Biology subjects

Huo, Y.

Publications and source records attributed to Huo, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Disruption of IL-17 signaling in the respiratory mucosa results in invasive streptococcal infection

Streptococcus pyogenes infection of the upper respiratory tract and skin can lead to severe invasive streptococcal disease (ISD). Previous studies have demonstrated that the deficiency of IL-17 in mice (IL-17-/-) reduces mucosal immunity against S. pyogenes. However, the impact of IL-17 deficiency on the development of ISD is unknown. Here, we model single or repeated non-lethal, intranasal (IN) S. pyogenes M1 strain infections in immunocompetent and IL-17-/-mice to assess bacterial dissemination following a final IN or skin challenge. Immunocompetent mice that received a single S. pyogenes IN infection displayed long-lasting mucosal immunity and no systemic infection. However, in the absence of IL-17, a single IN infection resulted in the dissemination of S. pyogenes to the spleens, which was further exacerbated by repeated IN infections. Interestingly, immunity following skin challenge did not show a correlation with IL-17 and was instead associated with the activation of germinal center responses and the accumulation of neutrophils in the spleen. Our results highlight the critical role of IL-17 in preventing ISD following S. pyogenes infection of the respiratory mucosa.

immunology↗

bioRxiv2023

The type of carbon source not the growth rate it supports can determine diauxie

How cells choose between potential carbon sources is a classic example of cellular decision-making, and we know that many organisms prioritise glucose. Yet there has been little investigation of whether other sugars are also preferred, blinkering our view of carbon sensing. Here we study eukaryotic budding yeast and its growth on mixtures of palatinose, an isomer of sucrose, with other sugars. We find that yeast prioritise galactose over palatinose, but not sucrose or fructose, despite all three of these sugars being able to support faster growth than palatinose. Our results therefore disfavour carbon flux-sensing as the sole mechanism. By using genetic perturbations and transcriptomics, we show that repression is active and through Gal4, the master regulator of the GAL regulon. Cells enforce their preference for galactose over palatinose by preventing runaway positive feedback in the MAL regulon, whose genes enable palatinose catabolism. They do so both by repressing MAL11, the gene encoding the palatinose transporter, and by first expressing the isomaltases, IMA1 and IMA5, which cleave palatinose and so prevent its intracellular concentration becoming enough to induce further MAL expression. Our results demonstrate that budding yeast actively maintain a preference for carbon sources other than glucose and that such preferences have been selected by more than differences in growth rates. They imply that carbon-sensing strategies even in unicellular organisms are more complex than previously thought.

systems biology↗

bioRxiv2023

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease

Crohns disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohns ileitis and Crohns colitis and identify novel biomarkers associated with disease activity and treatment response.

bioinformatics↗

bioRxiv2023

Hepatocyte-specific disruption of soluble epoxide hydrolase attenuates abdominal aortic aneurysm formation: novel role of the liver in aneurysm pathogenesis

IntroductionInflammation is a key pathogenic feature of abdominal aortic aneurysm (AAA). Soluble epoxide hydrolase (sEH) is a pro-inflammatory enzyme that converts cytochrome P450-derived epoxides of fatty acids to the corresponding diols, and pharmacological inhibition of sEH prevented AAA formation. Both cytochrome P450 enzymes and sEH are highly expressed in the liver. Here, we investigated the role of hepatic sEH in AAA using a selective pharmacological inhibitor of sEH and hepatocyte-specific Ephx2 (which encodes sEH gene) knockout (KO) mice in two models of AAA [angiotensin II (AngII) infusion and calcium chloride (CaCl2) application]. Methods and resultssEH expression and activity were strikingly higher in mouse liver compared with aorta and further increased the context of AAA, in conjunction with elevated expression of the transcription factor Sp1 and the epigenetic regulator Jarid1b, which have been reported to positively regulate sEH expression. Pharmacological sEH inhibition, or liver-specific sEH disruption, achieved by crossing sEH floxed mice with albumin-cre mice, prevented AAA formation in both models, concomitant with reduced expression of hepatic sEH as well as complement factor 3 (C3) and serum amyloid A (SAA), liver-derived factors linked to AAA formation. Moreover, sEH antagonism markedly reduced C3 and SAA protein accumulation in the aortic wall. Co-incubation of liver ex vivo with aneurysm-prone aorta resulted in induction of sEH in the liver, concomitant with upregulation of Sp1, Jarid1b, C3 and SAA gene expression, suggesting that the aneurysm-prone aorta secretes factors that activate sEH and downstream inflammatory signaling in the liver. Using an unbiased proteomic approach, we identified a number of dysregulated proteins [e.g., plastin-2, galectin-3 (gal-3), cathepsin S] released by aneurysm-prone aorta as potential candidate mediators of hepatic sEH induction. ConclusionWe provide the first direct evidence of the livers role in orchestrating AAA via the enzyme sEH. These findings not only provide novel insight into AAA pathogenesis, but they have potentially important implications with regard to developing effective medical therapies for AAA.

pharmacology and toxicology↗

bioRxiv2023

Nunchaku: Optimally partitioning data into piece-wise linear segments

When analysing two-dimensional data sets, scientists are often interested in regions where one variable depends linearly on the other. Typically they use an ad hoc method to do so. Here we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a data set into contiguous piece-wise linear segments. Our nunchaku algorithm is freely available. Focusing on microbial growth, we use nunchaku to identify the range of optical density where the density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and will facilitate data analysis for a broad range of scientists.

bioinformatics↗

bioRxiv2023

Plant Arbovirus Mobilizes a Vector Salivary Protein to Initiate Plant Infection

Plant viruses typically rely on insect vectors for transmission between plants, with insect salivary proteins playing critical roles in this process. In this study, we demonstrate how Laodelphax striatellus salivary carbonic anhydrase (LssaCA) promotes rice stripe virus (RSV) infection in plants. We discovered that LssaCA directly binds to RSV nucleocapsid protein (NP) in insect salivary glands. This LssaCA-NP complex interacts with a rice thaumatin-like protein (OsTLP) that possess endo-{beta}-1,3-glucanase activity potentially degrading callose. Upon binding, the LssaCA-NP complex significantly enhances OsTLP enzymatic activity. We further clarify that both L. striatellus feeding and RSV infection induce callose deposition. The tripartite LssaCA-NP-OsTLP interaction enhances callose degradation, thereby facilitating RSV infection via its insect vector. This study provides new insights into complex virus-insect-plant tripartite interactions mediated by insect salivary proteins, with broad implications for numerous plant viruses transmitted by insect vectors.

plant biology↗

bioRxiv2023

UBE3A and transsynaptic complex NRXN1-CBLN1-GluD1 in a hypothalamic VMHvl-arcuate feedback circuit regulates aggression

The circuit origins of aggression in autism spectrum disorder remain undefined. Here we report Tac1-expressing glutamatergic neurons in ventrolateral division of ventromedial hypothalamus (VMHvl) drive intermale aggression. Aggression is increased due to increases of Ube3a gene dosage in the VMHvl neurons when modeling autism due to maternal 15q11-13 triplication. Targeted deletion of increased Ube3a copies in VMHvl reverses the elevated aggression adult mice. VMHvl neurons form excitatory synapses onto hypothalamic arcuate nucleus AgRP/NPY neurons through a NRXN1-CBLN1-GluD1 transsynaptic complex and UBE3A impairs this synapse by decreasing Cbln1 gene expression. Exciting AgRP/NPY arcuate neurons leads to feedback inhibition of VMHvl neurons and inhibits aggression. Asymptomatic increases of UBE3A synergize with a heterozygous deficiency of presynaptic Nrxn1 or postsynaptic Grid1 (both ASD genes) to increase aggression. Targeted deletions of Grid1 in arcuate AgRP neurons impairs the VMHvl to AgRP/NPY neuron excitatory synapses while increasing aggression. Chemogenetic/optogenetic activation of arcuate AgRP/NPY neurons inhibits VMHvl neurons and represses aggression. These data reveal that multiple autism genes converge to regulate the VMHvl-arcuate AgRP/NPY glutamatergic synapse. The hypothalamic circuitry implicated by these data suggest impaired excitation of AgRP/NPY feedback inhibitory neurons may explain the increased aggression behavior found in genetic forms of autism. One Sentence SummaryA feedback circuit in the hypothalamus that inhibits aggression is impaired by converging autism genetic defects.

neuroscience↗

bioRxiv2022

Superficial white matter across the lifespan: volume, thickness, change, and relationship with cortical features

Superficial white matter (SWM) represents a significantly understudied part of the human brain, despite comprising a large portion of brain volume and making up a majority of cortical structural connections. Using multiple, high-quality, datasets with large sample sizes (N=2421, age range 5-100) in combination with methodological advances in tractography, we quantified features of SWM volume and thickness across the brain and across the lifespan. We address four questions: (1) How does U-fiber volume change with age? (2) What does U-fiber thickness look like across the brain? (3) How does SWM thickness change with age? (4) Are there relationships between SWM thickness and cortical features? Our main findings are that (1) SWM volume shows unique volumetric trajectories with age that are distinct from gray matter and other white matter trajectories; (2) SWM thickness varies across the brain, with patterns robust across individuals and across the population at the region-level and vertex-level; (3) SWM shows nonlinear changes across the lifespan that vary across regions; and (4) SWM thickness is associated with cortical thickness and curvature. For the first time, we show that SWM volume follows a similar trend as overall white matter volume, peaking at a similar time in adolescence, leveling off throughout adulthood, and decreasing with age thereafter. Notably, the relative fraction of total brain volume of SWM continuously increases with age, and consequently takes up a larger proportion of total white matter volume, unlike the other tissue types that decrease with respect to total brain volume. This study represents the first characterization of SWM features across the lifespan and provides the background for characterizing normal aging and insight into the mechanisms associated with SWM development and decline.

neuroscience↗

bioRxiv2021

DSCN: double-target selection guided by CRISPR screening and network

Cancer is a complex disease with usually multiple disease mechanisms. Target combination is a better strategy than a single target in developing cancer therapies. However, target combinations are generally more difficult to be predicted. Current CRISPR-cas9 technology enables genome-wide screening for potential targets, but only a handful of genes have been screend as target combinations. Thus, an effective computational approach for selecting candidate target combinations is highly desirable. Selected target combinations also need to be translational between cell lines and cancer patients. We have therefore developed DSCN (double-target selection guided by CRISPR screening and network), a method that matches expression levels in patients and gene essentialities in cell lines through spectral-clustered protein-protein interaction (PPI) network. In DSCN, a sub-sampling approach is developed to model first-target knockdown and its impact on the PPI network, and it also facilitates the selection of a second target. Our analysis first demonstrated high correlation of the DSCN sub-sampling-based gene knockdown model and its predicted differential gene expressions using observed gene expression in 22 pancreatic cell lines before and after MAP2K1 and MAP2K2 inhibition (R2 = 0.75). In our DSCN algorithm, various scoring schemes were evaluated. The diffusion-path method showed the most significant statistical power of differentialting known synthetic lethal (SL) versus non-SL gene pairs (P = 0.001) in pancreatic cancer. The superior performance of DSCN over existing network-based algorithms, such as OptiCon[1] and VIPER[2], in the selection of target combinations is attributable to its ability to calculate combinations for any gene pairs, whereas other approaches focus on the combinations among optimized regulators in the network. DSCNs computational speed is also at least ten times faster than that of other methods. Finally, in applying DSCN to predict target combinations and drug combinations for individual samples (DSCNi), we showed high correlation of DSCNi predicted target combinations with synergistic drug combinations (P = 1e-5) in pancreatic cell lines. In summary, DSCN is a highly effective computational method for the selection of target combinations. Author SummaryCancer therapies require targets to function. Compared to single target, target combination is a better strategy for developing cancer therapies. However, predicting target combination is much complicated than predicting single target. Current CRISPR technology enables whole genome screening of potential targets. But most of the experiments have been conducted on single target (gene) level. To facilitate the prediction of target combinations, we developed DSCN (double-target selection guided by CRISPR screening and network) that utilize single target-level CRISPR screening data and expression profiles for predicting target combinations by connecting cell-line omics-data with tissue omics-data. DSCN showed great accuracy on different cancer types and superior performance compared to existing network-based prediction tools. We also introduced DSCNi derived from DSCN and designed specific for predicting target combinations for single-paitent. We showed synergistic target combinations predicted by DSCNi accurately reflected synergies on drug combination levels. Thus, DSCN and DSCNi have the potential be further applied in personalized medicine field.

bioinformatics↗

bioRxiv2021

Allele-specific expression links diverse cis-regulatory mutations to recurrent gene dysregulation in high-risk neuroblastoma

Neuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few protein-coding mutations but contain extensive somatic copy number alterations (SCNAs) suggesting that mutations that alter gene dosage are important drivers of tumorigenesis. Here we analyze allele-specific expression (ASE) in 96 high-risk neuroblastoma tumors to discover genes with cis-acting mutations that alter dosage. We identify 1,049 genes with recurrent, neuroblastoma-specific ASE, 68% of which lie within common SCNA regions. However, many genes exhibit ASE in copy neutral samples and are enriched for mutations that cause nonsense-mediated decay, indicating that neuroblastoma tumors select for multiple types of mutations that alter gene expression. We also find 24 genes with reduced expression in stage 4 disease that have neuroblastoma-specific ASE that is independent of SCNAs. At least two of these genes have evidence for tumor suppressor activity including the transcription factor TFAP2B and the protein tyrosine phosphatase PTPRH. In summary, our ASE analysis discovers genes that are recurrently dysregulated by both large SCNAs and other cis-acting mutations in high-risk neuroblastoma.

cancer biology↗

bioRxiv2021

PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7 to suppress p53 dependent neurodegeneration

The PALB2 tumor suppressor plays key roles in DNA repair and has been implicated in redox homeostasis. Autophagy maintains mitochondrial quality, mitigates oxidative stress and suppresses neurodegeneration. Here we show that Palb2 deletion in the mouse brain leads to motor deficits and that co-deletion of Palb2 with the essential autophagy gene Atg7 accelerates and exacerbates neurodegeneration induced by ATG7 loss. Palb2 deletion leads to elevated DNA damage, oxidative stress and mitochondrial markers, especially in Purkinje cells, and co-deletion of Palb2 and Atg7 results in accelerated Purkinje cell loss. Further analyses suggest that the accelerated Purkinje cell loss and severe neurodegeneration in the double deletion mice are due to oxidative stress and mitochondrial dysfunction, rather than DNA damage, and partially dependent on p53 activity. Our studies uncover a role of PALB2 in mitochondrial regulation and a cooperation between PALB2 and ATG7/autophagy in maintaining redox and mitochondrial homeostasis essential for neuronal survival.

neuroscience↗

bioRxiv2021

A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340

BackgroundMaize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability. FindingsIn this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to "porphyrin-containing compound metabolic process", "tetrapyrrole biosynthetic process", and "tetrapyrrole metabolic process". ConclusionsThe completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding about of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement. Research AreasGenetics and Genomics; Agriculture, Plant Genetics Data Description

genomics↗

bioRxiv2020

Increased light availability enhances tolerance against ocean acidification stress in Halimeda opuntia

Although the adverse impacts of ocean acidification (OA) on marine calcifiers have been investigated substantially, the anti-stress abilities regulated by increased light availability are unclear. Herein, the interactive effects of three light levels combined with two pCO2 concentrations on the physiological acclimation of the calcifying macroalga Halimeda opuntia were investigated using a pCO2-light coupling experiment. The results indicate that OA exhibits an adverse role in influencing algal growth, calcification, photosynthesis and other physiological performances in H. opuntia. The relative growth rate in elevated pCO2 significantly declined by 13.14%-41.29%, while net calcification rates decreased by nearly three-fold under OA. Notably, increased light availability could enhance stress resistance by the accumulation of soluble organic molecules, especially soluble carbohydrate, soluble protein and free amino acids, and in combination with metabolic enzyme-driven activities alleviated OA stress. Carotenoid content in low light conditions accumulated remarkably and rapid light curves for relative electron transport rate was significantly enhanced by increasing light intensities, indicating that this new organization of the photosynthetic machinery in H. opuntia accommodated light variations and elevated pCO2 conditions. Taken together, the results describe stress resistance by the enhancement of metabolic performance in marine calcifiers to mitigate OA stress. One sentence summaryIncreased light availability enhances stress resistance in Halimeda opuntia by the accumulation of soluble organic molecules and enzyme-driven activities to alleviate ocean acidification stress. Credit authorship contribution statementFangfang Yang and Lijuan Long conceived and designed the experiments. Zhangliang Wei performed the experiments and wrote the paper. Yuanzi Huo analyzed the data, while Chao Long and Yating Zhang contributed materials and analysis tools. Lijuan Long agrees to serve as the author responsible for contact and communication. HighlightsO_LIElevated pCO2 adversely affects the physiological performance of Halimeda. C_LIO_LIModerately high light increases soluble organic molecules and enzymatic-driven activities. C_LIO_LIIncreased light availability enables H. opuntia to alleviate the negative effects of ocean acidification. C_LI

plant biology↗

bioRxiv2020

Mitochondria fragment and reassemble to initiate the formation and development of the nucleus

The function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).

cell biology↗

bioRxiv2020

Converting Escherichia coli MG1655 into a chemical overproducer through inactivating defense system against exogenous DNA

Escherichia coli strain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency and plasmid instability. Herein, we conducted genetic modifications at a serial of loci of MG1655 genome, generating a robust and universal host strain JW128 with higher transformation efficiency and plasmid stability that can be used to efficiently produce desired chemicals after introducing the corresponding synthetic pathways. Using JW128 as the host, the titer of isobutanol reached 5.76 g/L in shake-flask fermentation, and the titer of lycopene reached 1.91 g/L in test-tube fermentation, 40-fold and 5-fold higher than that of original MG1655, respectively. These results demonstrated JW128 is a promising chassis for high-level production of value-added chemicals.

genetics↗

bioRxiv2020

Immunity-and-Matrix-Regulatory Cells Derived from Human Embryonic Stem Cells Safely and Effectively Treat Mouse Lung Injury and Fibrosis

Lung injury and fibrosis represent the most significant outcomes of severe and acute lung disorders, including COVID-19. However, there are still no effective drugs to treat lung injury and fibrosis. In this study, we report the generation of clinical-grade human embryonic stem cells (hESCs)-derived immunity- and matrix-regulatory cells (IMRCs) produced under good manufacturing practice (GMP) requirements, that can treat lung injury and fibrosis in vivo. We generate IMRCs by sequentially differentiating hESCs with serum-free reagents. IMRCs possess a unique gene expression profile distinct from umbilical cord mesenchymal stem cells (UCMSCs), such as higher levels of proliferative, immunomodulatory and anti-fibrotic genes. Moreover, intravenous delivery of IMRCs inhibits both pulmonary inflammation and fibrosis in mouse models of lung injury, and significantly improves the survival rate of the recipient mice in a dose-dependent manner, likely through paracrine regulatory mechanisms. IMRCs are superior to both primary UCMSCs and FDA-approved pirfenidone, with an excellent efficacy and safety profile in mice and monkeys. In light of public health crises involving pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), our findings suggest that IMRCs are ready for clinical trials on lung disorders.

cell biology↗

bioRxiv2020

Engineering of critical enzymes and pathways for improved triterpenoid biosynthesis in yeast

Triterpenoids represent a diverse group of phytochemicals, widely distributed in the plant kingdom with many biological activities. Recently, the heterologous production of triterpenoids in Saccharomyces cerevisiae has been successfully implemented by introducing various triterpenoids biosynthetic pathways. By engineering related enzymes as well as yeast metabolism, the yield of various triterpenoids is significantly improved from milligram-scale per liter to gram-scale level per liter. This achievement demonstrates that engineering of critical enzymes is considered as a potential strategy to overcome the main hurdles of translation of these potent natural products into industry. Here, we review strategies for designing enzymes to improve the yield of triterpenoids in S. cerevisiae, which is mainly separated into three aspects: 1. elevating the supply of the precursor--2,3-oxidosqualene, 2. optimizing triterpenoid-involved reactions, 3. lowering the competition of the native sterol pathway. And then we provide challenges and prospects on further enhancing the triterpenoid production in S. cerevisiae.

synthetic biology↗

bioRxiv2019

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

Extensive epigenetic reprogramming occurs during preimplantation embryo development and is accompanied by zygotic genome activation (ZGA) and first cell fate specification. Recent studies using single-cell epigenome sequencing techniques have provided global views of the dynamics of different epigenetic layers during this period. However, it remains largely unclear how the drastic epigenetic reprogramming contributes to transcriptional regulatory network. Here, we developed a single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell with improved performance compared to that of earlier techniques. We applied this method to analyze the global dynamics of different molecular layers and their associations in mouse preimplantation embryos. We found that global DNA methylation remodeling facilitates the reconstruction of genetic lineages in early embryos and revealed that the gradual increases in heterogeneity among blastomeres are driven by asymmetric cleavage. Allele-specific DNA methylation pattern is maintained throughout preimplantation development and is accompanied by allele-specific associations between DNA methylation and gene expression in the gene body that are inherited from oocytes and sperm. Through integrated analyses of the collective dynamics between gene expression and chromatin accessibility, we constructed a ZGA-associated regulatory network and revealed coordination among multiple epigenetic layers, transcription factors (TFs) and repeat elements that instruct the proper ZGA process. Moreover, we found that inner cell mass (ICM)/trophectoderm (TE) lineage-associated cis-regulatory elements are stepwise activated in blastomeres during post-ZGA embryo stages. TE lineage-specific TFs play dual roles in promoting the TE program while repressing the ICM program, thereby separating the TE lineage from the ICM lineage. Taken together, our findings not only depict the first single-cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during mouse preimplantation development but also enhance the fundamental understanding of epigenetic regulation in early embryos.

developmental biology↗