Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information.

The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and produces the best results in a large-scale protein dynamics dataset; this model can accurately infer the dynamic information of a protein in only a few seconds. By learning effectively from experimental protein structure data and cryo-electron microscopy (cryo-EM) data integration, our approach is able to accurately identify the interactive bidirectional constraints and supervision between cryo-EM maps and PDB models in maximizing the dynamic prediction efficacy. Rigorous 5-fold cross-validation on the dataset demonstrates that RMSF-net achieves test correlation coefficients of 0.746 ± 0.127 at the voxel level and 0.765 ± 0.109 at the residue level, showcasing its ability to deliver dynamic predictions closely approximating molecular dynamics simulations. Additionally, it offers real-time dynamic inference with minimal storage overhead on the order of megabytes. RMSF-net is a freely accessible tool and is anticipated to play an essential role in the study of protein dynamics.

HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.

A CRISPR/Cas9 screen in embryonic stem cells reveals that Mdm2 regulates totipotency exit.

During early embryonic development, the transition from totipotency to pluripotency is a fundamental and critical process for proper development. However, the regulatory mechanisms governing this transition remain elusive. Here, we conducted a comprehensive genome-wide CRISPR/Cas9 screen to investigate the 2-cell-like cells (2CLCs) phenotype in mouse embryonic stem cells (mESCs). This effort led to the identification of ten regulators that play a pivotal role in determining cell fate during this transition. Notably, our study revealed Mdm2 as a significant negative regulator of 2CLCs, as perturbation of Mdm2 resulted in a higher proportion of 2CLCs. Mdm2 appears to influence cell fate through its impact on cell cycle progression and H3K27me3 epigenetic modifications. In summary, the results of our CRISPR/Cas9 screen have uncovered several genes with distinct functions in regulating totipotency and pluripotency at various levels, offering a valuable resource for potential targets in future molecular studies.

The preparation of edible water-soluble films comprising κ-carrageenan/carboxymethyl starch/gum ghatti and their application in instant coffee powder packaging.

This study successfully prepared an edible packaging film that rapidly dissolves in water by utilizing a combination of κ-carrageenan, carboxymethyl starch, and gum ghatti. We investigated the influence of these three materials on the microstructure and physical properties of the film, as well as the impact of the film's dissolution on the stability of beverages. SEM, FTIR, and XRD analyses revealed that the κ-carrageenan, carboxymethyl starch, and gum ghatti primarily interacted through hydrogen bonding, resulting in a more uniform and dense film structure. Surface hydrophilicity and swelling tests indicated an increased presence of hydrophilic groups in the composite film. The inclusion of carboxymethyl starch and gum ghatti significantly improves the film's physical properties, resulting in a notable reduction in water solubility time, an increase in elongation at break from 19.5 % to 26.0 %, a rise in the contact angle from 49.1° to 67.0°, and a decrease in water vapor permeability from 7.5 × 10-10 to 6.2 × 10-10 g/m·s·Pa. Furthermore, coffee packaging bags made from this composite film dissolved entirely in hot water in just 40 s. Dissolving these bags significantly improved the stability of instant coffee, reducing centrifugal sedimentation from 3.8 % to 1.7 %. This study highlights the substantial potential of the κ-carrageenan/carboxymethyl starch/gum ghatti composite film as a packaging material for solid beverages.

Integrated Lactylome Characterization Reveals the Molecular Dynamics of Protein Regulation in Gastrointestinal Cancers.

Lysine lactylation (Kla) plays a vital role in several physiological processes. However, the cancer-specific modulation of Kla in gastrointestinal (GI) tumors requires systematic elucidation. Here, global lactylome profiling of cancerous and adjacent tissues is conducted from 40 patients with GI cancer and identified 11698 Kla sites. Lactylome integration revealed that Kla affects proteins involved in hallmark cancer processes, including epigenetic rewiring, metabolic perturbations, and genome instability. Moreover, the study revealed pan-cancer patterns of Kla alterations, among which 37 Kla sites are consistently upregulated in all four GI cancers and are involved in gene regulation. It is further verified that lactylation of CBX3 at K10 mediates its interaction of CBX3 with the epigenetic marker H3K9me3 and facilitates GI cancer progression. Overall, this study provides an invaluable resource for understanding the lactylome landscape in GI cancers, which may provide new paths for drug discovery for these devastating diseases.

In Situ Polymerized Zwitterionic Copolymer Ionic Gel Electrolytes with High Performance for Lithium-Ion Batteries.

Gel electrolytes are a promising research direction due to their high safety. However, its poor room temperature conductivity along with complex preparation process hinder its practical application. In this article, a type of zwitterionic gel electrolyte is prepared by in situ polymerization. The introduction of charged but nonmigrating zwitterionic copolymer in the polymer chain is beneficial to the dissociation of the lithium salt, improving the ion transport of the electrolyte on this account. At room temperature, the conductivity of lithium ion reaches 9.1 × 10-4 S cm-1, which contributes to achieve excellent electrochemical performance at high rates. The assembled Li|LiFePO4 cell also shows a capacity retention rate of 90.5% after 150 cycles at 0.5 C at room temperature as well as remarkable cycle stability at 1 C. These offer a novel tactic for the efficient and safe commercial application of lithium-ion batteries.

Analysis of risk factors and construction of a prediction model for posttraumatic stress disorder among Chinese college students during the COVID-19 pandemic.

BACKGROUND: To explore the risk factors of post-traumatic stress disorder (PTSD) among Chinese college students during the COVID-19 pandemic and the construction and validation of risk prediction models. METHODS: A total of 10,705 university students were selected for the study. The questionnaire included the Generalized Anxiety Disorder 7 (GAD-7), Patient Health Questionnaire 9 (PHQ-9), PTSD Checklist for DSM-5 (PCL-5), and self-designed questionnaire. These assessments were conducted to facilitate the survey, construct the predictive model and validate the model's validity. RESULTS: Sex, left-behind experience, poverty status, anxiety score, and depression score were identified as independent risk factors influencing psychological trauma among Chinese college students during the COVID-19 pandemic, while COVID-19 infection emerged as a protective factor against psychological trauma. A column chart was constructed to visualize the six independent risk factors derived from logistic regression analysis. The Hosmer-Lemeshow test results (χ2 = 13.021, P = 0.111) indicated that the risk prediction model fitted well. The receiver operating characteristic (ROC) curve showed an area under the curve (AUC) of 0.864 in the model group and 0.855 in the validation group. The calibration curves of the model closely resembled the ideal curve. Decision curve analysis (DCA) revealed that the model provided net benefit and demonstrated good clinical utility. LIMITATIONS: The validation of the model is currently restricted to internal assessments. However, further confirmation through larger sample sizes, multicenter investigations, and prospective studies is necessary. CONCLUSIONS: The model effectively predicted PTSD risk among Chinese college students during the COVID-19 pandemic, indicating strong clinical applicability.

Dress me an outfit: advanced probiotics hybrid systems for intelligent IBD therapy.

Inflammation bowel disease (IBD) has emerged as a public health challenge worldwide; with high incidence and rapid prevalence, it has troubled billions of people and further induced multitudinous systemic complications. Recent decade has witnessed the vigorous application of food-borne probiotics for IBD therapy; however, the complicated and changeable environments of digestive tract have forced probiotics to face multiple in vivo pressures, consequently causing unsatisfied prophylactic or therapeutic efficacy attributed to off-targeted arrival, damaged viability, insufficient colonization efficiency, etc. Fortunately, arisen hybrid technology has provided versatile breakthroughs for the targeted transplantation of probiotics. By ingeniously modifying probiotics to form probiotics hybrid systems (PHS), the biological behaviors of probiotics in vivo could be mediated, the interactions between probiotics with intestinal components can be facilitated, and diverse advanced probiotic-based therapies for IBD challenge can be developed, which attribute to the intelligent response to microenvironment of PHS, and intelligent design of PHS for multiple functions combination. In this review, various PHS were categorized and their intestinal behaviors were elucidated systematically, their therapeutic effects and intrinsic mechanism were further analyzed. Besides, shortages of present PHS and the corresponding solutions have been discussed, based on which the future perspectives of this field have also been proposed. The undeniable fact is that PHS show an incomparable future to bring the next generation of advanced food science.

Dressing probiotics with versatile outfits would impart them with extended functions, including elevated targeted efficiency to the nidi, controlled in situ release, enhance intestinal colonization, comprehensive microecology regulation, and so on. In this article, we systematically analyzed and categorized PHS for intelligent IBD therapy published in recent decade, and discussed their pros and cons to further raise the future orientation for PHS development.

Insufficient Plasma Melatonin and Its Association With Neuropsychiatric Impairments in Patients With T2DM.

Purpose: Type 2 diabetes mellitus (T2DM) is associated with multiple neuropsychiatric impairments, including cognitive dysfunction, and melatonin (MLT) plays a crucial role in maintaining normal neuropsychiatric functions. This study is aimed at investigating the change in plasma MLT levels and its association with neuropsychiatric impairments in T2DM patients. Methods: One hundred twenty-six T2DM patients were recruited, and their demographics and clinical data were collected. Apart from the plasma glycated hemoglobin (HbA1c) levels and other routine metabolic indicators, the plasma concentrations of MLT, C-reactive protein (CRP), Interleukin 6 (IL-6), soluble myeloid triggered receptor 1 (sTREM 1), and receptor 2 (sTREM 2) were measured. Moreover, the executive function and depressive tendency were evaluated via the Behavior Rating Inventory of Executive Function-Adult Version (BRIEF-A) and the Epidemiological Research Center Depression Scale (CES-D), respectively. Result: Compared with the low HbA1c group, the T2DM patients in the high HbA1c group presented lower plasma MLT levels but higher plasma concentrations of inflammatory biomarker levels, together with higher scores in the BRIEF-A and CES-D scales. Moreover, results of the Pearson correlation test showed that the plasma MLT levels were negatively correlated with the BRIEF-A and CES-D scores, as well as plasma concentrations of HbA1c and inflammatory indications, indicating that MLT may mediate their neuroinflammation and neuropsychiatric impairments. Furthermore, the ROC curve results indicated that plasma MLT levels have a predictive effect on executive impairment and depressive status in T2DM patients. Conclusion: MLT levels decreased in patients with T2DM and were associated with neuropsychiatric impairments and inflammatory status, and MLT might be developed as a therapeutic agent and predictive indicator for T2DM-associated executive impairment and depression status.

Clinical study of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in hypertriglyceridemia-induced acute pancreatitis and acute biliary pancreatitis with persistent organ failure.

BACKGROUND: The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are novel inflammatory indicators that can be used to predict the severity and prognosis of various diseases. We categorize acute pancreatitis by etiology into acute biliary pancreatitis (ABP) and hypertriglyceridemia-induced acute pancreatitis (HTGP). AIM: To investigate the clinical significance of NLR and PLR in assessing persistent organ failure (POF) in HTGP and ABP. METHODS: A total of 1450 patients diagnosed with acute pancreatitis (AP) for the first time at Shanxi Bethune Hospital between January 2012 and January 2023 were enrolled. The patients were categorized into two groups according to the etiology of AP: ABP in 530 patients and HTGP in 241 patients. We collected and compared the clinical data of the patients, including NLR, PLR, and AP prognostic scoring systems, within 48 h of hospital admission. RESULTS: The NLR (9.1 vs 6.9, P < 0.001) and PLR (203.1 vs 160.5, P < 0.001) were significantly higher in the ABP group than in the HTGP group. In the HTGP group, both NLR and PLR were significantly increased in patients with severe AP and those with a SOFA score ≥ 3. Likewise, in the ABP group, NLR and PLR were significantly elevated in patients with severe AP, modified computed tomography severity index score ≥ 4, Japanese Severity Score ≥ 3, and modified Marshall score ≥ 2. Moreover, NLR and PLR showed predictive value for the development of POF in both the ABP and HTGP groups. CONCLUSION: NLR and PLR vary between ABP and HTGP, are strongly associated with AP prognostic scoring systems, and have predictive potential for the occurrence of POF in both ABP and HTGP.

Epitaxial Integration of Transferable High-κ Dielectric and 2D Semiconductor.

The synthesis of high-dielectric-constant (high-κ) dielectric materials and their integration with channel materials have been the key challenges in the state-of-the-art transistor architecture, as they can provide strong gate control and low operating voltage. For next-generation electronics, high-mobility two-dimensional (2D) layered semiconductors with dangling-bond-free surfaces and an atomic-thick thickness are being explored as channel materials to achieve shorter channel lengths and less interfacial scattering. Nowadays, the integration of high-κ dielectrics with high-mobility 2D semiconductors mainly relies on atomic layer deposition or transfer stacking, which may cause several undesirable problems, such as channel damage and interface traps. Here, we demonstrate the integration of high-mobility 2D semiconducting Bi2O2Se with transferable high-κ SrTiO3 as a 2D field-effect transistor by direct epitaxial growth. Remarkably, such 2D heterostructures can be efficiently transferred from the water-soluble Sr3Al2O6 sacrificial layer onto arbitrary substrates. The as-fabricated 2D Bi2O2Se/SrTiO3 transistors exhibit an on/off ratio over 104 and a subthreshold swing down to 90 mV/dec. Furthermore, the 2D Bi2O2Se/SrTiO3 heterostructures can be easily transferred onto flexible polyethylene terephthalate (PET) substrates, and the as-fabricated transistors exhibit good potential in flexible electronics. Our study opens up a new avenue for the integration of high-κ dielectrics with high-mobility 2D semiconductors and paves the way for the exploration of multifunctional electronic devices.

Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.

Intergeneric hybridization greatly reshapes regulatory interactions among allelic and non-allelic genes. However, their effects on growth diversity remain poorly understood in animals. In this study, we conducted whole-genome sequencing and RNA sequencing (RNA-seq) analyses in diverse hybrid varieties resulting from the intergeneric hybridization of goldfish (Carassius auratus red var.) and common carp (Cyprinus carpio). These hybrid individuals were characterized by distinct mitochondrial genomes and copy number variations. Through a weighted gene correlation network analysis, we identified 3693 genes as candidate growth-regulated genes. Among them, the expression of 3672 genes in subgenome R (originating from goldfish) displayed negative correlations with growth rate, whereas 20 genes in subgenome C (originating from common carp) exhibited positive correlations. Notably, we observed intriguing patterns in the expression of slc2a12 in subgenome C, showing opposite correlations with body weight that changed with water temperatures, suggesting differential interactions between feeding activity and weight gain in response to seasonal changes for hybrid animals. In 40.31% of alleles, we observed dominant trans-regulatory effects in the regulatory interaction between distinct alleles from subgenomes R and C. Integrating analyses of allelic-specific expression and DNA methylation data revealed that the influence of DNA methylation on both subgenomes shapes the relative contribution of allelic expression to the growth rate. These findings provide novel insights into the interaction of distinct subgenomes that underlie heterosis in growth traits and contribute to a better understanding of multiple allele traits in animals.

Storage protein SfSP8 mediates larval starvation tolerance of Spodoptera frugiperda.

BACKGROUND: Energy homeostasis is vital for insects to survive food shortages. This study investigated the starvation tolerance of Spodoptera frugiperda, which invaded China in 2019, focusing on its storage protein family, crucial for energy balance. 10 storage protein family members were identified and their expression patterns at different development stages and under different starvation stress were analyzed. METHODS AND RESULTS: We used qPCR to evaluate the expression levels of storage protein family members under various larval instars and starvation conditions. We discovered that, among above 10 members, only 2 storage proteins, SfSP8 and SfSP7 showed significant upregulation in response to starvation stress. Notably, SfSP8 upregulated markedly after 24 h of fasting, whereas SfSP7 exhibited a delayed response, with significant upregulation observed only after 72 h of starvation. Then we significantly reduced the starvation tolerance of larvae through RNAi-mediated knockdown of SfSP8 and also altered the starvation response of SfSP7 from a late to an early activation pattern. Finally, we constructed transgenic Drosophila melanogaster with heterologous overexpressing SfSP8 revealed that the starvation tolerance of the transgenic line was significantly stronger than that of wild-type lines. CONCLUSIONS: SfSP8 was the core storage protein member that mediated the starvation tolerance of larvae of S. frugiperda. Our study on the novel function of storage proteins in mediating larval starvation tolerance of S. frugiperda is conducive to understanding the strong colonization of this terrible invasive pest.

Comparison of early postoperative patient-reported outcomes after multiportal robotic-assisted thoracoscopic surgery and uniportal video-assisted thoracoscopic surgery for non-small cell lung cancer.

INTRODUCTION: We aimed to compare early postoperative patient-reported outcomes between multiportal robotic-assisted thoracoscopic surgery (M-RATS) and uniportal video-assisted thoracoscopic surgery (U-VATS) for non-small-cell lung cancer (NSCLC). MATERIALS AND METHODS: Symptom severity and functional status were measured using the Perioperative Symptom Assessment for Lung Surgery at pre-surgery, during postoperative hospitalisation, and within 4 weeks of discharge. A propensity score-matched (PSM) analysis of patients with NSCLC who were treated with M-RATS and U-VATS was performed. The symptom severity and daily functional status presented as proportion of moderate-to-severe scores on a 0-10-point scale, were compared using a generalised estimation equation model. RESULTS: We enrolled 762 patients with NSCLC from a prospective cohort (CN-PRO-Lung 3), including 151 and 611 who underwent M-RATS and U-VATS, respectively, before PSM analysis. After 1:1 PSM, two groups of 148 patients each were created. Pain severity (P = 0.019) and activity limitation (P = 0.001) during hospitalisation were higher in the M-RATS group. However, no significant differences existed post-discharge in pain (P = 0.383), cough (P = 0.677), shortness of breath (P = 0.526), disturbed sleep (P = 0.525), drowsiness (P = 0.304), fatigue (P = 0.153), distress (P = 0.893), walking difficulty (P = 0.242), or activity limitation (P = 0.513). M-RATS caused less intraoperative blood loss (P = 0.013), more stations of dissected lymph nodes (P = 0.001), more numbers of dissected lymph nodes (P = 0.001), and less tube drainage on the first postoperative day (P = 0.003) than U-VATS. CONCLUSION: M-RATS and U-VATS achieved comparable symptom burden and functional impairment after discharge. However, compared to U-VATS, M-RATS was associated with more severe pain and activity limitation in the short postoperative period. TRIAL REGISTRATION NUMBER: ChiCTR2000033016.

Electroencephalographic insights into the pathophysiological mechanisms of emergence delirium in children and corresponding clinical treatment strategies.

Emergence delirium is a common postoperative complication in patients undergoing general anesthesia, especially in children. In severe cases, it can cause unnecessary self-harm, affect postoperative recovery, lead to parental dissatisfaction, and increase medical costs. With the widespread use of inhalation anesthetic drugs (such as sevoflurane and desflurane), the incidence of emergence delirium in children is gradually increasing; however, its pathogenesis in children is complex and unclear. Several studies have shown that age, pain, and anesthetic drugs are strongly associated with the occurrence of emergence delirium. Alterations in central neurophysiology are essential intermediate processes in the development of emergence delirium. Compared to adults, the pediatric nervous system is not fully developed; therefore, the pediatric electroencephalogram may vary slightly by age. Moreover, pain and anesthetic drugs can cause changes in the excitability of the central nervous system, resulting in electroencephalographic changes. In this paper, we review the pathogenesis of and prevention strategies for emergence delirium in children from the perspective of brain electrophysiology-especially for commonly used pharmacological treatments-to provide the basis for understanding the development of emergence delirium as well as its prevention and treatment, and to suggest future research direction.

PRIORITI: Phase 4 study of triptorelin or active surveillance in high-risk prostate cancer.

AIM: To evaluate the efficacy and safety of triptorelin after radical prostatectomy (RP) in patients with negative lymph nodes. METHODS: PRIORITI (NCT01753297) was a prospective, open-label, randomized, controlled, phase 4 study conducted in China and Russia. Patients with high-risk (Gleason score ≥ 8 and/or pre-RP prostate-specific antigen [PSA] ≥ 20 ng/mL and/or primary tumor stage 3a) prostate adenocarcinoma without evidence of lymph node or distant metastases were randomized to receive triptorelin 11.25 mg at baseline (≤ 8 weeks after RP) and at 3 and 6 months, or active surveillance. The primary endpoint was biochemical relapse-free survival (BRFS), defined as the time from randomization to biochemical relapse (BR; increased PSA > 0.2 ng/mL). Patients were monitored every 3 months for at least 36 months; the study ended when 61 BRs were observed. RESULTS: The intention-to-treat population comprised 226 patients (mean [standard deviation] age, 65.3 [6.4] years), of whom 109 and 117 were randomized to triptorelin or surveillance, respectively. The median BRFS was not reached. The 25th percentile time to BRFS (95% confidence interval) was 39.1 (29.9-not estimated) months with triptorelin and 30.0 (18.6-42.1) months with surveillance (p = 0.16). There was evidence of a lower risk of BR with triptorelin versus surveillance but this was not statistically significant at the 5% level (p = 0.10). Chemical castration was maintained at month 9 in 93.9% of patients who had received triptorelin. Overall, triptorelin was well tolerated and had an acceptable safety profile. CONCLUSION: BRFS was observed to be longer with triptorelin than surveillance, but the difference was not statistically significant.

Enhanced Ferromagnetism and Tunable Magnetic Anisotropy in a van der Waals Ferromagnet.

2D van der Waals (vdW) magnets have recently emerged as a promising material system for spintronic device innovations due to their intriguing phenomena in the reduced dimension and simple integration of magnetic heterostructures without the restriction of lattice matching. However, it is still challenging to realize Curie temperature far above room temperature and controllable magnetic anisotropy for spintronics application in 2D vdW magnetic materials. In this work, the pressure-tuned dome-like ferromagnetic-paramagnetic phase diagram in an iron-based 2D layered ferromagnet Fe3GaTe2 is reported. Continuously tunable magnetic anisotropy from out-of-plane to in-plane direction is achieved via the application of pressure. Such behavior is attributed to the competition between intralayer and interlayer exchange interactions and enhanced DOS near the Fermi level. The study presents the prominent properties of pressure-engineered 2D ferromagnetic materials, which can be used in the next-generation spintronic devices.

Diagnosis and Treatment of Presumed Naltrexone-XR-precipitated Opioid Withdrawal in a Patient Chronically Treated With Buprenorphine-XR: A Case Report.

ABSTRACT: Naltrexone, buprenorphine, and methadone are Food and Drug Administration-approved medications for the treatment of opioid use disorder in the United States. Naltrexone, an opioid antagonist, can precipitate opioid withdrawal if administered too quickly after the use of full or partial opioid agonists for those with either dependence or use disorder. We describe a case of severe precipitated opioid withdrawal syndrome after reported buprenorphine extended-release (XR) administration, despite the patient having been stable on buprenorphine-XR for several years, with no missed doses or recent opioid use. Naltrexone levels were sent and helped to diagnose suspected inadvertent naltrexone-XR administration in this patient, which was likely the etiology of his precipitated opioid withdrawal syndrome. We suggest the use of high-dose buprenorphine, as well as adjunctive medications including benzodiazepines, as a treatment strategy for naltrexone-XR precipitated withdrawal in the setting of chronic buprenorphine-XR treatment.

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.