An atlas of DNA methylomes in porcine adipose and muscle tissues

It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth

Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives

Abstract Background: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings: We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression–based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions: These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments

MicroRNAome of Porcine Pre- and Postnatal Development

The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies

Hemoglobin: Kinetics of ligand binding and conformational change

Functional properties of two very unusual invertebrate hemoglobins, Artemia salina, and Paramphistomum epiclitum (P.E.), have been investigated through their ligand binding kinetics and equilibria. The conformational change of dimeric Artemia hemoglobin ($\alpha\beta,$ 9 heme domains per chain) is best described by a three-state model, $\rm R\rightarrow S\rightarrow T,$ revealed from CO binding kinetics. The rate constant for $\rm R\rightarrow S$ was too fast to be measured, whereas $\rm S\rightarrow T$ is very slow, 3.5 sec\sp{-1}, about 10,000 times slower than the $\rm R\rightarrow T$ change for human hemoglobin. The nanosecond geminate reactions for O\sb2 and NO are both biphasic; for CO the reaction was not detectable. In terms of the MWC allosteric model for oxygen binding, c = 0.046, L = 5.9 x 10\sp5, and n = 6 sites. P.E. hemoglobin has extraordinarily high affinity for oxygen, K\rm\sb{d}=0.5 nM, and a low CO/O\sb2 partition constant (0.062) at 20\sp\circC. The protein appears to have very different conformations for bound CO and O\sb2. Oxygen binding is favored over CO as the temperature decreases. The effects of the 2,4 vinyl groups on the heme periphery of horse Hb for geminate CO recombination and for the kinetics of the $\rm R\rightarrow T$ conformational change were compared with corresponding kinetics for horse deutero-, meso- and dibromohemoglobins. In the nanosecond time regime, the immediate CO recombination rate constant, k\sb2, for protoHb is much smaller than for the modified Hbs, but there were no large differences among the other rate constants. For each Hb, Arrhenius parameters were used in a global fitting for four rate constants to data at five different temperatures. The observed $\rm R\rightarrow T$ conformational change in the native and modified horse Hbs was very well simulated by an allosteric model together with linear free energy relations for the \rm R\ \sbsp{\to}{\gets}\ T equilibria. The modifications on the heme decrease the energy barrier for $\rm R\rightarrow T$ since protoHb has the highest activation energy. Except for protoHb, the transition state equilibrium constant, K\sp\ddagger, correlates well with the sizes of the substituents. The $\rm R\rightarrow T$ transition states of the modified Hbs appear very nearly R-like

Durability and Improvement of Cement-Based Revetment Materials Serving in Subtidal, Intertidal, and Supratidal Environments

To improve the durability of cement-based revetment materials serving in different positions relative to the water level, slag powder and polypropylene fibers were added into cement to prepare paste, mortar, and concrete. Based on three simulated experiments of high-humidity air, dry–wet cycles-coupled chloride erosion, and complete immersion-coupled chloride erosion, the half-year durability of cement-based revetment materials was investigated. An abundant amount of Ettringite containing chloride was formed in the pores of the cement, and its formation was accelerated by dry–wet cycles. Replacing 30% of cement by slag powder and adding 0.1 vol.% of polypropylene fibers helped concrete in the intertidal zone to obtain a compressive strength of 47.58 MPa after erosion, equal to 159% of the reference. Slag powder was found to induce cement to form Friedel’s salt and C-S-H with a more amorphous structure, increasing its chemical binding ability and physical adsorption ability to chloride ions, and reduce the chloride ions’ penetration depth of concrete from 22.5 to 12.6 mm. Polypropylene fibers controlled the direction of surface cracks to be perpendicular to the specimen’s sides. These findings lay a foundation for the design of high-durability cement-based revetment materials serving in costal environments

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

Lnc<i>PLAAT3</i>-AS Regulates <i>PLAAT3</i>-Mediated Adipocyte Differentiation and Lipogenesis in Pigs through miR-503-5p

Animal fat deposition has a significant impact on meat flavor and texture. However, the molecular mechanisms of fat deposition are not well understood. LncPLAAT3-AS is a naturally occurring transcript that is abundant in porcine adipose tissue. Here, we focus on the regulatory role of lncPLAAT3-AS in promoting preadipocyte proliferation and adipocyte differentiation. By overexpressing or repressing lncPLAAT3 expression, we found that lncPLAAT3-AS promoted the transcription of its host gene PLAAT3, a regulator of adipocyte differentiation. In addition, we predicted the region of lncPLAAT3-AS that binds to miR-503-5p and showed by dual luciferase assay that lncPLAAT3-AS acts as a sponge to absorb miR-503-5p. Interestingly, miR-503-5p also targets and represses PLAAT3 expression and helps regulate porcine preadipocyte proliferation and differentiation. Taken together, these results show that lncPLAAT3-AS upregulates PLAAT3 expression by absorbing miR-503-5p, suggesting a potential regulatory mechanism based on competing endogenous RNAs. Finally, we explored lncPLAAT3-AS and PLAAT3 expression in adipose tissue and found that both molecules were expressed at significantly higher levels in fatty pig breeds compared to lean pig breeds. In summary, we identified the mechanism by which lncPLAAT3-AS regulates porcine preadipocyte proliferation and differentiation, contributing to our understanding of the molecular mechanisms of lipid deposition in pigs

Genotype data of Chenghua pigs and Neijiang pigs.

The genotype datasets of 21 Chenghua pigs and 49 Neijiang pigs.</p