Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A.

Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40.

Efficient Chemical Synthesis of Multi-Monoubiquitylated and Diubiquitylated Histones by the α-Halogen Ketone-Mediated Strategy.

The chemical synthesis of homogeneously ubiquitylated histones is a powerful approach to decipher histone ubiquitylation-dependent epigenetic regulation. Among the various methods, α-halogen ketone-mediated conjugation chemistry has recently been an attractive strategy to generate single-monoubiquitylated histones for biochemical and structural studies. Herein, we report the use of this strategy to prepare not only dual- and even triple-monoubiquitylated histones but also diubiquitin-modified histones. We were surprised to find that the synthetic efficiencies of multi-monoubiquitylated histones were comparable to those of single-monoubiquitylated ones, suggesting that this strategy is highly tolerant to the number of ubiquitin monomers installed onto histones. The facile generation of a series of single-, dual-, and triple-monoubiquitylated H3 proteins enabled us to evaluate the influence of ubiquitylation patterns on the binding of DNA methyltransferase 1 (DNMT1) to nucleosomes. Our study highlights the potential of site-specific conjugation chemistry to generate chemically defined histones for epigenetic studies.

H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity.

Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.

Fabrication of levofloxacin-loaded porcine acellular dermal matrix hydrogel and functional assessment in urinary tract infection.

Bacterial cystitis, a commonly occurring urinary tract infection (UTI), is renowned for its extensive prevalence and tendency to recur. Despite the extensive utilization of levofloxacin as a conventional therapeutic approach for bacterial cystitis, its effectiveness is impeded by adverse toxic effects, drug resistance concerns, and its influence on the gut microbiota. This study introduces Lev@PADM, a hydrogel with antibacterial properties that demonstrates efficacy in the treatment of bacterial cystitis. Lev@PADM is produced by combining levofloxacin with decellularized porcine acellular dermal matrix hydrogel and exhibits remarkable biocompatibility. Lev@PADM demonstrates excellent stability as a hydrogel at body temperature, enabling direct administration to the site of infection through intravesical injection. This localized delivery route circumvents the systemic circulation of levofloxacin, resulting in a swift and substantial elevation of the antimicrobial agent's concentration specifically at the site of infection. The in vivo experimental findings provide evidence that Lev@PADM effectively prolongs the duration of levofloxacin's action, impedes the retention and invasion of E.coli in the urinary tract, diminishes the infiltration of innate immune cells into infected tissues, and simultaneously preserves the composition of the intestinal microbiota. These results indicate that, in comparison to the exclusive administration of levofloxacin, Lev@PADM offers notable benefits in terms of preserving the integrity of the bladder epithelial barrier and suppressing the recurrence of urinary tract infections.

Preparation of UFM1-Derived Probes through Highly Optimized Total Chemical Synthesis.

Ufmylation is involved in various cellular processes and associated with many human diseases. The understanding of this modification relies on the use of customized UFM1-derived probes for activity-based profiling of its related enzymes. This study presents a highly optimized total chemical synthesis for the generation of diverse UFM1-derived probes including UFM1-PA, Biotin-UFM1-PA and UFM1-AMC, in which a UFM1 C-terminal valine hydrazide was readily prepared by hydrazide-based ligation and used as a versatile handle for the installation of enzyme-sensitive warheads and fluorescent reporters. The resulting probes display high reactivity and selectivity for UFM1-specific enzymes in cell lysates. This strategy facilitates the generation and diversity of the UFM1-derived toolkit that can be employed to profile UFM1-specific enzymes, thereby shining insights into the dynamics of ufmylation.

Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes.

The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe the expedient syntheses of a selection of phosphorylated and ubiquitinated H2AX proteins in a strategy integrating expressed protein hydrazinolysis and auxiliary-mediated protein ligation. These modified H2AX proteins were then used to discover that although H2AXS139 phosphorylation can enhance the binding of the DNA damage repair factor 53BP1 to either an unmodified nucleosome or that bearing a single H2AXK15ub or H4K20me2 modification, it augments 53BP1's binding only weakly to nucleosomes bearing both H2AXK15ub and H4K20me2. To better understand why such a trivalent additive effect is lacking, we solved the cryo-EM structure (3.38 Å) of the complex of 53BP1 with the H2AXK15ub/S139ph_H4K20me2 nucleosome, which showed that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and 53BP1's UDR motif. Our study revealed that there is redundancy in the interplay of multiple histone PTMs, which may be useful for controlling the dynamic distribution of effector proteins onto nucleosomes bearing different histone variants and PTMs in a time-dependent fashion, through specific cellular biochemical events.

Real-world study on HBsAg loss of combination therapy in HBeAg-negative chronic hepatitis B patients.

Combination therapy with pegylated interferon (PEG-IFN) and nucleos(t)ide analogues (NAs) can enhance hepatitis B surface antigen (HBsAg) clearance. However, the specific treatment strategy and the patients who would benefit the most are unclear. Therefore, we assessed the HBsAg loss rate of add-on PEG-IFN and explored the factors associated with HBsAg loss in chronic hepatitis B (CHB) patients. This was a real-world cohort study of adults with CHB. Hepatitis B e antigen (HBeAg)-negative NAs-treated patients with baseline HBsAg ≤1500 IU/ml and HBV DNA < the lower limit of detection, or 100 IU/ml, received 48 weeks of add-on PEG-IFN. The primary outcome of the study was the rate of HBsAg loss at 48 weeks of combination treatment. Using multivariable logistic regression analysis, we determined factors associated with HBsAg loss. HBsAg loss in 2579 patients (mean age: 41.2 years; 80.9% male) was 36.7% (947 patients) at 48 weeks. HBsAg loss was highest in patients from south-central and southwestern China (40.0%). Factors independently associated with HBsAg loss included: increasing age (odds ratio = 0.961); being male (0.543); baseline HBsAg level (0.216); HBsAg decrease at 12 weeks (between 0.5 and 1.0 log10 IU/ml [2.405] and >1.0 log10 IU/ml [7.370]); alanine aminotransferase (ALT) increase at 12 weeks (1.365); haemoglobin (HGB) decrease at 12 weeks (1.558). There was no difference in the primary outcomes associated with the combination regimen. In conclusion, HBsAg loss by combination therapy was higher in patients from southern China than those from the north. An increased chance of HBsAg loss was associated with baseline characteristics and dynamic changes in clinical indicators.

Chemical methods for studying the crosstalk between histone H2B ubiquitylation and H3 methylation.

The reversible and dynamic post-translational modifications (PTMs) of histones in eukaryotic chromatin are intimately connected to cell development and gene function, and abnormal regulation of PTMs can result in cancer and neurodegenerative diseases. Specific combinations of these modifications are mediated by a series of chromatin proteins that write, erase, and read the "histone codes," but mechanistic studies of the precise biochemical and structural relationships between different sets of modifications and their effects on chromatin function constitute a unique challenge to canonical biochemical approaches. In the past decade, the development and application of chemical methods for investigating histone PTM crosstalks has received considerable attention in the field of chemical biology. In this review, taking the functional crosstalk between H2B ubiquitylation at Lys120 (H2BK120ub) and H3 methylation at Lys79 (H3K79me) as a typical example, we survey recent developments of different chemical methods, in particular, protein synthetic chemistry and protein-based chemical probes, for studying the mechanism of the functional crosstalks of histone PTMs.

Multistimuli Responsive Solid-State Emission of a Zinc(II) Complex with Multicolour Switching.

The development of smart luminescent materials, especially those stimulus-responsive fluorescent materials that can switch between different colors repeatedly under external stimulation based on a single molecule, is of great significance but a challenge. In this work, a novel zinc(II)-Schiff base complex (ZnL2) was obtained and characterized. Upon exposure to the HCl and NH3 vapors, it displayed remarkable tricolor acidochromic behavior with high contrast and rapid response under the ambient light as well as UV light (365 nm). The XPS analyses of ZnL2 crystals before and after HCl/NH3 fuming show that the acidochromism originates principally from the adsorption of vapor and the gas-solid reaction equilibrium on the crystal surface. The reddish-brown color of the HCl-fumigated ZnL2 crystals could be attributed to the generation of HL at the surface of ZnL2, and red-shifted emission could be ascribed to the self-absorption effect. The single crystal X-ray diffraction data indicate that these processes cause slight changes in the molecular conformation and crystal packing. ZnL2 shows reversible mechanochromic luminescence behavior between yellow and orange emission during the grinding-fuming/heating cycles due to the modulation between amorphous and crystalline states. Moreover, ZnL2 was successfully made into test paper for the rapid detection of HCl/NH3 vapors and mechanical stimuli.

A Multistimuli Responsive Crystalline Cd(II)-Viologen Coordination Polymer with Single-Crystal-Single-Crystal Transformation.

It is necessary to develop stable and fast multistimuli responsive materials due to the growing demand in our daily life. In this work, a new viologen-based Cd-complex (1) exhibits multiple thermochromic and photochromic behaviors through 10 states with 7 colors. For example, it responds to both Cu Kα/Mo Kα X-ray sources and UV dual light quickly with a color change from colorless to dark blue (1X) (Cu Kα/Mo Kα X-ray sources) and cyan (1-UV) (UV light), respectively. Interestingly, it exhibits a three-step coloration phenomenon when heated, which is unprecedented in viologen compounds. Crystal 1 undergoes a color change to pink, blue, and brown under 130, 180, and 240 °C, respectively. In addition, upon fumigation, both 1P and 1Q undergo a decoloration process to colorless (1K) and yellow (1T), respectively. Four more states (1P, 1K, 1T, and 1O) obtained via dehydration-hydration treatment are all photochromic. More importantly, via single-crystal-single-crystal transformation (SC-SC), the photochromic and thermochromic behaviors of 1 were investigated from the molecular level, which is also rather rare for thermochromic species. The detailed electron donor and the pathways for electron transfer were clearly given according to the results of crystal structure. The colorful states upon external stimuli may be attributed to the multiple pathways for electron transfer.

Multistimulus Response of Two Tautomeric Zn(II) Complexes and Their White-Light Emission Based on Different Mechanisms.

A triphenylamine (TPA)-based 2H-quinazoline Zn(II) complex (Q-TPA-Zn) exhibiting dual fluorescence and phosphorescence emission in the solid state was designed and prepared. It possesses mechanochromic luminescence and thermochromic luminescence properties. In the solid state, the white afterglow luminescence could be observed at 77 K (CIExy: 0.27, 0.33) while cyan luminescence could be observed at 297 K. After thermolysis at 300 °C, Q-TPA-Zn could be transformed into Schiff base complex S-TPA-Zn with white fluorescence in the powder state (CIExy: 0.32, 0.38), in methanol (CIExy: 0.32, 0.39), and in dimethylformamide (CIExy: 0.26, 0.32) at room temperature. This arises from dual emission of normal* emission and tautomeric* emission induced by excited-state intramolecular proton transfer (ESIPT) from the benzimidazole NH group to the Schiff base N atom. Q-TPA-Zn could also be transformed into its isomeric form, S-TPA-Zn, through photochemical ring-opening reaction upon irradiation under 365 nm in the solution, exhibiting high-contrast photochromic luminescence. Interestingly, S-TPA-Zn could further be transformed into its zwitterionic isomer after continuous irradiation. The same ring-opening reaction could also take place for the orgainc compound Q-TPA via heating or 365 nm irradiation. The ring-opening reaction mechanism and ESIPT emission were interpreted via theoretical calculation.

The Bre1/Rad6 machinery: writing the central histone ubiquitin mark on H2B and beyond.

Mono-ubiquitination on H2B (H2Bub1) is an evolutionarily conserved histone post-translational modification implicated in various important physiological processes including DNA replication, transcription activation, and DNA damage repair. The Bre1/Rad6 ubiquitination machinery is currently considered to be the sole writer of H2Bub1, but the mechanistic basis by which it operates is unclear. Recently, the RING-type E3 ligase Bre1 was proposed to associate with the E2 enzyme Rad6 through a novel interaction between Bre1 RBD (Rad6 binding domain) and Rad6; and the RING domain of Bre1 that is responsible for the nucleosomal acidic patch binding also interacts with Rad6 to stimulate its catalytic activity. Recent discoveries have yielded evidence for the phenomenon of liquid-liquid phase separation in the context of H2Bub1, and its regulation by other histone post-translational modifications. This review summarizes current knowledge about Bre1/Rad6-mediated H2B ubiquitination, including the physiological functions and the molecular basis for writing and regulation of this central histone ubiquitin mark. Possible models for the Bre1/Rad6 machinery bound to nucleosomes bearing different modifications in the writing step are also disclosed.

Low Vitamin D Status Is Associated with Epithelial-Mesenchymal Transition in Patients with Chronic Obstructive Pulmonary Disease.

Vitamin D deficiency is correlated with the increased morbidity of chronic obstructive pulmonary disease (COPD). However, the mechanisms underlying these effects have largely remained elusive. This study analyzed the correlations among COPD, vitamin D concentration, and epithelial-mesenchymal transition (EMT). Ninety-five patients with newly diagnosed COPD and 190 age- and sex-matched healthy subjects were recruited for this research. Serum 25(OH)D levels were detected, and pulmonary EMT biomarkers and TGF-ß/Smad signaling were evaluated. Serum 25(OH)D level was remarkably decreased in COPD patients compared with that in control subjects. Furthermore, serum 25(OH)D concentration gradually decreased in COPD patients ranging from grade 1-2 to 4. However, reduced expression of the epithelial biomarker E-cadherin and increased expression of the mesenchymal biomarkers vimentin and α-SMA were found in COPD patients. Mechanistic analysis showed that pulmonary nuclear vitamin D receptor (VDR) was decreased in patients with COPD. In contrast, TGF-ß/Smad signaling was obviously activated in COPD patients. Furthermore, the level of serum TGF-ß in COPD patients increased in parallel with COPD severity. Serum 25(OH)D concentration was inversely associated with TGF-ß levels in COPD patients. In vitro experiments showed that active vitamin D3 inhibits TGF-ß-induced Smad2/3 phosphorylation in MRC-5 cells. Furthermore, vitamin D concentration was inversely correlated with TGF-ß/Smad signaling and EMT in COPD patients, suggesting EMT as a vital mediator of COPD development in patients with low vitamin D concentrations.

Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins.

Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA. The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64-179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.

Clinical application and effect of dexmedetomidine in combination with continuous positive airway pressure on one-lung ventilation in lung surgery of elder patients.

In this study, 126 elder patients who underwent thoracic surgery under general anesthesia were divided into three groups randomly, i.e. dexmedetomidine group, positive ventilation group and combination group. All patients received varying strategies in addition to the one-lung ventilation, and changes in oxidative stress and indicators of inflammation at different time points were observed. In comparison to the dexmedetomidine group and the positive ventilation group, patients in the combination group at T2-3 had lower levels of malonaldehyde, cortisol, C-reaction protein, interleukin-6 (IL-6) and tumor necrosis factor α in serum (p<0.05); one day after surgery, the incidence of complications in lungs of patients in the combination group was significantly lower than those in the dexmedetomidine group and the positive ventilation group (p<0.05). Dexmedetomidine in combination with continuous positive airway pressure can alleviate the oxidative stress and inflammation of lung tissues in one-lung ventilation during the thoracic surgery of elder patients, thus, reducing the incidence of postoperative complications.

[General situation and comprehensive utilization of medicinal fungi resources in Heilongjiang province].

In order to develop and utilize the macrofungi in Heilongjiang province, numerous literatures have been investigated to make a comprehensive analysis of the number of known species of fungi in Heilongjiang province. There exists a total of 546 species of macrofungus in Heilongjiang province belonging to 53 families and 13 orders of 6 classes and 2 subdivisions. And its application value is classified, summarized and reviewed. Three hundred and twenty kinds of edible fungi, 214 species of fungi with medicinal value, medicinal value in the anti-cancer effects of 167 species of fungi, 141 wood rot fungi, 141 species of ectomycorrhizal fungi, 88 poisonous species, 67 macrofungus which are not clarified whether could be edible or toxic. It shows a broad prospects for development and utilization of macrofungus resources in Heilongjiang province.

Predict esophageal varices via routine trans-abdominal ultrasound: A design of classification analysis model.

BACKGROUND AND AIMS: Upper gastrointestinal endoscopy remains the gold standard for diagnosis of esophageal varices. Trans-abdominal ultrasound, as a noninvasive routine examination for the follow-up of cirrhosis patient, is safe, cheap, easy to perform, and plays an important role. In this study, we attempt to design a practical classification analysis model to predict esophageal varices via ultrasound. METHODS: Compared with endoscopy, the ultrasound qualitative signs (lower esophageal Doppler signals, left gastric vein hepatofugal flow, and paraumbilical vein recanalization) and quantitative parameters (spleen diameter, spleen vein diameter, portal vein diameter, and portal vein velocity) have been evaluated in 286 cirrhosis patients. RESULTS: The classification analysis model is designed as that: the patients are defined with esophageal varices high risk, who with any ultrasound qualitative signs or who with spleen diameter greater than 162 mm without qualitative parameters. The sensitivity for detecting esophageal varices is 97.5% and the specificity is 82.6%, while the positive predictive value is 96.7%, negative predictive value is 83.4%, and the omission diagnostic rate is 2.5%. CONCLUSIONS: This classification analysis model design includes ultrasound qualitative signs and spleen diameter, which can be detected easily via routine ultrasound without other auxiliary. The classification analysis model is useful in detecting esophageal varices, which may be a supplement for predicting of esophageal varices, and reducing the frequency of endoscopy in the follow-up of cirrhosis patients.

Stool vs. Serum Hepatitis B Virus DNA in Patients with Chronic Hepatitis B.

BACKGROUND Serum hepatitis B virus (HBV) DNA and hepatitis B e antigen (HBeAg) liver function in patients with chronic hepatitis B (CHB) are significantly associated. A comparison of clinical significance of fecal HBV DNA and serum HBV DNA has not yet been reported. MATERIAL AND METHODS Stool and serum samples were collected from 66 patients with CHB. Fecal HBV DNA, serum HBV DNA, and intestinal microbiota DNA were detected by real-time quantitative fluorescence polymerase chain reaction (PCR). Liver function and HBeAg were analyzed. RESULTS The stool and serum HBV DNA were positively correlated (r=0.57, P=0.001). Fecal HBV DNA was higher in the HBeAg-positive group than in the HBeAg-negative group (P=0.02). Fecal HBV DNA was negatively correlated with alkaline phosphatase (ALP) (r=-0.41, P=0.001) and TBIL (r=-0.29, P=0.02), and was positively correlated with Enterococcus (r=0.38, P=0.002). Serum HBV DNA was negatively correlated with alanine aminotransferase (ALT) (r=-0.30,P=0.02), aminotransferase (AST) (r=-0.26, P=0.049), and Lactobacillus (r=-0.31, P=0.01). CONCLUSIONS These observations suggest that fecal HBV DNA and serum HBV DNA in patients with CHB have different effects. Fecal HBV DNA might be associated with changes in Enterococcus concentrations, but serum HBV DNA is not.

New semi-synthesis of ubiquitin C-terminal conjugate with 7-amino-4-methylcoumarin.

The ligation of peptide hydrazides at a Gly site carrying a removal auxiliary was found to be an efficient process. This technology was successfully used for the synthesis of ubiquitin C-terminal conjugates. Recombinant Ub(1-75)-NHNH2 was prepared through the hydrozinolysis of the Ub(1-75)-intein fusion protein. It was ligated with a glycine derivative modified with an acid-sensitive thiol auxiliary. The final acid treatment produced the desired bioactive ubiquitin conjugates in practical quantities. Thus, the method described here extends the protocols of expressed protein ligation.

Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16.

Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16-H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A-H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16.