitination assays, ChIP, mitochondrial imaging and in vivo IRI/gouty-arthritis models

    PMID:37488647 PMID:37777507

    Open questions at the time
    • Whether USP16 acts on these substrates in the cytoplasm versus mitochondria not fully localized
    • Linkage specificities partly undefined
  17. 2023 High

    Chemoproteomics revealed dual ubiquitin/Fubi cleavage activity, showing USP16 deISGylates metabolic enzymes and contributes to Fubi-S30 maturation for ribosome function.

    Evidence ISG15 activity-based profiling, in vitro cleavage, cell-based ISGylation with depletion, MS interactome, and crystallographic context (USP36 complexes)

    PMID:37443395 PMID:38055744

    Open questions at the time
    • Structural basis of USP16 Fubi versus Ub discrimination not directly solved
    • Physiological balance between deISGylation and deubiquitination unclear
  18. 2024 High

    The cryo-EM USP16–nucleosome structure defined an acidic-patch-independent recognition mode for H2AK119ub, distinguishing USP16 mechanistically from PR-DUB.

    Evidence Cryo-EM structure determination of the USP16–H2AK119Ub nucleosome complex

    PMID:38918638

    Open questions at the time
    • Conformational heterogeneity in Ub motif limits full atomic interpretation
    • Disease-mutation effects predicted but not functionally tested
  19. 2024 High

    Mapping O-GlcNAcylation at Thr203/Ser214 showed a second post-translational layer that tunes catalysis and antagonizes CDK1 phosphorylation to control localization and mitotic fidelity.

    Evidence Site-directed mutagenesis, in vitro deubiquitination, phospho-specific detection, nuclear-export and chromosome-segregation imaging

    PMID:38462164

    Open questions at the time
    • O-GlcNAc transferase/hydrolase enzymes acting on USP16 not identified
    • Crosstalk dynamics with Ser552 in vivo not fully resolved
  20. 2025 Medium

    Localization of USP16 (and PRC1) to mitochondria and identification of S-nitrosylation regulating KDM1A deubiquitination opened mitochondrial and redox-signaling dimensions of USP16 biology.

    Evidence IF, PLA, fractionation, degron depletion and mitochondrial proteomics; plus S-nitrosylation/Co-IP/ChIP with CME mouse model for the KDM1A axis

    PMID:41086206 PMID:41339351

    Open questions at the time
    • USP16-specific mitochondrial function not dissected from PRC1
    • Direct mitochondrial USP16 substrates in this context undefined
  21. 2025 Medium

    Kinetic dissection showed the ZnF-UBP domain relieves product inhibition in cis, providing a mechanism for how the recognition module accelerates catalytic turnover.

    Evidence Biochemical kinetics, domain mutagenesis and in trans activation experiments (preprint)

    PMID:bio_10.1101_2025.09.28.679104

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • In vivo relevance of product-inhibition relief untested
  22. 2026 Medium

    Identifying TOM40 and MFRN2 deubiquitination, plus NLRP3 and E2F1 stabilization, consolidated USP16 as a regulator of mitochondrial integrity, iron homeostasis, inflammasome and tumor-microenvironment signaling.

    Evidence Co-IP, site- and linkage-specific deubiquitination assays, ChIP, KO/rescue and disease models (mitochondrial dysfunction, psoriasis, ALI, CRC)

    PMID:41591834 PMID:41873345 PMID:41894390 PMID:42236685

    Open questions at the time
    • Most rely on single-lab Co-IP without in vitro reconstitution
    • How a predominantly cytoplasmic enzyme accesses outer-membrane substrates not structurally defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how USP16's growing roster of substrates is spatially and temporally partitioned—how localization control, post-translational modifications, and the ZnF-UBP activation mechanism collectively dictate which substrate is engaged in a given compartment and physiological state.
  • No unified model coupling localization to substrate choice
  • E3 ligases counteracted by USP16 are largely unidentified for most substrates
  • Disease-causing USP16 mutations not yet functionally characterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 7 GO:0016787 hydrolase activity 4 GO:0098772 molecular function regulator activity 4 GO:0042393 histone binding 2
Localization
GO:0000228 nuclear chromosome 3 GO:0005634 nucleus 3 GO:0005739 mitochondrion 2 GO:0005829 cytosol 2 GO:0005840 ribosome 2
Pathway
R-HSA-1640170 Cell Cycle 4 R-HSA-168256 Immune System 4 R-HSA-4839726 Chromatin organization 4 R-HSA-392499 Metabolism of proteins 3 R-HSA-73894 DNA Repair 2 R-HSA-8953854 Metabolism of RNA 2
Partners
HERC2IKBKBJAK1KEAP1MYCPLK1PPP3CBTOMM40
Complex memberships
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) deubiquitinates histone H2A in vitro. The protein is phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition; the C-terminal domain can be phosphorylated by cdc2/cyclin B complexes. Wild-type Ubp-M localizes to the cytoplasm, while catalytic-site cysteine mutants associate with mitotic chromosomes and remain in the nucleus post-mitosis. Expression of the catalytic mutant blocks cell division and induces apoptosis. In vitro deubiquitination assay, in vitro kinase assay with mitotic extracts and purified cdc2/cyclin B, GFP-fusion live-cell imaging, transfection of mutant constructs with cell division/apoptosis readout Proceedings of the National Academy of Sciences of the United States of America High 10077596
2007 The BUZ domain of USP16 (Ubp-M) adopts a solution structure featuring three zinc-binding sites (two cross-braced ring fingers within a third zinc finger). It binds specifically to the free C-terminal tail of ubiquitin (RLRGG-COOH); modification of the G76 carboxylate by a peptide or isopeptide bond abolishes binding. The ubiquitin-binding site maps to a concave surface formed by helix α3 and the central β-sheet. NMR solution structure determination, binding affinity measurements with ubiquitin peptides and full-length ubiquitin Journal of molecular biology High 17512543
2010 The BUZ domain of USP16 (Ubp-M) requires a C-terminal Gly-Gly motif for binding and has distinct sequence specificity from HDAC6-BUZ at more N-terminal positions. In vitro pull-down showed the Ubp-M BUZ domain can bind the histone H3–H4 tetramer complex. One-bead-one-compound peptide library screen, alanine scanning, fluorescence polarization binding assays, in vitro pull-down Biochemistry Medium 21090589
2013 USP16 removes ubiquitin from histone H2A at lysine 119 (H2AK119), antagonizing PRC1/Bmi1 function. Triplication of Usp16 in Ts65Dn (Down syndrome model) mice reduces self-renewal of hematopoietic stem cells, mammary epithelial cells, neural progenitors, and fibroblasts, associated with decreased H2AK119 ubiquitination of Cdkn2a and accelerated senescence. Downregulation of a single Usp16 allele or siRNA knockdown rescues these defects. Mouse genetic model (Ts65Dn trisomy), siRNA knockdown, in vitro and in vivo self-renewal assays, senescence assays, histone ubiquitination analysis Nature High 24025767
2013 CDK1/cyclin B phosphorylates USP16 (Ubp-M) at serine 552 in vitro and in vivo. This phosphorylation is required for cell cycle G2/M progression. Phospho-S552 reduces USP16 interaction with nuclear export protein CRM1, facilitating USP16 nuclear localization. S552 phosphorylation does not affect USP16 tetramer formation, deubiquitination activity, substrate specificity, or gene expression regulation. In vitro kinase assay, mass spectrometry, in vivo phosphorylation assay, Co-IP (CRM1 interaction), cell cycle analysis, nuclear localization imaging Cell cycle (Georgetown, Tex.) High 24013421
2014 USP16 interacts with HERC2 through its coiled-coil domain (USP16 side) and the C-terminal HECT domain (HERC2 side). HERC2 knockdown alters ubiquitinated H2A levels through USP16. In response to DNA damage, USP16 levels increase in a HERC2-dependent manner, and increased USP16 negatively regulates DNA damage-induced ubiquitin foci formation and downstream factor recruitment. USP16 can deubiquitinate both H2AK119 and H2AK15 ubiquitination in vitro. Co-immunoprecipitation, domain-mapping, siRNA knockdown, in vitro deubiquitination assay, DNA damage assays (ubiquitin foci, downstream factor recruitment) The Journal of biological chemistry High 25305019
2015 USP16 deubiquitinates Plk1, enhancing its interaction with kinetochore-localized BubR1, and thereby retains Plk1 on kinetochores to promote proper chromosome alignment in early mitosis. Downregulation of USP16 causes increased Plk1 ubiquitination and decreased Plk1 kinetochore localization. siRNA knockdown, co-immunoprecipitation, ubiquitination assays, immunofluorescence of kinetochore localization, chromosome alignment assays The Journal of cell biology High 26323689
2015 Conditional deletion of Usp16 in mouse bone marrow significantly increases global H2AK119 ubiquitination and causes lethality. Usp16 deletion leads to dramatic reduction of mature and progenitor hematopoietic cell populations (affecting HSC lineage commitment) without changing HSC number. The altered gene expression is partly rescued by knockdown of PRC1 subunits, demonstrating that Usp16 and PRC1 counterbalance each other for H2AK119 ubiquitination control. Knockdown of Cdkn1a (p21) rescued cell cycle and differentiation defects of Usp16-deleted HSCs. Conditional knockout mouse, ChIP-seq, RNA-seq, PRC1 subunit knockdown epistasis, Cdkn1a knockdown rescue, flow cytometry of hematopoietic populations Proceedings of the National Academy of Sciences of the United States of America High 26699484
2019 USP16 deubiquitinates calcineurin A (CNA, encoded by PPP3CB/PPP3CC) at lysine 327, removing K29-linked polyubiquitin chains in response to intracellular calcium stimulation. K29-linked ubiquitination of CNA impairs NFAT recruitment and transcription of NFAT target genes. USP16 deficiency prevents calcium-triggered CNA deubiquitination, leading to defective maintenance and proliferation of peripheral T cells. T cell-specific USP16 knockout mice show reduced severity of experimental autoimmune encephalitis and IBD. Co-immunoprecipitation, ubiquitination assays, T cell-specific knockout mice, NFAT transcription reporter assays, EAE and IBD mouse models The Journal of clinical investigation High 31135381
2020 USP16 is predominantly cytoplasmic in all cell cycle phases due to a nuclear export signal (NES) that actively excludes it from the nucleus. A non-canonical nuclear localization signal (NLS) plays a minimal role in nuclear entry. USP16 is only transiently retained in the nucleus following mitosis. Enforced nuclear localization of USP16 abolishes DNA double-strand break repair, likely due to unrestrained DUB activity. USP16 does not accumulate in the nucleus following DNA damage. Live-cell imaging, nuclear export signal mutagenesis, nuclear localization signal mutagenesis, forced nuclear localization constructs, DSB repair assays Journal of cell science High 32005696
2020 USP16 is a component of late cytoplasmic pre-40S ribosomal subunits and deubiquitinates an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion causes 18S rRNA processing defects and retarded recycling of late-acting ribosome biogenesis factors, revealing a role in the final maturation of human 40S subunits. RPS27a ubiquitination appears to depend on active translation. Mass spectrometry of RIOK1-trapped pre-ribosomal subunits, USP16 deletion, pre-rRNA processing assays, ribosome biogenesis factor recycling assays eLife High 32129764
2021 USP16 deubiquitinates and stabilizes c-Myc protein. Co-immunoprecipitation and ubiquitination assays confirmed USP16 as a direct deubiquitinase of c-Myc; overexpression of c-Myc rescued effects of USP16 depletion on prostate cancer cell proliferation. Co-immunoprecipitation, ubiquitination assay, protein co-localization, shRNA knockdown, xenograft mouse model, c-Myc rescue experiment Journal of experimental & clinical cancer research : CR Medium 33546726
2021 USP16 deubiquitinates IKKβ at lysine 238, and this deubiquitination selectively affects IKKβ-mediated phosphorylation of p105 without directly affecting p65 or IκBα phosphorylation. USP16 was identified as a regulator of IKKβ ubiquitination by mass spectrometry. Myeloid-conditional USP16 knockout mice showed reduced IBD severity. Mass spectrometry identification, ubiquitination assay, phosphorylation assays for downstream substrates, myeloid-conditional knockout mice, IBD mouse model Science advances High 33523871
2021 USP16 interacts with and deubiquitinates JAK1, promoting JAK1 signaling and lung tumor growth downstream of K-RAS. USP16 upregulation upon RAS activation also averts ROS-induced p38 activation. Usp16 deletion significantly attenuates K-rasG12D-mutation-induced lung tumorigenesis in mice. Co-immunoprecipitation, deubiquitination assay, conditional Usp16 deletion in K-rasG12D mouse lung tumor model, ROS and p38 signaling assays Oncogene Medium 34294846
2022 USP16 is the major H2AK119ub1 deubiquitinase in mouse oocytes. Conditional knockout of Usp16 in oocytes does not impair survival, growth, or meiotic maturation, but oocytes lacking USP16 have defects in zygotic genome activation and developmental competence after fertilization, associated with high levels of maternal H2AK119ub1 deposition. USP16-dependent H2AK119ub1 removal during oocyte maturation is required for zygotic transcriptional reprogramming. Conditional knockout mouse, ChIP-seq (genome-wide H2AK119ub1 mapping), RNA-seq, immunostaining, fertilization and embryo development assays Nucleic acids research High 35640597
2022 Genetic reduction of USP16 decreases Cdkn2a expression and mitigates aberrant BMP signaling, rescuing neural precursor cell (NPC) self-renewal defects and downstream cognitive defects in an Alzheimer's disease mouse model. Genetic reduction (heterozygous knockout), NPC self-renewal assays, cognitive behavioral testing in AD mouse model, Cdkn2a and BMP pathway analysis eLife Medium 35311644
2023 USP16 interacts with and deubiquitinates KEAP1, leading to increased KEAP1 ubiquitination when USP16 is reduced (by FGF18 treatment) and subsequent Nrf2 activation. Nrf2 directly binds to the USP16 promoter, forming a negative feedback loop. This USP16/KEAP1/Nrf2 axis mediates FGF18's protective effect in hepatic ischemia-reperfusion injury. Co-immunoprecipitation, deubiquitination assay, ChIP (Nrf2 binding to USP16 promoter), USP16 knockout/overexpression, mouse IRI model Nature communications High 37777507
2023 USP16 deubiquitinates and stabilizes Drp1 through direct interaction, promoting Drp1-dependent mitochondrial fission and NLRP3 inflammasome activation in macrophages, contributing to gouty arthritis pathology. Co-immunoprecipitation, GST pull-down, ubiquitination assay, transmission electron microscopy of mitochondria, NLRP3 inflammasome activation assays, mouse MSU-induced gouty arthritis model Arthritis research & therapy Medium 37488647
2023 USP16 has dual Ub/Fubi cleavage activity, discovered by chemoproteomics. USP16 cleaves pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro and deISGylates substrates from cell lysates. Depletion of USP16 increases interferon-induced ISGylation. USP16-dependent ISG15 targets include metabolic enzymes (malate dehydrogenase, SOD1, fructose-bisphosphate aldolase A, and cytoplasmic GOT1). ISG15 activity-based profiling (chemoproteomics), in vitro cleavage assays, cell-based ISGylation assays with USP16 depletion, ISG15 interactome by MS Proceedings of the National Academy of Sciences of the United States of America High 38055744
2023 USP16 has dual ubiquitin/Fubi cleavage activity identified by chemoproteomics. USP16 plays a synergistic role with USP36 in Fubi-S30 maturation required for translationally competent ribosomes. Chemoproteomics, crystal structures of USP36-Fubi and USP36-ubiquitin complexes, Fubi C-terminal hydrolase measurements, USP16 functional assays in Fubi-S30 maturation Nature chemical biology High 37443395
2024 Cryo-EM structure of the USP16–H2AK119Ub nucleosome complex reveals that USP16 recognizes the H2AK119Ub nucleosome via a mode independent of the H2A–H2B acidic patch, distinct from PR-DUB. The structure shows conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail, and provides a structural framework for understanding disease-causing USP16 mutations. Cryo-EM structure determination of USP16-H2AK119Ub nucleosome complex Nature structural & molecular biology High 38918638
2024 USP16 is O-GlcNAcylated at Thr203 and Ser214. Mutation of Thr203 (adjacent to catalytic Cys204) reduces deubiquitination of H2AK119ub in vitro and in cells, while mutation of Ser214 has the opposite effect. O-GlcNAcylation antagonizes CDK1-mediated Ser552 phosphorylation and promotes USP16 nuclear export. O-GlcNAcylation is required for deubiquitination of Polo-like kinase 1 and proper chromosome segregation and cytokinesis. Site-directed mutagenesis, in vitro deubiquitination assay, phosphorylation-specific antibodies, nuclear export assays, chromosome segregation/cytokinesis imaging The Journal of biological chemistry High 38462164
2025 Both PRC1 and USP16 localize to mitochondria in addition to the nucleus. Mitochondria-specific depletion of PRC1 subunit RING2 alters ubiquitination of mitochondrial proteins including H2Aub. Double KO of RING1/RING2 or mitochondria-specific RING2 deletion causes profound alterations in mitochondrial proteome, integrity, and respiratory function. Immunofluorescence, proximity ligation assay, cell fractionation, biochemical analysis of isolated/affinity-purified mitochondria, auxin-inducible degron system for mitochondria-specific depletion, mitochondrial proteomics Proceedings of the National Academy of Sciences of the United States of America Medium 41086206
2025 S-nitrosylation of USP16 at C731 by iNOS inhibits USP16 deubiquitinase activity toward KDM1A, leading to increased K27-linked ubiquitination of KDM1A at K355, KDM1A degradation, reduced H3K9me1/2 demethylation at GCLM and GLS promoters, glutathione depletion, and epithelial ferroptosis during coronary microembolization. S-nitrosylation assay, co-immunoprecipitation, ubiquitination assay (K27-linkage specific), ChIP, KDM1A overexpression rescue, mouse CME model Nature communications Medium 41339351
2026 USP16 interacts with and deubiquitinates TOM40 (core subunit of the TOM complex in the mitochondrial outer membrane), removing K48-linked ubiquitin chains from lysines 175, 184, and 309 of TOM40. USP16 knockout disrupts mitochondrial membrane potential, elevates ROS, reduces ATP synthesis, and alters oxygen consumption. Re-expression of USP16 restores TOM40 levels and mitochondrial function; TOM40 re-expression in USP16 KO partially restores mitochondrial function. Co-immunoprecipitation, deubiquitination assay (K48-linkage specific, site-specific mutagenesis on TOM40), USP16 knockout, mitochondrial functional assays (membrane potential, ROS, ATP, OCR), rescue experiments Cell death & disease High 42236685
2026 USP16 directly binds and deubiquitinates NLRP3 at K48-linked ubiquitin, preventing its degradation and stabilizing NLRP3 protein to activate the inflammasome and promote keratinocyte hyperproliferation in psoriasis. Therapeutic effects of USP16 reduction on psoriasis were counteracted by NLRP3 activator or NLRP3 overexpression. Co-immunoprecipitation, deubiquitination assay, keratinocyte-specific knockdown in mouse psoriasis model, NLRP3 rescue experiments JCI insight Medium 41591834
2026 USP16 deubiquitinates and stabilizes the transcription factor E2F1, and stabilized E2F1 transcriptionally activates Notch1, driving M2 macrophage polarization in colorectal cancer. USP16 directly interacted with E2F1 in Co-IP assays; silencing E2F1 or Notch1 abrogated USP16 overexpression effects. Co-immunoprecipitation, deubiquitination assay, siRNA epistasis (E2F1, Notch1), macrophage polarization assays, conditioned medium experiments Cytotechnology Medium 41873345
2026 USP16 deubiquitinates mitoferrin-2 (MFRN2) at lysine 97, removing K27-linked ubiquitin chains, thereby stabilizing MFRN2. RUNX2 transcriptionally activates USP16 expression upon LPS stimulation. USP16-mediated MFRN2 stabilization leads to mitochondrial iron dyshomeostasis and promotes epithelial ferroptosis in sepsis-induced acute lung injury. ChIP (RUNX2 binding to USP16 promoter), co-immunoprecipitation, ubiquitination assay (K27-linkage specific, site K97), LPS stimulation model, epistasis experiments Cell reports Medium 41894390
2025 The ZnF-UBP domain of USP16 binds the free C-terminal GlyGly motif of ubiquitin and serves as a crucial regulator of enzyme kinetics by relieving product inhibition: after catalytic cleavage, slow ubiquitin release from the catalytic domain causes product inhibition, which is overcome in cis by ZnF-UBP-mediated product release. Supplying a high-affinity ZnF-UBP domain in trans activates USP16 and other USP enzymes. Biochemical kinetics assays, domain mutagenesis, in trans activation experiments, binding assays for ZnF-UBP–ubiquitin interaction bioRxivpreprint Medium bio_10.1101_2025.09.28.679104
2020 USP16 deubiquitinates and stabilizes LDLR (LDL receptor), preventing ubiquitylation-dependent LDLR degradation and promoting LDL uptake. Ubiquitination assay, protein stability assay, LDL uptake assay International heart journal Low 32999190
2018 USP16 modulates Wnt pathway activity in mammary epithelial cells, fibroblasts, and MEFs at least in part through Cdkn2a activation, affecting Rspo-mediated phosphorylation of LRP6. Reduced Usp16 increases tissue responsiveness to Wnt signaling, expands the basal mammary compartment, and increases epithelial regeneration. Genetic allele reduction in Ts65Dn mice, mammary epithelial regeneration assays, Wnt reporter (Axin2) analysis, LRP6 phosphorylation assay, siRNA knockdown in human fibroblasts Scientific reports Medium 30504774

Source papers

Stage 0 corpus · 37 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2013 Usp16 contributes to somatic stem-cell defects in Down's syndrome. Nature 105 24025767
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
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 67 26699484
2014 The histone H2A deubiquitinase USP16 interacts with HERC2 and fine-tunes cellular response to DNA damage. The Journal of biological chemistry 62 25305019
2021 USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc. Journal of experimental & clinical cancer research : CR 59 33546726
2023 FGF18 alleviates hepatic ischemia-reperfusion injury via the USP16-mediated KEAP1/Nrf2 signaling pathway in male mice. Nature communications 58 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 47 31135381
2015 Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis. The Journal of cell biology 45 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 37 32129764
2021 Substrate-specific recognition of IKKs mediated by USP16 facilitates autoimmune inflammation. Science advances 36 33523871
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
2010 HDAC6 and Ubp-M BUZ domains recognize specific C-terminal sequences of proteins. Biochemistry 26 21090589
2023 Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36. Nature chemical biology 21 37443395
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
2024 Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Nature structural & molecular biology 20 38918638
2023 Deubiquitinase USP16 induces gouty arthritis via Drp1-dependent mitochondrial fission and NLRP3 inflammasome activation. Arthritis research & therapy 19 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 13 35311644
2021 The deubiquitinase USP16 functions as an oncogenic factor in K-RAS-driven lung tumorigenesis. Oncogene 11 34294846
2024 O-GlcNAcylation stimulates the deubiquitination activity of USP16 and regulates cell cycle progression. The Journal of biological chemistry 10 38462164
2013 Usp16: key controller of stem cells in Down syndrome. The EMBO journal 10 24076652
2018 Usp16 modulates Wnt signaling in primary tissues through Cdkn2a regulation. Scientific reports 9 30504774
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
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 2 41086206
2025 USP16 S-nitrosylation aggravates coronary microembolization-induced myocardial injury via repressing KDM1A-mediated glutathione homeostasis. Nature communications 2 41339351
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
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
2026 USP16 regulates mitochondrial function by deubiquitinating TOM40, a core component of the translocase in the mitochondrial outer membrane. Cell death & disease 0 42236685

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