Haplotype-resolved 3D chromatin architecture of the hybrid pig.

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs.

Tibetan pigs are indigenous to the Qinghai-Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.

Mapping the global, regional, and national burden of diarrheal diseases attributable to unsafe water.

Background: Diarrheal diseases are major contributors to deaths. Data on global and country-specific levels and trends of diarrheal diseases resulting from unsafe water are essential for policymakers to allocate resources. Aims: This study aimed to describe the global, regional, and national spatiotemporal burden of diarrheal diseases resulting from unsafe water exposure. Methods: According to the Global Burden of Disease (GBD) 2019 dataset, deaths, disability-adjusted life years (DALYs) of diarrheal diseases, and their age-standardized rates (ASRs) were analyzed by age and sex in 204 countries and territories. Moreover, the average annual percentage change (AAPC) was estimated by a log-linear regression model to reflect the time trend. The association between ASR of diarrheal diseases due to unsafe water and socio-demographic index (SDI) levels was also analyzed. Results: From 1990 to 2019, the number of deaths and DALYs of diarrheal diseases resulting from unsafe water decreased by 50 and 59%, respectively. Moreover, the ASR of deaths and DALYs also decreased during the study period, with AAPCs of -3.69 (95% CI [95% confidence interval]: -3.91 to -3.47) and - 3.66 (95% CI: -3.8 to -3.52), respectively. High diarrheal diseases resulting from unsafe water occurred mainly in low SDI regions and Africa. Males exhibited greater diarrheal deaths attributable to unsafe water than females, which was contrary to the condition in terms of DALYs. The age-specific burden of diarrheal deaths attributable to unsafe water is concentrated in children younger than 5 years. The AAPCs of the ASR of both deaths and DALYs showed a strong negative correlation with the SDI levels. Conclusion: The current study indicated that the global burden of unsafe water exposure-related diarrheal diseases decreased from 1990 to 2019 and varied significantly according to age, sex, and geographical location. Effective health promotion and health communication strategies and policies should be adopted to prevent and control diarrheal diseases resulting from unsafe water exposure.

Transcriptomic and lipidomic profiling of subcutaneous and visceral adipose tissues in 15 vertebrates.

The storage of lipids as energy in adipose tissue (AT) has been conserved over the course of evolution. However, substantial differences in ATs physiological activities were reported among species. Hence, establishing the mechanisms shaping evolutionarily divergence in ATs transcriptomes could provide a deeper understanding of AT regulation and its roles in obesity-related diseases. While previous studies performed anatomical, physiological and morphological comparisons between ATs across different species, little is currently understood at the molecular phenotypic levels. Here, we characterized transcriptional and lipidomic profiles of available subcutaneous and visceral ATs samples across 15 vertebrate species, spanning more than 300 million years of evolution, including placental mammals, birds and reptiles. We provide detailed descriptions of the datasets produced in this study and report gene expression and lipid profiles across samples. We demonstrate these data are robust and reveal the AT transcriptome and lipidome vary greater among species than within the same species. These datasets may serve as a resource for future studies on the functional differences among ATs in vertebrate species.

Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss.

Using an adult female miniature pig model with diet-induced weight gain/weight loss, we investigated the regulatory mechanisms of three-dimensional (3D) genome architecture in adipose tissues (ATs) associated with obesity. We generated 249 high-resolution in situ Hi-C chromatin contact maps of subcutaneous AT and three visceral ATs, analyzing transcriptomic and chromatin architectural changes under different nutritional treatments. We find that chromatin architecture remodeling underpins transcriptomic divergence in ATs, potentially linked to metabolic risks in obesity development. Analysis of chromatin architecture among subcutaneous ATs of different mammals suggests the presence of transcriptional regulatory divergence that could explain phenotypic, physiological, and functional differences in ATs. Regulatory element conservation analysis in pigs and humans reveals similarities in the regulatory circuitry of genes responsible for the obesity phenotype and identified non-conserved elements in species-specific gene sets that underpin AT specialization. This work provides a data-rich tool for discovering obesity-related regulatory elements in humans and pigs.

Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis.

Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is essential for understanding human-specific metabolic regulation, but the functional importance and evolutionary dynamics of three-dimensional (3D) genome organizations of ATs are not well defined. Here, we compared the 3D genome architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation in ATs at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI), which have not been described previously. We found PEI are much more evolutionarily dynamic with respect to compartmentalization and topologically associating domain. Compared to conserved PEIs, human-specific PEIs are enriched for human-specific sequence, and the binding motifs of their potential mediators (transcription factors) are less conserved. Our data also demonstrated that genes involved in the evolutionary dynamics of chromatin organization have weaker transcriptional conservation than those associated with conserved chromatin organization. Furthermore, the genes involved in energy metabolism and the maintenance of metabolic homeostasis are enriched in human-specific chromatin organization, while housekeeping genes, health-related genes, and genetic variations are enriched in evolutionarily conserved compared to human-specific chromatin organization. Finally, we showed extensively divergent human-specific 3D genome organizations among one subcutaneous and three visceral ATs. Together, these findings provide a global overview of 3D genome architecture dynamics between ATs from human and mammalian models and new insights into understanding the regulatory evolution of human ATs.

Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues.

BACKGROUND: A growing body of evidence has revealed that the mammalian genome is organized into hierarchical layers that are closely correlated with and may even be causally linked with variations in gene expression. Recent studies have characterized chromatin organization in various porcine tissues and cell types and compared them among species and during the early development of pigs. However, how chromatin organization differs among pig breeds is poorly understood. RESULTS: In this study, we investigated the 3D genome organization and performed transcriptome characterization of two adipose depots (upper layer of backfat [ULB] and greater omentum [GOM]) in wild boars and Bama pigs; the latter is a typical indigenous pig in China. We found that over 95% of the A/B compartments and topologically associating domains (TADs) are stable between wild boars and Bama pigs. In contrast, more than 70% of promoter-enhancer interactions (PEIs) are dynamic and widespread, involving over a thousand genes. Alterations in chromatin structure are associated with changes in the expression of genes that are involved in widespread biological functions such as basic cellular functions, endocrine function, energy metabolism and the immune response. Approximately 95% and 97% of the genes associated with reorganized A/B compartments and PEIs in the two pig breeds differed between GOM and ULB, respectively. CONCLUSIONS: We reported 3D genome organization in adipose depots from different pig breeds. In a comparison of Bama pigs and wild boar, large-scale compartments and TADs were mostly conserved, while fine-scale PEIs were extensively reorganized. The chromatin architecture in these two pig breeds was reorganized in an adipose depot-specific manner. These results contribute to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar.

Generation and characterization of stable pig pregastrulation epiblast stem cell lines.

Pig epiblast-derived pluripotent stem cells are considered to have great potential and broad prospects for human therapeutic model development and livestock breeding. Despite ongoing attempts since the 1990s, no stably defined pig epiblast-derived stem cell line has been established. Here, guided by insights from a large-scale single-cell transcriptome analysis of pig embryos from embryonic day (E) 0 to E14, specifically, the tracing of pluripotency changes during epiblast development, we developed an in vitro culture medium for establishing and maintaining stable pluripotent stem cell lines from pig E10 pregastrulation epiblasts (pgEpiSCs). Enabled by chemical inhibition of WNT-related signaling in combination with growth factors in the FGF/ERK, JAK/STAT3, and Activin/Nodal pathways, pgEpiSCs maintain their pluripotency transcriptome features, similar to those of E10 epiblast cells, and normal karyotypes after more than 240 passages and have the potential to differentiate into three germ layers. Strikingly, ultradeep in situ Hi-C analysis revealed functional impacts of chromatin 3D-spatial associations on the transcriptional regulation of pluripotency marker genes in pgEpiSCs. In practice, we confirmed that pgEpiSCs readily tolerate at least three rounds of successive gene editing and generated cloned gene-edited live piglets. Our findings deliver on the long-anticipated promise of pig pluripotent stem cells and open new avenues for biological research, animal husbandry, and regenerative biomedicine.

Allele-specific regulatory effects on the pig transcriptome.

BACKGROUND: Allele-specific expression (ASE) refers to the preferential expression of one allele over the other and contributes to adaptive phenotypic plasticity. Here, we used a reciprocal cross-model between phenotypically divergent European Berkshire and Asian Tibetan pigs to characterize 2 ASE classes: imprinting (i.e., the unequal expression between parental alleles) and sequence dependent (i.e., unequal expression between breed-specific alleles). We examined 3 transcript types, including protein-coding genes (PCGs), long noncoding RNAs, and transcripts of unknown coding potential, across 7 representative somatic tissues from hybrid pigs generated by reciprocal crosses. RESULTS: We identified a total of 92 putative imprinted transcripts, 69 (75.00%) of which are described here for the first time. By combining the transcriptome from purebred Berkshire and Tibetan pigs, we found ∼6.59% of PCGs are differentially expressed between breeds that are regulated by trans-elements (e.g., transcriptional factors), while only ∼1.35% are attributable to cis (e.g., promoters). The higher prevalence of trans-PCGs indicates the dominated effects of trans-regulation in driving expression differences and shaping adaptive phenotypic plasticity between breeds, which were supported by functional enrichment analysis. We also found strong evidence that expression changes mediated by cis-effects were associated with accumulated variants in promoters. CONCLUSIONS: Our study provides a comprehensive map of expression regulation that constitutes a valuable resource for the agricultural improvement of pig breeds.

Upregulation of deubiquitinase USP7 by transcription factor FOXO6 promotes EC progression via targeting the JMJD3/CLU axis.

Esophageal carcinoma (EC) is recognized as one of the most frequently occurring malignancies worldwide, and its high morbidity rate motivates efforts to identify potential therapeutic targets. Notably, forkhead box (FOX) family genes are highlighted as possible biomarkers for diagnostics, prognostics, and therapeutics of various malignancies, including EC. Our present study was performed to investigate the underlying mechanism of FOXO6 on the development of EC. We observed a significant upregulation of FOXO6 in EC tissues, contributing to the migration and proliferation in EC cells through gain- and loss-of-function assays. FOXO6 directly interacted with the ubiquitin-specific processing protease 7 (USP7) gene promoter and enhanced its transcriptional activity, which resulted in suppressed cancer cell apoptosis as revealed by chromatin immunoprecipitation (ChIP)-qPCR. USP7 enhanced the ubiquitination of Jumonji domain-containing protein D3 (JMJD3), elevated JMJD3-promoted growth of EC cells, and transcriptionally activated clusterin (CLU) expression at the promoter region via histone H3 lysine 27 tri-methyl (H3K27me3) demethylation, according to immunoprecipitation and ubiquitination assays. Finally, we verified that FOXO6 mediated effects on the USP7/JMJD3/CLU axis to exert an oncogenic role in vivo, which was blocked by USP7 and JMJD3 inhibitor. Our findings demonstrate an important role of the FOXO6/USP7/JMJD3/CLU pathway in EC progression and thus provide attractive potential therapeutic targets for EC patients.

Silencing of long non-coding RNA LINC01270 inhibits esophageal cancer progression and enhances chemosensitivity to 5-fluorouracil by mediating GSTP1methylation.

Esophageal cancer (EC) is a serious digestive malignancy which remains the sixth leading cause of cancer-related deaths worldwide. Emerging evidence suggests the involvement of long non-coding RNAs (lncRNAs) in the tumorigenesis of EC and thus, in this study we explored the potential effects of lncRNA LINC01270 on EC cell proliferation, migration, invasion and, drug resistance via regulation of glutathione S-transferase P1 (GSTP1) methylation. First, we screened out the EC-related differentially expressed lncRNAs, and the expression of our top candidate LINC01270 was quantified in EC tissues and cells. To define the role of LINC01270 in EC progression, we evaluated the proliferation, migration and invasion of EC cells when the LINC01270 was overexpressed or knocked down, in the presence of the GSTP1 methylation inhibitor SGI-1027 and 5-fluorouracil (5-FU). In addition, interaction between LINC01270 and methylation of the GSTP1 promoter was identified. Finally, we assessed transplantable tumor growth in nude mice. LINC01270 was up-regulated and GSTP1 was down-regulated in EC tissues and cells. Silencing of LINC01270 inhibited migration and invasion, and enhanced the sensitivity of 5-FU in EC cells. We found that LINC01270 recruited the DNA methyltransferases DNMT1, DNMT3A and DNMT3B initiating GSTP1 promoter methylation, thereby leading to the proliferation, migration, invasion and drug resistance of EC cells. Moreover, GSTP1 overexpression was observed to reverse the effects of LINC01270 overexpression on EC cells and their response to 5-FU. Taken together, this study shows that inhibition of LINC01270 can lead to suppression of EC progression via demethylation of GSTP1, highlighting this lncRNA as a potential target for EC treatment.

Current Situation of Methamphetamine Abuse and Related Research Progress.

Drug problem is a major social and public security problem in the world. Drug abuse poses a great threat to economic development, social stability and public health. In recent years, synthetic drugs represented by methamphetamine have surpassed traditional drugs such as morphine, heroin, ketamine and become one of the most abused drugs in the world. In order to solve the problem of drug abuse, it is of great theoretical value and practical significance to carry out all-round and multi-level scientific research on drug-related issues. Based on the current situation of drug abuse, this article reviews research progresses on the epidemiology of methamphetamine abuse, the monitoring technology, the basic researches on toxicity damage, the withdrawal drug screening, the related clinical comorbidity and the testing technologies, comprehensively presenting the development trend of methamphetamine abuse related issues.

Endoscopic Esophageal Submucosal Tunnel Dissection for Cystic Lesions Originating from the Muscularis Propria of the Gastric Cardia.

OBJECTIVE: To analyze the types and properties of cystic lesions originating from the muscularis propria of the gastric cardia (CLMPGC), explore the growth pattern and anatomical characteristics, and evaluate the safety, feasibility, and clinical efficacy of endoscopic esophageal submucosal tunnel dissection (ESTD). METHODS: From September 2013 to July 2018, we treated 6 patients with CLMPGC whom we had diagnosed using endoscopy, endoscopic ultrasound (EUS), and Computed Tomography (CT) before the operations. ESTD was the best option for treatment for all these patients. Postoperative observation and follow-ups were performed, and the operational, clinical data, and treatment results are analyzed. RESULTS: The mean age of the patients was 50.67 ± 11.59 years (male : female = 1 : 1). The only clinical manifestations the patients exhibited were upper abdominal discomfort. The diameter of the masses was 2.05 ± 0.73 (1.1-3.0) cm. The duration of the ESTD operation was 93.5 (82-256) mins, and the length of hospital stay was 7.50 ± 1.38 days. Postoperative pathology showed 4 cases of an epithelioid cyst, and 2 cases of mucocele with xanthogranuloma. There were no complications, such as hemorrhage, pneumothorax, and pleural effusion during and after the operation. No recurrence during the follow-ups was observed. CONCLUSION: The CLMPGC were mainly mucocele and epidermoid cyst, in an expansive growth pattern, and these lesions had no distinct borders with the muscularis propria. The muscularis propria formed a complete wall of the lesion. There was no direct blood supply to the lesions from big blood vessels. Endoscopic esophageal submucosal tunnel dissection was a safe, feasible, and effective treatment for CLMPGC.

Circular RNA-hsa-circ-0000670 promotes gastric cancer progression through the microRNA-384/SIX4 axis.

Circular RNAs (circRNAs), a special type of non-coding RNA molecules, have been addressed to be implicated in gastric cancer progression. The GSE93541 and GSE83521 microarrays found hsa-circRNA-000670 (hsa-circ-0000670) as an up-regulated circRNAin gastric cancer. We mainly investigated the function and molecular mechanisms of hsa-circ-0000670 involved in gastric cancer. The expression of hsa-circ-0000670 was determined by RT-qPCR to be highly expressed in gastric cancer tissues relative to corresponding adjacent normal tissues, as well as in gastric cancer cell lines relative to normal gastric mucosal epithelial cell line. By conducting EdU, scratch test and Transwell assays, hsa-circ-000670 was found to be a tumor promoter by potentiating the proliferative, invasive and migrating capabilities of gastric cancer cells. Consistently, a tumor-promotive role of hsa-circ-000670 was validated in vivo. Dual-luciferase reporter gene and RIP assays identified the binding of hsa-circ-0000670 to microRNA-384 (miR-384) and the binding of miR-384 to sine oculis-related homeobox 4 (SIX4). The oncogenic potential of hsa-circ-0000670 in gastric cancer cells were inhibited by overexpressed miR-384. Mechanistically, SIX4 was targeted by miR-384 and was upregulated in gastric cancer. High SIX4 expression was suggested to correlate with the poor prognosis of gastric cancer patients. Additionally, silencing of SIX4 delayed tumor growth and progression, which were reversed by overexpression of hsa-circ-0000670. Taken together, hsa-circ-0000670 acts as a tumor promotor in gastric cancer progression and might be a potential target for gastric cancer treatment.

Endoscopic Submucosal Dissection of the Angiolipoma at Hypopharynx-Esophageal Introitus.

Angiolipoma in the region of the hypopharynx-esophageal introitus is a rare occurrence. Surgical treatment was performed in the few cases reported in the literature. Endoscopic submucosal dissection (ESD) is a minimally invasive treatment for hypopharyngeal and esophageal lesions. Our objective was to evaluate the feasibility, safety, and efficacy of ESD for treatment of angiolipoma at the hypopharynx-esophageal introitus. The patients with submucosal tumors at the hypopharynx-esophageal introitus were diagnosed as angiolipoma by preoperative evaluation with endoscopy, endoscopic ultrasonography, and computed tomography (CT). The patients who were diagnosed with angiolipoma agreed to undergo endoscopic submucosal dissection. Under general anesthesia and endotracheal intubation, ESD was used to remove the lesions. Preoperative, intraoperative, and postoperative data were collected and analyzed to evaluate the feasibility, safety, and effectiveness of endoscopic submucosal dissection. From January 2013 to December 2018, 6 cases of angiolipoma were treated with ESD with a success rate of 100%. The average operation time was 107.0 ± 69.4 minutes. Intraoperative blood loss is the main risk. Endoscopic thermocoagulation successfully stopped bleeding in all cases. Pharyngeal pain and painful swallowing were the main clinical signs. There was no stricture at the hypopharynx-esophageal introitus after the operation. ESD treatment of angiolipoma at hypopharynx-esophageal introitus is feasible, safe, and effective.

Knockdown of ST7-AS1 inhibits migration, invasion, cell cycle progression and induces apoptosis of gastric cancer.

Role of ST7-AS1 in the malignant progression of gastric cancer (GC) and its molecular mechanisms were investigated. ST7-AS1 level in GC tissues and matched normal tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Its level in GC patients presenting different tumor stages and tumor sizes was determined. Subsequently, ST7-AS1 level in epithelial cells of gastric mucosa and GC cell lines was examined. Cellular behavior of GC cells, including viability, apoptosis, migration, invasion and cell cycle, influenced by ST7-AS1 was evaluated. The interaction between ST7-AS1 and EZH2 was assessed by RNA immunoprecipitation (RIP) assay. The involvement of EZH2 in the progression of GC mediated by ST7-AS1 was identified. ST7-AS1 was upregulated in GC tissues and cell lines. Its level was positively correlated to tumor stage and tumor size of GC. Knockdown of ST7-AS1 attenuated proliferative, migratory and invasive abilities, arrested cell cycle progression and induced apoptosis of GC cells. EZH2 was identified to interact with ST7-AS1, which attenuated the regulatory effects of ST7-AS1 on migratory and invasive abilities of GC cells. Upregulated ST7-AS1 in GC accelerated proliferation, migration and invasion, and inhibited apoptosis, thus aggravating the progression of GC.

Transcriptional Differences of Coding and Non-Coding Genes Related to the Absence of Melanocyte in Skins of Bama Pig.

Skin is the body's largest organ, and the main function of skin is to protect underlying organs from possible external damage. Melanocytes play an important role in skin pigmentation. The Bama pig has a "two-end-black" phenotype with different coat colors across skin regions, e.g., white skin (without melanocytes) and black skin (with melanocytes), which could be a model to investigate skin-related disorders, specifically loss of melanocytes. Here, we generated expression profiles of mRNAs and long noncoding RNAs in Bama pig skins with different coat colors. In total, 14,900 mRNAs and 7549 lncRNAs were expressed. Overall, 2338 mRNAs/113 lncRNAs with FDR-adjusted p-value ≤ 0.05 were considered to be differentially expressed (DE) mRNAs/lncRNAs, with 1305 down-regulated mRNAs and 1033 up-regulated mRNAs in white skin with|log2(fold change)| > 1. The genes down-regulated in white skin were associated with pigmentation, melanocyte-keratinocyte interaction, and keratin, while up-regulated ones were mainly associated with cellular energy metabolisms. Furthermore, those DE lncRNAs were predicted to be implicated in pigmentation, keratin synthesis and cellular energy metabolism. In general, this study provides insight into the transcriptional difference involved in melanocyte-loss-induced keratinocyte changes and promotes the Bama pig as a biomedical model in skin research.

Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs.

Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules to control gene expression. However, studies on the NATs of pigs are relatively rare. Here, we identified a novel antisense transcript, designated PLA2G16-AS, transcribed from the phospholipase A2 group XVI locus (PLA2G16) in the porcine genome, which is a well-known regulatory molecule of fat deposition. PLA2G16-AS and PLA2G16 were dominantly expressed in porcine adipose tissue, and were differentially expressed between Tibetan pigs and Rongchang pigs. In addition, PLA2G16-AS has a weak sequence conservation among different vertebrates. PLA2G16-AS was also shown to form an RNA-RNA duplex with PLA2G16, and to regulate PLA2G16 expression at the mRNA level. Moreover, the overexpression of PLA2G16-AS increased the stability of PLA2G16 mRNA in porcine cells. We envision that our findings of a NAT for a regulatory gene associated with lipolysis might further our understanding of the molecular regulation of fat deposition.

Long non-coding RNAs and mRNAs profiling during spleen development in pig.

Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development.