Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components.

The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) and analyzed chromatome reorganizations during major phases of pluripotency. This enabled us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the ground, formative and primed pluripotency states, and to pinpoint the specific binding and rearrangement of regulatory components. These comprehensive datasets combined with extensive analyses identified phase-specific factors like QSER1 and JADE1/2/3 and provide a detailed foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency. The technical advances reported here can be readily applied to other models in development and disease.

Probing protein ubiquitination in live cells.

The reversible attachment of ubiquitin governs the interaction, activity and degradation of proteins whereby the type and target of this conjugation determine the biological response. The investigation of this complex and multi-faceted protein ubiquitination mostly relies on painstaking biochemical analyses. Here, we employ recombinant binding domains to probe the ubiquitination of proteins in living cells. We immobilize GFP-fused proteins of interest at a distinct cellular structure and detect their ubiquitination state with red fluorescent ubiquitin binders. With this ubiquitin fluorescent three-hybrid (ubiF3H) assay we identified HP1ß as a novel ubiquitination target of UHRF1. The use of linkage specific ubiquitin binding domains enabled the discrimination of K48 and K63 linked protein ubiquitination. To enhance signal-to-noise ratio, we implemented fluorescence complementation (ubiF3Hc) with split YFP. Using in addition a cell cycle marker we could show that HP1ß is mostly ubiquitinated by UHRF1 during S phase and deubiquitinated by the protease USP7. With this complementation assay we could also directly detect the ubiquitination of the tumor suppressor p53 and monitor its inhibition by the anti-cancer drug Nutlin-3. Altogether, we demonstrate the utility of the ubiF3H assay to probe the ubiquitination of specific proteins and to screen for ligases, proteases and small molecules controlling this posttranslational modification.

Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.

Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.

Phosphorylation of the HP1ß hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency.

Heterochromatin binding protein HP1ß plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1ß-/- embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1ß is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1ß-/- and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1-/- cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.

Chemical characteristics, oxidative potential, and sources of PM2.5 in wintertime in Lahore and Peshawar, Pakistan.

The chemical characteristics, oxidative potential, and sources of PM2.5 were analyzed at the urban sites of Lahore and Peshawar, Pakistan in February 2019. Carbonaceous species, water soluble ions, and metal elements were measured to investigate the chemical composition and sources of PM2.5. The dithiothreitol (DTT) consumption rate was measured to evaluate the oxidative potential of PM2.5. Both cities showed a high exposure risk of PM2.5 regarding its oxidative potential (DTTv). Carbonaceous and some of the elemental species of PM2.5 correlated well with DTTv in both Lahore and Peshawar. Besides, the DTTv of PM2.5 in Lahore showed significant positive correlation with most of the measured water soluble ions, however, ions were DTT-inactive in Peshawar. Due to the higher proportions of carbonaceous species and metal elements, Peshawar showed higher mass-normalized DTT activity of PM2.5 compared to Lahore although the average PM2.5 concentration in Peshawar was lower. The high concentrations of toxic metals also posed serious non-carcinogenic and carcinogenic risks to the residents of both cities. Principle component analysis coupled with multiple linear regression was applied to investigate different source contributions to PM2.5 and its oxidative potential. Mixed sources of traffic and road dust resuspension and coal combustion, direct vehicle emission, and biomass burning and formation of secondary aerosol were identified as the major sources of PM2.5 in both cities. The findings of this study provide important data for evaluation of the potential health risks of PM2.5 and for formulation of efficient control strategies in major cities of Pakistan.

DNMT1 mutations found in HSANIE patients affect interaction with UHRF1 and neuronal differentiation.

DNMT1 is recruited to substrate sites by PCNA and UHRF1 to maintain DNA methylation after replication. The cell cycle dependent recruitment of DNMT1 is mediated by the PCNA-binding domain (PBD) and the targeting sequence (TS) within the N-terminal regulatory domain. The TS domain was found to be mutated in patients suffering from hereditary sensory and autonomic neuropathies with dementia and hearing loss (HSANIE) and autosomal dominant cerebellar ataxia deafness and narcolepsy (ADCA-DN) and is associated with global hypomethylation and site specific hypermethylation. With functional complementation assays in mouse embryonic stem cells, we showed that DNMT1 mutations P496Y and Y500C identified in HSANIE patients not only impair DNMT1 heterochromatin association, but also UHRF1 interaction resulting in hypomethylation. Similar DNA methylation defects were observed when DNMT1 interacting domains in UHRF1, the UBL and the SRA domain, were deleted. With cell-based assays, we could show that HSANIE associated mutations perturb DNMT1 heterochromatin association and catalytic complex formation at methylation sites and decrease protein stability in late S and G2 phase. To investigate the neuronal phenotype of HSANIE mutations, we performed DNMT1 rescue assays and could show that cells expressing mutated DNMT1 were prone to apoptosis and failed to differentiate into neuronal lineage. Our results provide insights into the molecular basis of DNMT1 dysfunction in HSANIE patients and emphasize the importance of the TS domain in the regulation of DNA methylation in pluripotent and differentiating cells.

A modular open platform for systematic functional studies under physiological conditions.

Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1, Dnmt3a, Dnmt3b, Tet1, Tet2, Tet3 and Uhrf1, we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions.

Gallic acid induces apoptosis in human cervical epithelial cells containing human papillomavirus type 16 episomes.

The high-risk human papillomaviruses (HPV) that infect the anogenital tract are strongly associated with the development of cervical carcinoma, which is the second most common cancer in women worldwide. Therapeutic drugs specifically targeting HPV are not available. Polyphenolic compounds have gained considerable attention because of their cytotoxic effects against a variety of cancers and certain viruses. In this study, we examined the effects of several polyphenols on cellular proliferation and death of the human cervical cancer cells and human cervical epithelial cells containing stable HPV type 16 episomes (HPVep). Our results show that three polyphenols inhibited proliferation of HeLa cells dose-dependently. Furthermore, one of the examined polyphenols, gallic acid (GA), also inhibited the proliferation of HPVep cells and exhibited significant specificity towards HPV-positive cells. The anti-proliferative effect of GA on HPVep and HeLa cells was associated with apoptosis and upregulation of p53. These results suggest that GA can be a potential candidate for the development of anti-HPV agents.

Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling.

DNA methyltransferase 1 (Dnmt1) reestablishes methylation of hemimethylated CpG sites generated during DNA replication in mammalian cells. Two subdomains, the proliferating cell nuclear antigen (PCNA)-binding domain (PBD) and the targeting sequence (TS) domain, target Dnmt1 to the replication sites in S phase. We aimed to dissect the details of the cell cycle-dependent coordinated activity of both domains. To that end, we combined super-resolution 3D-structured illumination microscopy and fluorescence recovery after photobleaching (FRAP) experiments of GFP-Dnmt1 wild type and mutant constructs in somatic mouse cells. To interpret the differences in FRAP kinetics, we refined existing data analysis and modeling approaches to (i) account for the heterogeneous and variable distribution of Dnmt1-binding sites in different cell cycle stages; (ii) allow diffusion-coupled dynamics; (iii) accommodate multiple binding classes. We find that transient PBD-dependent interaction directly at replication sites is the predominant specific interaction in early S phase (residence time Tres ≤ 10 s). In late S phase, this binding class is taken over by a substantially stronger (Tres ∼22 s) TS domain-dependent interaction at PCNA-enriched replication sites and at nearby pericentromeric heterochromatin subregions. We propose a two-loading-platform-model of additional PCNA-independent loading at postreplicative, heterochromatic Dnmt1 target sites to ensure faithful maintenance of densely methylated genomic regions.

Heterochromatin organization and phase separation.

The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.

Effect of chemical regulation combined with mechanical filtration on deep dewatering and consolidation characteristics of sludge.

To reveal the mechanism underlying deep dewatering of municipal sludge, this paper investigated the sludge characteristics from the perspective of soil mechanics, and analyzed the sludge physical and mechanical properties, stress as well as dewatering behavior during the dewatering process. Before and after cationic polyacrylamide (CPAM) and chitosan (HACC) conditioning, the pressure filtration dewatering time of treated sludge was shorter than that of raw sludge, and the water removal rate was greater than 70% at the 6 MPa pressure. However, with the increase in filter pressing time, the filtration resistance coefficient of sludge increased, and the water pressure in sludge pores rose up, and a longer time was needed for dissipation at the larger pressure, resulting in the slowdown of sludge consolidation. In addition, based on the three-stage Terzaghi Voigt model, when the pressure rose from 2 to 6 MPa, the time from filtration stage to compression stage of raw sludge was shortened, and the second stage played the most important role in the dewatering process. Compared with the raw sludge, the sludge filtration stage was shortened after CPAM or HACC conditioning, and the main dewatering mechanism changed from the second compression stage to the first compression stage, which means the bound water in sludge flocs was transformed into free water. This was also the reason why the dewatering, compression and consolidation rate of the conditioned sludge was faster than that of the raw sludge.

Pollution characteristics and light-driven evolution of environmentally persistent free radicals in PM2.5 in two typical northern cities of China.

Environmentally persistent free radicals (EPFRs) in PM2.5 can pose significant health risks by generating reactive oxygen species (ROS). In this study, Beijing and Yuncheng were chosen as two representative northern cities of China that mainly relied on natural gas and coal respectively as the energy source for domestic heating in winter. The pollution characteristics and exposure risks of EPFRs in PM2.5 around the heating season of 2020 were investigated and compared between the two cities. Through laboratory simulation experiments, the decay kinetics and secondary formation of EPFRs in PM2.5 collected in both cities were also studied. EPFRs in PM2.5 collected in Yuncheng in the heating period showed longer lifetime and lower reactivity, suggesting that EPFRs originated from coal combustion were more stable in the atmosphere. However, the generation rate of hydroxyl radical (·OH) by the newly formed EPFRs in PM2.5 in Beijing under ambient conditions was 4.4 times of that in Yuncheng, suggesting higher oxidative potential of EPFRs from the atmospheric secondary processes. Accordingly, the control strategies of EPFRs and their health risks were raised for the two cities, which would also have direct implication for the control of EPFRs in other areas of similar atmospheric emission and reaction patterns.

The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5.

UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, the mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for the termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.

Synergistic effects on d-band center via coordination sites of M-N3P1 (M = Co and Ni) in dual single atoms that enhances photocatalytic dechlorination from tetrachlorobispheonl A.

Transition metal single atoms (TM-SAs) coordinated with highly electronegative N atoms often suffer from low activity and poor stability, which limiting their application in catalysis. To solve it, a PH3-assisted annealing strategy is designed to synthesize atomically dispersed TM-SAs (CCoNiP), which is stemmed from a pyrolysis approach of pre-designed CoNi layered double hydroxide (LHD) as a soft-template, and further coordinated with P atoms for adjusting the coordination environment. Characterization results show that the atomically dispersed Co and Ni atoms anchor on the carbon nitride substrate with Co/Ni-N3P1 coordination sites. Combined with density functional theory calculations, it is confirmed that multiple coordination sites of Co/Ni-N and Co/Ni-P can modulate d-band center position which increases the catalytic activity of TM-SAs. The formed multiple midgap levels can extend optical absorption ranges. Meanwhile, P-introduction can change the coordination environment, suppress the conversion trend of SAs to high valence state and improve electron separation. All the above characteristics can improve effective degradation from Tetrachlorobisphenol A (TCBPA) under visible light irradiation, achieving 100% removal and 44.1% dechlorination rate.

Oxidative potential associated with water-soluble components of PM2.5 in Beijing: The important role of anthropogenic organic aerosols.

Oxidative stress is the mainstream toxicological mechanism for the adverse health outcomes of ambient aerosols. However, our understanding of the crucial redox-active species affecting the oxidative potential of water-soluble aerosols (OPWS) remains limited. In this study, the OPWS of PM2.5 in Beijing was measured using dithiothreitol (DTT) assay, including DTT consumption rate and ·OH formation rate. OPWS was more closely related to water-soluble organic compounds (WSOC) rather than transition metals. Laboratory simulations were conducted to investigate the effects of individual target species in the context of complex metal-organic interactions. The results showed that reducing WSOC can effectively decrease OPWS, while reducing Cu2+ increased OPWS. Parallel factor analysis demonstrated that OPWS was the most significantly correlated with the highly oxidized humic-like or quinone-like substances. Multiple linear regression showed that aromatic secondary organic carbon (SOC) (34.4%), other primary combustion sources of WSOC (20.0%), primary biomass burning WSOC (19.8%), transition metal ions (12.9%) and biomass burning SOC (12.8%) made significant contributions to DTTV. In addition to the anthropogenic sources of WSOC, the aged biogenic SOC also contributed to OHV, particularly in summer. Reducing anthropogenic WSOC was the key to the effective control of OPWS of PM2.5 in Beijing.

Enhanced Heterogeneous Fenton-like Process for Sulfamethazine Removal via Dual-Reaction-Center Fe-Mo/rGO Catalyst.

A heterogeneous Fenton-like catalyst with single redox site has a rate-limiting step in oxidant activation, which limited its application in wastewater purification. To overcome this, a bimetallic doping strategy was designed to prepare a heterogeneous Fenton-like catalyst (Fe-Mo/rGO) with a double-reaction center. Combined with electrochemical impedance spectroscopy and density functional theory calculation, it was confirmed that the formation of an electron-rich Mo center and an electron-deficient Fe center through the constructed Fe-O-Mo and Mo-S-C bonding bridges induced a higher electron transfer capability in the Fe-Mo/rGO catalyst. The designed Fe-Mo/rGO catalyst exhibited excellent sulfamethazine (SMT) degradation efficiency in a broad pH range (4.8-8.4). The catalytic performance was hardly affected by inorganic anions (Cl-, SO42- and HCO3-) in the complicated and variable water environment. Compared to Fe/rGO and Mo/rGO catalysts, the SMT degradation efficiency increased by about 14.6 and 1.6 times in heterogeneous Fenton-like reaction over Fe-Mo/rGO catalyst. The electron spin resonance and radical scavenger experiments proved that ·O2-/HO2· and 1O2 dominate the SMT removal in the Fe-Mo/rGO/H2O2 system. Fe and Mo, as active centers co-supported on rGO, significantly enhanced the electron transfer between catalyst, oxidant, and pollutants, which accelerated the reactive oxygen species generation and effectively improved the SMT degradation. Our findings offer a novel perspective to enhance the performance of heterogeneous Fenton-like catalysts by accelerating the electron transfer rate in the degradation of organic pollutants.

Gas-PM2.5 partitioning, health risks, and sources of atmospheric PAHs in a northern China city: Impact of domestic heating.

The diurnal variation, gas-particle partitioning, health risks, and sources of polycyclic aromatic hydrocarbons (PAHs) were investigated in a northern basin city of China in winter, 2020. The mean concentrations of particulate and gaseous PAHs were 87.90 ng m-3 and 69.65 ng m-3, respectively, and their concentrations were considerably enhanced during the domestic heating period. The relationship between the gas-particle partitioning coefficient of PAHs (KP) and subcooled liquid vapor pressure of PAHs (PL0) indicated organic absorption as the mechanism for this partitioning. However, the dual sorption model confirmed adsorption onto elemental carbon (EC). The health risks indicated by several equivalent parameters showed an important health effect of PAHs, especially of particulate PAHs bound onto PM2.5 during the heating period. Environmentally persistent free radicals (EPFRs) were also studied as an auxiliary parameter to evaluate the health impact of PAHs. According to the diagnostic ratios of PAHs and PMF model results, petroleum volatilization and coal combustion were the dominant sources of particulate PAHs during the non-heating and heating periods, respectively. The source apportionment results can help efficiently control PAHs and their health risks.

MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid-liquid phase separation and restricted by DNA methylation.

Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid-liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations in vitro and in vivo to explore the mechanism of MeCP2-driven heterochromatin organization and dynamics. We show that MeCP2 alone forms liquid-like spherical droplets via multivalent electrostatic interactions and with isotropic mobility. Crowded environments and DNA promote MeCP2 LLPS and slow down MeCP2 mobility. DNA methylation, however, restricts the growth of heterochromatin compartments correlating with immobilization of MeCP2. Furthermore, MeCP2 self-interaction is required for LLPS and is disrupted by Rett syndrome mutations. In summary, we are able to model the heterochromatin compartmentalization as well as MeCP2 concentration and heterogeneous motion in the minimal in vitro system.

Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1.

In mammals Dnmt1 is the DNA methyltransferase chiefly responsible for maintaining genomic methylation patterns through DNA replication cycles, but how its maintenance activity is controlled is still not well understood. Interestingly, Uhrf1, a crucial cofactor for maintenance of DNA methylation by Dnmt1, is endowed with E3 ubiquitin ligase activity. Here, we show that both Dnmt1 and Uhrf1 coprecipitate with ubiquitin specific peptidase 7 (Usp7), a de-ubiquitinating enzyme. Overexpression of Uhrf1 and Usp7 resulted in opposite changes in the ubiquitination status and stability of Dnmt1. Our findings suggest that, by balancing Dnmt1 ubiquitination, Usp7 and Uhrf1 fine tune Dnmt1 stability.

HP1ß carries an acidic linker domain and requires H3K9me3 for phase separation.

Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1ß. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1ß which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1ß mutants defective in H3K9me3 binding were less efficient in phase separationin vitro and failed to accumulate at heterochromatin in vivo. We propose that multivalent interactions of HP1ß with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments in vivo.