Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.

The immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we used multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after immunization with the mRNA vaccine BNT162b2. Our data indicated distinct subpopulations of CD8+ T cells, which reliably appeared 28 days after prime vaccination. Using a suite of cross-modality integration tools, we defined their transcriptome, accessible chromatin landscape and immunophenotype, and we identified unique biomarkers within each modality. We further showed that this vaccine-induced population was SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we identified these CD8+ T cell populations in scRNA-seq datasets from COVID-19 patients and found that their relative frequency and differentiation outcomes were predictive of subsequent clinical outcomes.

Structural basis of tethered agonism of the adhesion GPCRs ADGRD1 and ADGRF1.

Adhesion G protein-coupled receptors (aGPCRs) are essential for a variety of physiological processes such as immune responses, organ development, cellular communication, proliferation and homeostasis1-7. An intrinsic manner of activation that involves a tethered agonist in the N-terminal region of the receptor has been proposed for the aGPCRs8,9, but its molecular mechanism remains elusive. Here we report the G protein-bound structures of ADGRD1 and ADGRF1, which exhibit many unique features with regard to the tethered agonism. The stalk region that proceeds the first transmembrane helix acts as the tethered agonist by forming extensive interactions with the transmembrane domain; these interactions are mostly conserved in ADGRD1 and ADGRF1, suggesting that a common stalk-transmembrane domain interaction pattern is shared by members of the aGPCR family. A similar stalk binding mode is observed in the structure of autoproteolysis-deficient ADGRF1, supporting a cleavage-independent manner of receptor activation. The stalk-induced activation is facilitated by a cascade of inter-helix interaction cores that are conserved in positions but show sequence variability in these two aGPCRs. Furthermore, the intracellular region of ADGRF1 contains a specific lipid-binding site, which proves to be functionally important and may serve as the recognition site for the previously discovered endogenous ADGRF1 ligand synaptamide. These findings highlight the diversity and complexity of the signal transduction mechanisms of the aGPCRs.

The F-box protein RhSAF destabilizes the gibberellic acid receptor RhGID1 to mediate ethylene-induced petal senescence in rose.

Roses are among the most popular ornamental plants cultivated worldwide for their great economic, symbolic, and cultural importance. Nevertheless, rapid petal senescence markedly reduces rose (Rosa hybrida) flower quality and value. Petal senescence is a developmental process tightly regulated by various phytohormones. Ethylene accelerates petal senescence, while gibberellic acid (GA) delays this process. However, the molecular mechanisms underlying the crosstalk between these phytohormones in the regulation of petal senescence remain largely unclear. Here, we identified SENESCENCE-ASSOCIATED F-BOX (RhSAF), an ethylene-induced F-box protein gene encoding a recognition subunit of the SCF-type E3 ligase. We demonstrated that RhSAF promotes degradation of the GA receptor GIBBERELLIN INSENSITIVE DWARF1 (RhGID1) to accelerate petal senescence. Silencing RhSAF expression delays petal senescence, while suppressing RhGID1 expression accelerates petal senescence. RhSAF physically interacts with RhGID1s and targets them for ubiquitin/26S proteasome-mediated degradation. Accordingly, ethylene-induced RhGID1C degradation and RhDELLA3 accumulation are compromised in RhSAF-RNAi lines. Our results demonstrate that ethylene antagonizes GA activity through RhGID1 degradation mediated by the E3 ligase RhSAF. These findings enhance our understanding of the phytohormone crosstalk regulating petal senescence and provide insights for improving flower longevity.

Endogenous cell membrane interactome mapping for the GLP-1 receptor in different cell types.

The GLP-1 receptor, one of the most successful drug targets for the treatment of type 2 diabetes and obesity, is known to engage multiple intracellular signaling proteins. However, it remains less explored how the receptor interacts with proteins on the cell membrane. Here, we present a ligand-based proximity labeling approach to interrogate the native cell membrane interactome for the GLP-1 receptor after agonist simulation. Our study identified several unreported putative cell membrane interactors for the endogenous receptor in either a pancreatic ß cell line or a neuronal cell line. We further uncovered new regulators of GLP-1 receptor-mediated signaling and insulinotropic responses in ß cells. Additionally, we obtained a time-resolved cell membrane interactome map for the receptor in ß cells. Therefore, our study provides a new approach that is generalizable to map endogenous cell membrane interactomes for G-protein-coupled receptors to decipher the molecular basis of their cell-type-specific functional regulation.

Widespread Enhancer Dememorization and Promoter Priming during Parental-to-Zygotic Transition.

The epigenome plays critical roles in controlling gene expression and development. However, how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show that parental-to-zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory, starting with methylating gametic enhancers. Surprisingly, this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4-cell stage, and zygotic enhancers are not activated until around zygotic genome activation (ZGA). By contrast, many promoters remain hypomethylated and, unexpectedly, acquire histone acetylation before ZGA at as early as the 4-cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally, such reprogramming is largely driven by maternal factors, with zygotic products mainly contributing to embryonic enhancer activation. These data reveal widespread enhancer dememorization and promoter priming during parental-to-zygotic transition.

Affinity selection of double-click triazole libraries for rapid discovery of allosteric modulators for GLP-1 receptor.

The recently developed double-click reaction sequence [G. Meng et al., Nature 574, 86-89 (2019)] is expected to vastly expand the number and diversity of synthetically accessible 1,2,3-triazole derivatives. However, it remains elusive how to rapidly navigate the extensive chemical space created by double-click chemistry for bioactive compound discovery. In this study, we selected a particularly challenging drug target, the glucagon-like-peptide-1 receptor (GLP-1R), to benchmark our new platform for the design, synthesis, and screening of double-click triazole libraries. First, we achieved a streamlined synthesis of customized triazole libraries on an unprecedented scale (composed of 38,400 new compounds). By interfacing affinity-selection mass spectrometry and functional assays, we identified a series of positive allosteric modulators (PAMs) with unreported scaffolds that can selectively and robustly enhance the signaling activity of the endogenous GLP-1(9-36) peptide. Intriguingly, we further revealed an unexpected binding mode of new PAMs which likely act as a molecular glue between the receptor and the peptide agonist. We anticipate the merger of double-click library synthesis with the hybrid screening platform allows for efficient and economic discovery of drug candidates or chemical probes for various therapeutic targets.

Crystal structure of the Frizzled 4 receptor in a ligand-free state.

Frizzled receptors (FZDs) are class-F G-protein-coupled receptors (GPCRs) that function in Wnt signalling and are essential for developing and adult organisms1,2. As central mediators in this complex signalling pathway, FZDs serve as gatekeeping proteins both for drug intervention and for the development of probes in basic and in therapeutic research. Here we present an atomic-resolution structure of the human Frizzled 4 receptor (FZD4) transmembrane domain in the absence of a bound ligand. The structure reveals an unusual transmembrane architecture in which helix VI is short and tightly packed, and is distinct from all other GPCR structures reported so far. Within this unique transmembrane fold is an extremely narrow and highly hydrophilic pocket that is not amenable to the binding of traditional GPCR ligands. We show that such a pocket is conserved across all FZDs, which may explain the long-standing difficulties in the development of ligands for these receptors. Molecular dynamics simulations on the microsecond timescale and mutational analysis uncovered two coupled, dynamic kinks located at helix VII that are involved in FZD4 activation. The stability of the structure in its ligand-free form, an unfavourable pocket for ligand binding and the two unusual kinks on helix VII suggest that FZDs may have evolved a novel ligand-recognition and activation mechanism that is distinct from that of other GPCRs.

Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals.

Polycomb group proteins and the related histone modification H3K27me3 can maintain the silencing of key developmental regulators and provide cellular memory. However, how such an epigenetic state is reprogrammed and inherited between generations is poorly understood. Using an ultra-sensitive approach, STAR ChIP-seq, we investigated H3K27me3 across 14 developmental stages along mouse gametogenesis and early development. Interestingly, highly pervasive H3K27me3 is found in regions depleted of transcription and DNA methylation in oocytes. Unexpectedly, we observed extensive loss of promoter H3K27me3 at Hox and other developmental genes upon fertilization. This is accompanied by global erasure of sperm H3K27me3 but inheritance of distal H3K27me3 from oocytes. The resulting allele-specific H3K27me3 patterns persist to blastocysts before being converted to canonical forms in postimplantation embryos, where both H3K4me3/H3K27me3 bivalent promoter marks are restored at developmental genes. Together, these data revealed widespread resetting of epigenetic memory and striking plasticity of epigenome during gametogenesis and early development.

Adipokines in atopic dermatitis: the link between obesity and atopic dermatitis.

Atopic dermatitis (AD) is a chronic skin condition with intense pruritus, eczema, and dry skin. The recurrent intense pruritus and numerous complications in patients with AD can profoundly affect their quality of life. Obesity is one of its comorbidities that has been confirmed to be the hazard factor of AD and also worsen its severity. Nevertheless, the specific mechanisms that explain the connection between obesity and AD remain incompletely recognized. Recent studies have built hopes on various adipokines to explain this connection. Adipokines, which are disturbed by an obese state, may lead to immune system imbalances in people with AD and promote the development of the disease. This review focuses on the abnormal expression patterns of adipokines in patients with AD and their potential regulatory molecular mechanisms associated with AD. The connection between AD and obesity is elucidated through the involvement of adipokines. This conduces to the in-depth exploration of AD pathogenesis and provides a new perspective to develop therapeutic targets.

An Algorithm for Generating Outdoor Floor Plans and 3D Models of Rural Houses Based on Backpack LiDAR.

As the Rural Revitalization Strategy continues to progress, there is an increasing demand for the digitization of rural houses, roads, and roadside trees. Given the characteristics of rural areas, such as narrow roads, high building density, and low-rise buildings, the precise and automated generation of outdoor floor plans and 3D models for rural areas is the core research issue of this paper. The specific research content is as follows: Using the point cloud data of the outer walls of rural houses collected by backpack LiDAR as the data source, this paper proposes an algorithm for drawing outdoor floor plans based on the topological relationship of sliced and rasterized wall point clouds. This algorithm aims to meet the needs of periodically updating large-scale rural house floor plans. By comparing the coordinates of house corner points measured with RTK, it is verified that the floor plans drawn by this algorithm can meet the accuracy requirements of 1:1000 topographic maps. Additionally, based on the generated outdoor floor plans, this paper proposes an algorithm for quickly generating outdoor 3D models of rural houses using the height information of wall point clouds. This algorithm can quickly generate outdoor 3D models of rural houses by longitudinally stretching the floor plans, meeting the requirements for 3D models in spatial analyses such as lighting and inundation. By measuring the distance from the wall point clouds to the 3D models and conducting statistical analysis, results show that the distances are concentrated between -0.1 m and 0.1 m. The 3D model generated by the method proposed in this paper can be used as one of the basic data for real 3D construction.

Impact of COVID-19 on epidemic trend of hepatitis C in Henan Province assessed by interrupted time series analysis.

OBJECTIVE: Hepatitis C presents a profound global health challenge. The impact of COVID-19 on hepatitis C, however, remain uncertain. This study aimed to ascertain the influence of COVID-19 on the hepatitis C epidemic trend in Henan Province. METHODS: We collated the number of monthly diagnosed cases in Henan Province from January 2013 to September 2022. Upon detailing the overarching epidemiological characteristics, the interrupted time series (ITS) analysis using autoregressive integrated moving average (ARIMA) models was employed to estimate the hepatitis C diagnosis rate pre and post the COVID-19 emergence. In addition, we also discussed the model selection process, test model fitting, and result interpretation. RESULTS: Between January 2013 and September 2022, a total of 267,968 hepatitis C cases were diagnosed. The yearly average diagnosis rate stood at 2.42/100,000 persons. While 2013 witnessed the peak diagnosis rate at 2.97/100,000 persons, 2020 reported the least at 1.7/100,000 persons. The monthly mean hepatitis C diagnosed numbers culminated in 2291 cases. The optimal ARIMA model chosen was ARIMA (0,1,1) (0,1,1)12 with AIC = 1459.58, AICc = 1460.19, and BIC = 1472.8; having coefficients MA1=-0.62 (t=-8.06, P < 0.001) and SMA1=-0.79 (t=-6.76, P < 0.001). The final model's projected step change was - 800.0 (95% confidence interval [CI] -1179.9 ~ -420.1, P < 0.05) and pulse change was 463.40 (95% CI 191.7 ~ 735.1, P < 0.05) per month. CONCLUSION: The measures undertaken to curtail COVID-19 led to a diminishing trend in the diagnosis rate of hepatitis C. The ARIMA model is a useful tool for evaluating the impact of large-scale interventions, because it can explain potential trends, autocorrelation, and seasonality, and allow for flexible modeling of different types of impacts.

Interruption time series analysis using autoregressive integrated moving average model: evaluating the impact of COVID-19 on the epidemic trend of gonorrhea in China.

BACKGROUND: Interrupted time series (ITS) analysis is a growing method for assessing intervention impacts on diseases. However, it remains unstudied how the COVID-19 outbreak impacts gonorrhea. This study aimed to evaluate the effect of COVID-19 on gonorrhea and predict gonorrhea epidemics using the ITS-autoregressive integrated moving average (ARIMA) model. METHODS: The number of gonorrhea cases reported in China from January 2005 to September 2022 was collected. Statistical descriptions were applied to indicate the overall epidemiological characteristics of the data, and then the ITS-ARIMA was established. Additionally, we compared the forecasting abilities of ITS-ARIMA with Bayesian structural time series (BSTS), and discussed the model selection process, transfer function, check model fitting, and interpretation of results. RESULT: During 2005-2022, the total cases of gonorrhea were 2,165,048, with an annual average incidence rate of 8.99 per 100,000 people. The highest incidence rate was 14.2 per 100,000 people in 2005 and the lowest was 6.9 per 100,000 people in 2012. The optimal model was ARIMA (0,1, (1,3)) (0,1,1)12 (Akaike's information criterion = 3293.93). When predicting the gonorrhea incidence, the mean absolute percentage error under the ARIMA (16.45%) was smaller than that under the BSTS (22.48%). The study found a 62.4% reduction in gonorrhea during the first-level response, a 46.47% reduction during the second-level response, and an increase of 3.6% during the third-level response. The final model estimated a step change of - 2171 (95% confidence interval [CI] - 3698 to - 644) cases and an impulse change of - 1359 (95% CI - 2381 to - 338) cases. Using the ITS-ARIMA to evaluate the effect of COVID-19 on gonorrhea, the gonorrhea incidence showed a temporary decline before rebounding to pre-COVID-19 levels in China. CONCLUSION: ITS analysis is a valuable tool for gauging intervention effectiveness, providing flexibility in modelling various impacts. The ITS-ARIMA model can adeptly explain potential trends, autocorrelation, and seasonality. Gonorrhea, marked by periodicity and seasonality, exhibited a downward trend under the influence of COVID-19 intervention. The ITS-ARIMA outperformed the BSTS, offering superior predictive capabilities for the gonorrhea incidence trend in China.

Computational Insights and In Silico Characterization of a Novel Mini-Lipoxygenase from Nostoc Sphaeroides and Its Application in the Quality Improvement of Steamed Bread.

Lipoxygenase (EC1.13.11.12, LOX) has been potentially used in the food industry for food quality improvement. However, the low activity, poor thermal stability, narrow range of pH stability, as well as undesirable isoenzymes and off-flavors, have hampered the application of current commercial LOX. In this study, a putative mini-lipoxygenase gene from cyanobacteria, Nostoc sphaeroides (NsLOX), was cloned and expressed in E. coli BL21. NsLOX displayed only 26.62% structural identity with the reported LOX from Cyanothece sp., indicating it as a novel LOX. The purified NsLOX showed the maximum activity at pH 8.0 and 15 °C, with superior stability at a pH range from 6.0 to 13.0, retaining about 40% activity at 40 °C for 90 min. Notably, NsLOX exhibited the highest specific activity of 78,080 U/mg towards linoleic acid (LA), and the kinetic parameters-Km, kcat, and kcat/Km-attain values of 19.46 µM, 9199.75 s-1, and 473.85 µM-1 s-1, respectively. Moreover, the activity of NsLOX was obviously activated by Ca2+, but it was completely inhibited by Zn2+ and Cu2+. Finally, NsLOX was supplied in steamed bread and contributed even better improved bread quality than the commercial LOX. These results suggest NsLOX as a promising substitute of current commercial LOX for application in the food industry.

Sustainable recovery of melanoidins from thermal hydrolyzed sludge by macroporous resin and properties characterization.

Melanoidins, the dark-color recalcitrant Maillard reaction by-products in thermal hydrolyzed sludge (THS), cause significant adverse effects on wastewater treatment. This study aimed to develop an efficient adsorption method for recovering melanoidins from THS by macroporous resin. The adsorptive characteristics of six macroporous resins (XAD761, XAD8, XAD16HP, FPX66, HPD-600 and IRA958Cl) showed that XAD761, not yet reported for melanoidins extraction, was the most appropriate with the highest recovery ratio. The adsorption kinetics followed pseudo-second-order model, and the adsorption process was confirmed to be physical, spontaneous, and exothermic, without changing the structure of the adsorbed melanoidins. In the dynamic adsorption, the breakthrough point increased with a decreasing flow rate. After five consecutive regeneration cycles, XAD761 resin maintained stable adsorption efficiency and thus had a good potential for reuse. Furthermore, the physicochemical properties of the extracted THS melanoidins were compared with model melanoidins to lay the foundation for their management, in terms of morphology, molecular weight (MW), and spectrophotometric properties. These results demonstrate that XAD761 resin extraction is a promising sustainable method for practical application in the recovery of melanoidins from THS.

Slightly acidic electrolyzed water-slurry ice: shelf-life extension and quality maintenance of mackerel (Pneumatophorus japonicus) during chilled storage.

BACKGROUND: Different ice treatments were applied for the preservation of mackerel (Pneumatophorus japonicus). The quality changes of samples treated with flake ice (Control), slurry ice (SI) and slightly acidic electrolyzed water-slurry ice (SAEW-SI) in microbiological, physicochemical, protein characteristic, and sensory evaluation were investigated during chilled storage. RESULTS: SAEW-SI showed a significant advantage for the inhibition of microbial growth, which could extend the shelf-life for another 144 h at least, compared with Control group. SAEW-SI treatment also showed a strong inhibition for the increase in pH, total volatile basic nitrogen (TVB-N), K-value, histamine and metmyoglobin (MetMb) content. Results of texture profile analysis (TPA) and water holding capacity (WHC) indicated that SAEW-SI can obviously suppress the decrease of hardness value, and have a better protective effect on muscle structure compared to flake ice and SI (P < 0.05). During the whole experiment, the highest sensory scores and a* were obtained in the SAEW-SI group, which indicated that SAEW-SI treatment could maintain better sensory characteristics. According to the results of thiobarbituric acid reactive substances (TBARS) and fluorescence spectroscopy analysis, SAEW-SI treatment could effectively retard protein degradation and lipid oxidation compared with Control and SI group. In maintaining the quality of mackerel, SAEW-SI shows a better effect than SI due to the synergistic effect of fence factors. CONCLUSION: The results demonstrated that the shelf-life of mackerel could be extended and the quality of mackerel could be maintained effectively with SAEW-SI treatment during chilled storage. © 2022 Society of Chemical Industry.

ortho-Terphenylene Viologens with Through-Space Conjugation for Enhanced Photocatalytic Oxidative Coupling and Hydrogen Evolution.

A series of novel ortho-terphenylene viologen derivatives (o-TPV2+) with through-space conjugation (TSC) via the combination of ortho-terphenylene skeletons with viologen structure is reported. Their optoelectronic properties can be adjusted by N-arylation or N-alkylation reactions. Compared with other viologen derivatives, o-TPV2+ not only exhibits strong photoluminescence but also retards the charge recombination process and stabilizes the diradical state without forming a quinoid structure due to the special TSC effect. Based on their special redox characteristics, o-TPV2+ was applied to the photocatalytic oxidative coupling of benzylamine with 96% yield. In addition, pTA-o-TPV2+ (tethered with p-toluic acid)-modified g-C3N4 was used for visible-light-driven hydrogen production for the first time, exceeding 15 times the rate over unmodified g-C3N4.

Tolerogenic Dendritic Cells Generated by BAFF Silencing Ameliorate Collagen-Induced Arthritis by Modulating the Th17/Regulatory T Cell Balance.

Tolerogenic dendritic cells (tolDCs) have received much attention because of their capacity to restore immune homeostasis. RNA interference techniques have been used in several studies to generate tolDCs by inactivating certain molecules that regulate DC maturation and immunologic function. BAFF is a key B cell survival factor that is not only essential for B cell function but also T cell costimulation, and DCs are the major source of BAFF. In this study, we determined whether BAFF gene silencing in mature DCs could lead to a tolerogenic phenotype as well as the potential therapeutic effect of BAFF-silenced DCs on collagen-induced arthritis (CIA) in mice. Meanwhile, CRISPR/Cas9-mediated BAFF-/- DC2.4 cells were generated to verify the role of BAFF in DC maturation and functionality. BAFF-silenced DCs and BAFF-/- DC2.4 cells exhibited an immature phenotype and functional state. Further, the transplantation of BAFF-silenced DCs significantly alleviated CIA severity in mice, which correlated with a reduction in Th17 populations and increased regulatory T cells. In vitro, BAFF-silenced DCs promoted Foxp3 mRNA and IL-10 expression but inhibited ROR-γt mRNA and IL-17A expression in CD4+ T cells. Together, BAFF-silenced DCs can alleviate CIA, partly by inducing Foxp3+ regulatory T cells and suppressing Th17 subsets. Collectively, BAFF plays an important role in interactions between DCs and T cells, which might be a promising genetic target to generate tolDCs for autoimmune arthritis treatment.

Structural optimizations and bioevaluation of N-H aporphine analogues as Gq-biased and selective serotonin 5-HT2C receptor agonists.

The concept of subtype selectivity and functional bias has recently reshaped current GPCR drug discovery for G protein-coupled receptors. A series of new N-H aporphines with A-ring modifications have been synthesized, and their efficacy on 5-HT2 receptor activation was evaluated. SAR analysis led to the discovery of several more potent and selective 5-HT2C receptor agonists (e.g., 11b and 11f) with low nanomolar activity. Molecular docking analysis of this series of aporphines was in accordance with our SAR results. The functional selectivity of specific compounds was tested via both Gq-mediated calcium flux and ß-arrestin recruitment assays, which revealed that these compounds exhibited no ß-arrestin recruitment activity. Further ADMET study combined with behavioral assessment using a methamphetamine-induced hyperactivity model identified compound 11b and 11f possessing promising drug-like profiles and having antipsychotic potential. These agonists with an exclusive bias toward Gq signaling may serve as valuable pharmacological probes to facilitate the elucidation of therapeutically relevant 5-HT2C signaling pathways and the development of alternative antipsychotic medications.

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development.

Histone modifications are fundamental epigenetic regulators that control many crucial cellular processes. However, whether these marks can be passed on from mammalian gametes to the next generation is a long-standing question that remains unanswered. Here, by developing a highly sensitive approach, STAR ChIP-seq, we provide a panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation, from developing gametes to post-implantation embryos. We find that upon fertilization, extensive reprogramming occurs on the paternal genome, as H3K4me3 peaks are depleted in zygotes but are readily observed after major zygotic genome activation at the late two-cell stage. On the maternal genome, we unexpectedly find a non-canonical form of H3K4me3 (ncH3K4me3) in full-grown and mature oocytes, which exists as broad peaks at promoters and a large number of distal loci. Such broad H3K4me3 peaks are in contrast to the typical sharp H3K4me3 peaks restricted to CpG-rich regions of promoters. Notably, ncH3K4me3 in oocytes overlaps almost exclusively with partially methylated DNA domains. It is then inherited in pre-implantation embryos, before being erased in the late two-cell embryos, when canonical H3K4me3 starts to be established. The removal of ncH3K4me3 requires zygotic transcription but is independent of DNA replication-mediated passive dilution. Finally, downregulation of H3K4me3 in full-grown oocytes by overexpression of the H3K4me3 demethylase KDM5B is associated with defects in genome silencing. Taken together, these data unveil inheritance and highly dynamic reprogramming of the epigenome in early mammalian development.

The landscape of accessible chromatin in mammalian preimplantation embryos.

In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.