Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.

Oxidative stress is a central part of innate immune-induced neurodegeneration. However, the transcriptomic landscape of central nervous system (CNS) innate immune cells contributing to oxidative stress is unknown, and therapies to target their neurotoxic functions are not widely available. Here, we provide the oxidative stress innate immune cell atlas in neuroinflammatory disease and report the discovery of new druggable pathways. Transcriptional profiling of oxidative stress-producing CNS innate immune cells identified a core oxidative stress gene signature coupled to coagulation and glutathione-pathway genes shared between a microglia cluster and infiltrating macrophages. Tox-seq followed by a microglia high-throughput screen and oxidative stress gene network analysis identified the glutathione-regulating compound acivicin, with potent therapeutic effects that decrease oxidative stress and axonal damage in chronic and relapsing multiple sclerosis models. Thus, oxidative stress transcriptomics identified neurotoxic CNS innate immune populations and may enable discovery of selective neuroprotective strategies.

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.

A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development.

Directed differentiation of human embryonic stem cells (ESCs) into cardiovascular cells provides a model for studying molecular mechanisms of human cardiovascular development. Although it is known that chromatin modification patterns in ESCs differ markedly from those in lineage-committed progenitors and differentiated cells, the temporal dynamics of chromatin alterations during differentiation along a defined lineage have not been studied. We show that differentiation of human ESCs into cardiovascular cells is accompanied by programmed temporal alterations in chromatin structure that distinguish key regulators of cardiovascular development from other genes. We used this temporal chromatin signature to identify regulators of cardiac development, including the homeobox gene MEIS2. Using the zebrafish model, we demonstrate that MEIS2 is critical for proper heart tube formation and subsequent cardiac looping. Temporal chromatin signatures should be broadly applicable to other models of stem cell differentiation to identify regulators and provide key insights into major developmental decisions.

Asynchronous carbon sink saturation in African and Amazonian tropical forests.

Structurally intact tropical forests sequestered about half of the global terrestrial carbon uptake over the 1990s and early 2000s, removing about 15 per cent of anthropogenic carbon dioxide emissions1-3. Climate-driven vegetation models typically predict that this tropical forest 'carbon sink' will continue for decades4,5. Here we assess trends in the carbon sink using 244 structurally intact African tropical forests spanning 11 countries, compare them with 321 published plots from Amazonia and investigate the underlying drivers of the trends. The carbon sink in live aboveground biomass in intact African tropical forests has been stable for the three decades to 2015, at 0.66 tonnes of carbon per hectare per year (95 per cent confidence interval 0.53-0.79), in contrast to the long-term decline in Amazonian forests6. Therefore the carbon sink responses of Earth's two largest expanses of tropical forest have diverged. The difference is largely driven by carbon losses from tree mortality, with no detectable multi-decadal trend in Africa and a long-term increase in Amazonia. Both continents show increasing tree growth, consistent with the expected net effect of rising atmospheric carbon dioxide and air temperature7-9. Despite the past stability of the African carbon sink, our most intensively monitored plots suggest a post-2010 increase in carbon losses, delayed compared to Amazonia, indicating asynchronous carbon sink saturation on the two continents. A statistical model including carbon dioxide, temperature, drought and forest dynamics accounts for the observed trends and indicates a long-term future decline in the African sink, whereas the Amazonian sink continues to weaken rapidly. Overall, the uptake of carbon into Earth's intact tropical forests peaked in the 1990s. Given that the global terrestrial carbon sink is increasing in size, independent observations indicating greater recent carbon uptake into the Northern Hemisphere landmass10 reinforce our conclusion that the intact tropical forest carbon sink has already peaked. This saturation and ongoing decline of the tropical forest carbon sink has consequences for policies intended to stabilize Earth's climate.

The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes.

BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells, and it was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BRG1-associated factors (BAF), an SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromodomain and extraterminal (ET) domain, and this isoform was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using chromatin immunoprecipitation sequencing (ChIP-seq) combined with assay for transposase-accessible chromatin coupled to high-throughput sequencing (ATAC-seq) data, we found that the latent HIV-1 promoter phenotypically resembles endogenous long terminal repeat (LTR) sequences, pointing to a select role of BRD4S-BRG1 complexes in genomic silencing of invasive retroelements.

Biochar effects on NTFP-enriched secondary forest growth and soil properties in Amazonian Ecuador.

Deforestation in the Amazon has resulted in large areas of depleted soils on abandoned pastures and agricultural sites that present a restoration challenge central to protecting biodiversity and ecosystem function in the region. Biochar - charcoal made from waste materials - can improve soil physical, chemical, and biological properties, but the few tropical field trials to date do not give consistent results regarding tree growth. This study presents three years of soil performance and tree growth of a secondary forest shading nontimber forest product (NTFP) plantations of Ocotea quixos (Lauraceae), Myroxylon balsamum (Fabaceae), and their mixture. Open kiln and traditional mound biochars were added at 10 t ha-1 at two sites with contrasting soil types. Biochar additions resulted in pronounced effects on soil properties that varied over time and with depth in the soil profile. Biochar additions generally increased soil organic matter, electrical conductivity, and plant nutrients (in particular K, Ca, and N), but there were interactive effects of NTFP treatments, and stronger responses on the poorer soil type. Biochar amendments resulted in increased tree growth, with a 29 ± 12% increase in aboveground biomass (AGB) on plots amended with kiln biochar and a 23 ± 9% increase in plots with mound biochar compared to controls. Tree species also varied in growth responses to biochar additions, with the largest increases observed in Jaccaranda copaia and Piptocoma discolor. Significant interactions between biochar and NTFP treatments were also seen for tree growth responses, such as Cecropia spp., which only showed increased biomass on mound biochar plots planted with Ocotea quixos. Overall, our results demonstrate a stronger effect of biochar in less favorable soil conditions, and an overriding effect of the legume NTFP in richer soils, and suggest that additions of biochar and legumes are important options to increase productivity and ecological resilience in tropical forest restoration.

The effect of spanning external fixation on entrapped structures in tibial pilon fractures.

PURPOSE: Pilon fractures are often complex injuries involving severe soft tissue injury. Studies have shown pilon fractures may entrap soft tissue structures between fracture fragments. Staged fixation of pilon fractures with spanning external fixation (SEF) is important for soft tissue rest and plays an important role in the management of these injuries. While SEF has been shown to promote soft tissue rest prior to definitive fixation, no studies have shown the effect SEF has on entrapped structures (ES). The purpose of this study was to evaluate how SEF effects ES in pilon fractures. METHODS: A retrospective review of 212 pilon fractures treated at our institution between 2010 and 2022 was performed. Patients with a CT scan pre-SEF and post-SEF met inclusion criteria. CTs were reviewed to characterize ES in pre- and post-SEF imaging. RESULTS: Of the 19 patients with ES identified on CT pre-SEF, seven (36.8%) had full release of ES post-SEF and 12 (63.2%) had no release of ES. The posterior tibial tendon was the most commonly ES and remained entrapped in 62.5% of cases. Only 25% of 43-C3 fractures had release of ES post-SEF, while 100% of 43-C1 and 43-C2 fractures demonstrated complete release of ES post-SEF. CONCLUSION: Entrapped structures in pilon fractures are likely to remain entrapped post-SEF, with only one-third of our cohort demonstrating release. In 43-C3 patterns, if ES are identified on CT pre-SEF, surgeons should consider addressing these either through mini open versus open approaches at the time of SEF as they are likely to remain entrapped post-SEF.

High Lethality of Mycobacterium tuberculosis Infection in Mice Lacking the Phagocyte Oxidase and Caspase1/11.

Immune networks that control antimicrobial and inflammatory mechanisms have overlapping regulation and functions to ensure effective host responses. Genetic interaction studies of immune pathways that compare host responses in single and combined knockout backgrounds are a useful tool to identify new mechanisms of immune control during infection. For disease caused by pulmonary Mycobacterium tuberculosis (Mtb) infections, which currently lacks an effective vaccine, understanding the genetic interactions between protective immune pathways may identify new therapeutic targets or disease-associated genes. Previous studies have suggested a direct link between the activation of NLRP3-Caspase1 inflammasome and the NADPH-dependent phagocyte oxidase complex during Mtb infection. Loss of the phagocyte oxidase complex alone resulted in increased activation of Caspase1 and IL-1ß production during Mtb infection, resulting in failed disease tolerance during the chronic stages of disease. To better understand this interaction, we generated mice lacking both Cybb, a key subunit of the phagocyte oxidase, and Caspase1/11. We found that ex vivo Mtb infection of Cybb-/-Caspase1/11-/- macrophages resulted in the expected loss of IL-1ß secretion but an unexpected change in other inflammatory cytokines and bacterial control. Mtb infected Cybb-/-Caspase1/11-/- mice rapidly progressed to severe TB, succumbing within 4 weeks to disease characterized by high bacterial burden, increased inflammatory cytokines, and the recruitment of granulocytes that associated with Mtb in the lungs. These results uncover a key genetic interaction between the phagocyte oxidase complex and Caspase1/11 that controls protection against TB and highlight the need for a better understanding of the regulation of fundamental immune networks during Mtb infection.

Biochar mitigates allelopathic effects in temperate trees.

Many invasive and some native tree species in North America exhibit strong allelopathic effects that may contribute to their local dominance. Pyrogenic carbon (PyC; including soot, charcoal, and black carbon) is produced by the incomplete combustion of organic matter and is widespread in forest soils. Many forms of PyC have sorptive properties that can reduce the bioavailability of allelochemicals. We investigated the potential for PyC produced by controlled pyrolysis of biomass ("biochar" [BC]) to reduce the allelopathic effects of black walnut (Juglans nigra) and Norway maple (Acer platanoides), a common native tree species and a widespread invasive species in North America, respectively. Seedling growth of two native tree species (Acer saccharinum [silver maple] and Betula papyrifera [paper birch]) in response to leaf-litter-incubated soils was examined; litter incubation treatments included leaves of black walnut, Norway maple, and a nonallelopathic species (Tilia americana [American basswood]) in a factorial design with varying dosages; responses to the known primary allelochemical of black walnut (juglone) were also examined. Juglone and leaf litter of both allelopathic species strongly suppressed seedling growth. BC treatments substantially mitigated these effects, consistent with the sorption of allelochemicals; in contrast no positive effects of BC were observed in leaf litter treatments involving controls or additions of nonallelopathic leaf litter. Treatments of leaf litter and juglone with BC increased the total biomass of silver maple by ~35% and in some cases more than doubled the biomass of paper birch. We conclude that BCs have the capacity to largely counteract allelopathic effects in temperate forest systems, suggesting the effects of natural PyC in determining forest community structure, and also the applied use of BC as a soil amendment to mitigate allelopathic effects of invasive tree species.

Direct growth of crystalline SiGe nanowires on superconducting NbTiN thin films.

Novel heterostructures created by coupling one-dimensional semiconductor nanowires with a superconducting thin film show great potential toward next-generation quantum computing. Here, by growing high-crystalline SiGe nanowires on a NbTiN thin film, the resulting heterostructure exhibits Ohmic characteristics as well as a shift of the superconducting transition temperature (Tc). The structure was characterized at atomic resolution showing a sharp SiGe/NbTiN interface without atomic interdiffusion. Lattice spacing, as calculated from large-area x-ray diffraction experiments, suggests a potential preferredd-spacing matching between (200) NbTiN and (110) SiGe grains. The observed out-of-plane compressive strain within the NbTiN films coupled with SiGe nanowires explains the downward shift of the superconductivity behavior. The presented results post scientific insights toward functional heterostructures by coupling multi-dimensional materials, which could enable tunable superconductivity that benefits the quantum science applications.

Biochar Benefits Green Infrastructure: Global Meta-Analysis and Synthesis.

Urbanization has degraded ecosystem services on a global scale, and cities are vulnerable to long-term stresses and risks exacerbated by climate change. Green infrastructure (GI) has been increasingly implemented in cities to improve ecosystem functions and enhance city resilience, yet GI degradation or failure is common. Biochar has been recently suggested as an ideal substrate additive for a range of GI types due to its favorable properties; however, the generality of biochar benefits the GI ecosystem function, and the underlying mechanisms remain unclear. Here, we present a global meta-analysis and synthesis and demonstrate that biochar additions pervasively benefit a wide range of ecosystem functions on GI. Biochar applications were found to improve substrate water retention capacity by 23% and enhance substrate nutrients by 12-31%, contributing to a 33% increase in plant total biomass. Improved substrate physicochemical properties and plant growth together reduce discharge water volume and improve discharge water quality from GI. In addition, biochar increases microbial biomass on GI by ∼150% due to the presence of biochar pores and enhanced microbial growth conditions, while also reducing CO2 and N2O emissions. Overall results suggest that biochar has great potential to enhance GI ecosystem functions as well as urban sustainability and resilience.

Biochar granulation, particle size, and vegetation effects on leachate water quality from a green roof substrate.

Biochar, due to its favourable physiochemical properties, has been promoted as an ideal substrate additive on green roofs, with potential benefits to hydrological function. However, biochar is susceptible to water erosion, which may result in biochar loss and water pollution. The use of granulated biochars or biochars in large particle sizes could potentially alleviate biochar erosion loss, but effects on leachate quality have not been investigated. Also, biochar type and particle size influence plant performance, and effects on discharge quality may vary with vegetation. We assessed the effects of unprocessed and granulated biochars at five (0.25-0.5 mm, 0.5-1 mm, 1-2 mm, 2-2.8 mm, 2.8-4 mm) and four (1-2 mm, 2-2.8 mm, 2.8-4 mm, and 4-6.3 mm) particle size ranges, respectively, on leachate quality on a typical green roof substrate, with presence and absence of vegetation (Agastache foeniculum - a drought-tolerant native forb). We evaluated integrated leachate quality using the CCME Water Quality Index (WQI). Unprocessed biochars reduced nutrient leaching due to increased water retention capacity (WRC) and total porosity. In contrast, granulated biochars, although showing less pronounced mitigation of nutrient leaching, reduced total suspended solids (TSS) and improved WQI in leachate due to enhanced plant performance. In addition, small biochar particles better reduced nutrient leaching and particle loss than large biochar particles, possibly due to increased WRC and formation of water-stable aggregates. The presence of vegetation generally reduced the leaching of nutrients and TSS, consistent with plant nutrient uptake and root substrate stabilization. However, plant biomass was correlated with increased total N leaching, likely due to litter inputs and rapid litter decomposition. We conclude that applications of granulated biochars may best improve discharge quality from green roofs through sorption effects and by enhancing plant performance.

Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.

Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.

Fighting Persistence: How Chronic Infections with Mycobacterium tuberculosis Evade T Cell-Mediated Clearance and New Strategies To Defeat Them.

Chronic bacterial infections are caused by pathogens that persist within their hosts and avoid clearance by the immune system. Treatment and/or detection of such pathogens is difficult, and the resulting pathologies are often deleterious or fatal. There is an urgent need to develop protective vaccines and host-directed therapies that synergize with antibiotics to prevent pathogen persistence and infection-associated pathologies. However, many persistent pathogens, such as Mycobacterium tuberculosis, actively target the very host pathways activated by vaccination. These immune evasion tactics blunt the effectiveness of immunization strategies and are impeding progress to control these infections throughout the world. Therefore, it is essential that M. tuberculosis immune evasion-related pathogen virulence strategies are considered to maximize the effectiveness of potential new treatments. In this review, we focus on how Mycobacterium tuberculosis infects antigen-presenting cells and evades effective immune clearance by the adaptive response through (i) manipulating antigen presentation, (ii) repressing T cell-activating costimulatory molecules, and (iii) inducing ligands that drive T cell exhaustion. In this context, we will examine the challenges that bacterial virulence strategies pose to developing new vaccines. We will then discuss new approaches that will help dissect M. tuberculosis immune evasion mechanisms and devise strategies to bypass them to promote long-term protection and prevent disease progression.

The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.

The human genome is structurally organized in three-dimensional space to facilitate functional partitioning of transcription. We learned that the latent episome of the human Epstein-Barr virus (EBV) preferentially associates with gene-poor chromosomes and avoids gene-rich chromosomes. Kaposi's sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not. Contacts on the EBV side localize to OriP, the latent origin of replication. This genetic element and the EBNA1 protein that binds there are sufficient to reconstitute chromosome association preferences of the entire episome. Contacts on the human side localize to gene-poor and AT-rich regions of chromatin distant from transcription start sites. Upon reactivation from latency, however, the episome moves away from repressive heterochromatin and toward active euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during reactivation. Involvement of myriad interchromosomal associations also suggests a role for this type of long-range association in gene regulation.IMPORTANCE The human genome is structurally organized in three-dimensional space, and this structure functionally affects transcriptional activity. We set out to investigate whether a double-stranded DNA virus, Epstein-Barr virus (EBV), uses mechanisms similar to those of the human genome to regulate transcription. We found that the EBV genome associates with repressive compartments of the nucleus during latency and with active compartments during reactivation. This study advances our knowledge of the EBV life cycle, adding three-dimensional relocalization as a novel component to the molecular events that occur during reactivation. Furthermore, the data add to our understanding of nuclear compartments, showing that disperse interchromosomal interactions may be important for regulating transcription.

Features that define the best ChIP-seq peak calling algorithms.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in the analysis of these data. Peak calling consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. We surveyed 30 methods and identified 12 features of the two sub-problems that distinguish methods from each other. We picked six methods GEM, MACS2, MUSIC, BCP, Threshold-based method (TM) and ZINBA] that span this feature space and used a combination of 300 simulated ChIP-seq data sets, 3 real data sets and mathematical analyses to identify features of methods that allow some to perform better than the others. We prove that methods that explicitly combine the signals from ChIP and input samples are less powerful than methods that do not. Methods that use windows of different sizes are more powerful than the ones that do not. For statistical testing of candidate peaks, methods that use a Poisson test to rank their candidate peaks are more powerful than those that use a Binomial test. BCP and MACS2 have the best operating characteristics on simulated transcription factor binding data. GEM has the highest fraction of the top 500 peaks containing the binding motif of the immunoprecipitated factor, with 50% of its peaks within 10 base pairs of a motif. BCP and MUSIC perform best on histone data. These findings provide guidance and rationale for selecting the best peak caller for a given application.

Brg1 modulates enhancer activation in mesoderm lineage commitment.

The interplay between different levels of gene regulation in modulating developmental transcriptional programs, such as histone modifications and chromatin remodeling, is not well understood. Here, we show that the chromatin remodeling factor Brg1 is required for enhancer activation in mesoderm induction. In an embryonic stem cell-based directed differentiation assay, the absence of Brg1 results in a failure of cardiomyocyte differentiation and broad deregulation of lineage-specific gene expression during mesoderm induction. We find that Brg1 co-localizes with H3K27ac at distal enhancers and is required for robust H3K27 acetylation at distal enhancers that are activated during mesoderm induction. Brg1 is also required to maintain Polycomb-mediated repression of non-mesodermal developmental regulators, suggesting cooperativity between Brg1 and Polycomb complexes. Thus, Brg1 is essential for modulating active and repressive chromatin states during mesoderm lineage commitment, in particular the activation of developmentally important enhancers. These findings demonstrate interplay between chromatin remodeling complexes and histone modifications that, together, ensure robust and broad gene regulation during crucial lineage commitment decisions.

Epidemiology and Detrimental Impact of Opioid Use in Patients Undergoing Arthroscopic Treatment of Femoroacetabular Impingement Syndrome.

PURPOSE: To determine the prevalence of preoperative opioid use in patients with femoroacetabular impingement (FAI) syndrome and to define how opioid use influences preoperative hip pain and function at a single center. METHODS: Between February 2015 and September 2016, patients undergoing hip arthroscopy at a single Midwest institution for FAI syndrome were retrospectively reviewed. Patients undergoing arthroscopy for non-FAI conditions and those with undocumented preoperative opioid use were excluded. Baseline validated measures (Hip Disability and Osteoarthritis Outcome Score [HOOS] pain and physical function; University of California, Los Angeles, activity scores; Veterans RAND 12 Item Health Survey) of health were collected at the time of surgery. Articular cartilage status was documented at the time of surgery. Opioid use was extracted from the electronic medical record retrospectively, and patients were designated current users, past users, or nonusers. Analysis of variance and 2-tailed Student's t-tests were used to detect differences between groups according to preoperative opioid use, and significance was set to P < .05. RESULTS: During the study period 321 patients underwent arthroscopic hip surgery for FAI and met the inclusion criteria (75 were excluded). Preoperatively, 55 patients (17%) were current opioid users, 89 (28%) were past users (not within 3 months of surgery), and 177 (55%) were opioid naive. Current opioid use was associated with significantly worse measures of joint and general health including HOOS-Pain (15.3 point difference, P < .001), HOOS-Physical Function (13.6 point difference, P < .001), University of California, Los Angeles, activity score (1.7 point difference, P < .001), and Veterans RAND 12 Item Health Survey mental component score (5.5 point difference, P < .001). Outerbridge cartilage grading and presence or length of labral tears were not worse in opioid users (P = .2-.61). CONCLUSIONS: Preoperative opioid use is common prior to arthroscopy for FAI and has detrimental impacts on hip pain and function. The present data also suggest cessation of opioid medication for 3 months prior to surgery may have meaningful impacts on baseline measures of hip and general health. LEVEL OF EVIDENCE: Level III, prognostic.

Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature.

Maintenance of vascular integrity is required for embryogenesis and organ homeostasis. However, the gene expression programs that stabilize blood vessels are poorly understood. Here, we show that the histone methyltransferase Ezh2 maintains integrity of the developing vasculature by repressing a transcriptional program that activates expression of Mmp9. Inactivation of Ezh2 in developing mouse endothelium caused embryonic lethality with compromised vascular integrity and increased extracellular matrix degradation. Genome-wide approaches showed that Ezh2 targets Mmp9 and its activators Fosl1 and Klf5. In addition, we uncovered Creb3l1 as an Ezh2 target that directly activates Mmp9 gene expression in the endothelium. Furthermore, genetic inactivation of Mmp9 rescued vascular integrity defects in Ezh2-deficient embryos. Thus, epigenetic repression of Creb3l1, Fosl1, Klf5 and Mmp9 by Ezh2 in endothelial cells maintains the integrity of the developing vasculature, potentially linking this transcriptional network to diseases with compromised vascular integrity.