Xiangyang Miao

Sheep production is vital to the global agricultural economy, particularly for meat and wool. However, fertility varies significantly among breeds, influenced by genetics, nutrition, and environment. MicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression, binding to target messenger RNAs (mRNAs) to inhibit translation or trigger degradation. Despite their importance, little is known about ovary-specific miRNAs and their target genes in high and low fecundity sheep breeds. Here, we investigated miRNA expression profiles in ovarian tissues from Small Tail Han (high fecundity) and Dolang sheep (low fecundity) using miRNA sequencing. The analysis identified 51 significantly differentially expressed miRNAs (DEmiRNAs), with only nine mapping to the reference genome (including oar-miR-103, oar-miR-16b). We predicted 88,699, 176,629, and 240,753 target mRNAs for these DEmiRNAs from sheep, goat, and cow, respectively. Functional enrichment analysis revealed significant biological processes and signaling pathways potentially associated with fecundity. Subsequently, we constructed a DEmiRNA-mRNA regulatory network, highlighting candidate miRNA-mRNA pairs like chi-miR-130a-3p-WNT2B, oar-miR-103-FSHR, and oar-miR-16b-AMH. These findings provide insights into the potential regulators of sheep fecundity. We further validated these candidate miRNA-mRNA interactions using qRT-PCR to explore their roles in regulating sheep fecundity. Overall, this study utilized miRNA sequencing to analyze ovarian miRNA expression in sheep and identified potential miRNA-mRNA targets associated with fecundity. This lays the foundation for future research on the molecular mechanisms underlying sheep ovarian physiology and improving reproductive traits.

Background Low fertility is considered the major constraint in sheep rearing industry depending on several factors like, estrus cycle, ovulation rate and litter size but fecundity of ewe plays a key role in sheep reproduction, influenced by several intrinsic and extrinsic factors. However, genetic improvements of traits associated with reproduction through conventional breeding is a very complex and slow process. In current study, we went through a comprehensive integration of high throughput transcriptomic and metabolomics approaches to understand the role of key regulatory genes and metabolites in fecundity of two different and widely raised sheep breeds (Small Tail Han & Dolang) in different regions of China. Result UPLC/MS/MS system based metabolomic profiling of ovarian tissue from both breeds results into the identification of 1,423 metabolites, including 542 DEMs (379 upregulated and 163 downregulated). Integration of metabolomics and transcriptomics data identified 48 pathways contributed by 37 genes and 85 metabolites through regulatory network analysis. Functional enrichment analysis showed significantly enriched pathways associated with fecundity including Riboflavin metabolism, xenobiotics, bile acid biosynthesis, and Drug metabolism, which produces hormones for regulation of ovarian function, ovulation, and establishment of pregnancy. Further, analyzed two restrictive constrained plots analyzed via multivariate statistical analysis. In one plot complement component C3 associated with Leukotriene D4, and Uridine 5’-diphosphate involved in the processes of Neuroactive legend receptor interaction pathway and in second plot IFNGR1 associated with Progesterone, Fumaric acid, and Cortisone involved in the processes of cancer pathway and any disruptions in hormonal balance may induce cancer, which can affect fertility, menstrual cycles, and overall reproductive health. Conclusion Expression profiling, functional enrichments, co-expression network analysis and integrated transcriptomemetabolome data showed gene-metabolite association in energy metabolism, Inflammation, and drug metabolism, all of which play a role in ovarian physiology and ovarian metabolic disorders. Identification and validation of genes, metabolites, and gene-metabolite interactions will help to elucidate the regulatory mechanisms and pathways underlying sheep fecundity and could be leveraged to improve reproductive traits.

Circular RNAs (circRNAs), as important non-coding RNAs (ncRNAs), are involved in many biological activities. However, the exact chemical mechanism behind fat accumulation is unknown. In this paper, we obtained the expression profiles of circRNAs using high-throughput sequencing and investigated their differential expression in subcutaneous fat tissue of Duolang and Small Tail Han sheep. From the transcriptomic analysis, 141 differentially expressed circRNAs were identified, comprising 61 up-regulated circRNAs and 80 down-regulated circRNAs. These host genes were primarily enriched in the MAPK and AMPK signaling pathways which is closely associated with fat deposition regulation. We identified circRNA812, circRNA91, and circRNA388 as vital genes in fat deposition by miRNA-circRNA target gene prediction. The functional annotation results of target genes of key circRNAs showed that the signaling pathways mainly included PI3K-Akt and AMPK. We constructed the competing endogenous RNA (ceRNA) regulatory network to study the role of circRNAs in sheep lipid deposition, and circRNA812, circRNA91, and circRNA388 can adsorb more miRNAs. NC_040253.1_5757, as the source of miRNA response element (MRE) among the three, may play an important role during the process of sheep fat deposition. Our study gives a systematic examination of the circRNA profiles expressed in sheep subcutaneous fat. These results from this study provide some new basis for understanding circRNA function and sheep fat metabolism.

Reproductive traits play a vital role in determining the production efficiency of sheep. Maximizing the production is of paramount importance for breeders worldwide due to the growing population. Circular RNAs (circRNAs) act as miRNA sponges by absorbing miRNA activity through miRNA response elements (MREs) and participate in ceRNA regulatory networks (ceRNETs) to regulate mRNA expression. Despite of extensive research on role of circRNAs as miRNA sponges in various species, their specific regulatory roles and mechanism in sheep ovarian tissue are still not well understood. In this study, we performed whole genome sequencing of circRNAs, miRNA and mRNA employing bioinformatic techniques on ovine tissues of two contrasting sheep breeds "Small tail Han (X_LC) and Dolang sheep (D_LC)", which results into identification of 9,878 circRNAs with a total length of 23,522,667 nt and an average length of 2,381.32 nt. Among them, 44 differentially expressed circRNAs (DECs) were identified. Moreover, correlation between miRNA-mRNA and lncRNA-miRNA provided us with to prediction of miRNA binding sites on nine differentially expressed circRNAs and 165 differentially expressed mRNAs using miRanda. miRNA-mRNA and lncRNA-miRNA pairs with negative correlation were selected to determine the ceRNA score along with positively correlated pairs from lncRNA and mRNA network. Integration of ceRNA score and positively correlated pairs exhibit a significant ternary relationship among circRNAs-miRNA-mRNA demonestrated by ceRNA, comprising of 50 regulatory pairs sharring common nodes and predicted potential differentially expressed circRNAs-miRNAs-mRNAs regulatory axis. Based on functional enrichment analysis shortlisted key ceRNA regulatory pairs associated with reproduction including circRNA_3257-novel579_mature-EPHA3, circRNA_8396-novel130_mature-LOC101102473, circRNA_4140- novel34_mature > novel661_mature-KCNK9, and circRNA_8312-novel339_mature-LOC101110545. Furthermore, expression profiling, functional enrichments and qRT-PCR analysis of key target genes infer their implication in reproduction and metabolism. ceRNA target mRNAs evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations following genomic organizations will provide new insights underlying molecular mechanisms of reproduction, and establish a solid foundation for future research. Graphical Abstract Graphical abstract summarizing the scheme of study

Introduction: Titanium Dioxide (TiO2) has gained a lot of focus in today’s world owing to its wide usage in several industries. The hazardous effects of TiO2 and its nanoparticles are also slowly revealing. The need for a proper cure of these toxic effects is of utmost importance. Due to its few side effects, medicinal plants can be an efficient source of remedy but are least considered compared to synthetic medicines. Cinnamomum cassia and Azadirachta indica are the most common of such medicinal plants used extensively in Pakistan and India. In this study, we carried out experiments to know the toxic effects of TiO2 nanoparticles in kidneys using a murine model and observed the ameliorating effects of Cinnamomum cassia and Azadirachta indica on the toxicity of TIO2 nanoparticles.Methods: Rats were given a subcutaneous injection of TiO2 nanoparticles at the dose of 150mg/kg body weight for 28 days along with oral administration of Cinnamomum cassia and Azadirachta indica alone and in combination.Results and Discussion: Both Cinnamomum cassia and Azadirachta indica at doses of 100 or 150mg/kg reduced the toxic effects of TiO2 nanoparticles evident from reduced alterations in kidney histopathology and also decreased DNA damage.Conclusion: It was concluded that Cinnamomum cassia and Azadirachta indica showed remedial or healing effects against nephrotoxicity in rats exposed to TiO2 sublethal doses.

Background Circular RNAs (circRNAs), as important non-coding RNAs (ncRNAs), are involed in many biological activities. However, the exact chemical mechanism behind fat accumulation is unknown. In this paper, we obtained the expression profiles of circRNAs using high-throughput sequencing and investigated their differential expression in subcutaneous fat tissue of Duolang and Small Tail Han sheep. Results From the transcriptomic analysis, 141 differentially expressed circRNAs were identified, comprising 61 up-regulated circRNAs and 80 down-regulated circRNAs. These host genes were primarily enriched in the MAPK and AMPK signaling pathway which is closely associated with fat deposition regulation. We identified circRNA812, circRNA91, and circRNA388 as vital genes in fat deposition by miRNA-circRNA target gene prediction. The functional annotation results of target genes of key circRNAs showed that the signaling pathways mainly included PI3K-Akt and AMPK. We constructed the ceRNA regulatory network to study the role of circRNAs in sheep lipid deposition, and circRNA812, circRNA91, and circRNA388 can adsorb more miRNAs. NC_040253.1_5757, as the source of miRNA response element (MRE) among the three, may play an important role during the process of sheep fat deposition. Conclusions Our study gives a systematic examination of the circRNA profles expressed in sheep subcutaneous fat. These results from this study provide some new basis for understanding circRNA function and sheep fat metabolism.

Background: Long non-coding RNAs (lncRNAs) regulate adipocyte differentiation and metabolism, However, their function on subcutaneous and intramuscular adipose tissues in pigs is unclear. Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), which severely affects the meat rate of pigs. It is of great significance for porcine breeding to study the mechanism of lncRNA related to adipogenesis and lipid metabolism.Methods: We identified differentially expressed lncRNAs, miRNAs and mRNAs in subcutaneous and intramuscular adipose tissues in three female Laiwu pigs by deep RNA-sequencing(|log2foldchange|≥1, P_value ≤ 0.05). The gene expression profiles of IMF and SCF in Laiwu pigs were comparatively analyzed by Bioinformatics methods to identify key lncRNAs, miRNAs, and mRNAs associated with lipid metabolism and adipogenesis.Results: A total of 1209 lncRNAs (DElncRNAs), 286 miRNAs (DEmiRNAs), and 1597 mRNAs (DEgenes) were differentially expressed between two types of adipose. Among them, 17 DElncRNAs and 103 target genes play a role in the co-expression network, as well as 59 DElncRNAs, 44 DEmiRNAs, and 88 DEgenes involved in ceRNA network. In GO(Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DElncRNAs their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as PPAR signaling pathway, Wnt signaling pathway, MAPK signaling pathway.Conclusions: By constructing co-expression and ceRNAs network we found that Wnt signaling pathway play a critical regulatory role in intramuscular adipogenesis and lipid accumulation in Laiwu pigs. TCONS_00006525, TCONS_00046551 and TCONS_00000528 may target WNT5A, WNT10B and FDZ3 in co-expression network, TCONS_00026517 and other lncRNAs regulate the expression of PPARG, RXRG and SCD in ceRNA network, and were involved in Wnt signaling pathway. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation, predicting and treating diseases caused by ectopic fat.

CircRNAs, as miRNA sponges, participate in many important biological processes. However, it remains unclear whether circRNAs can regulate lipid metabolism. This study aimed to explore the competing endogenouse RNA (ceRNA) regulatory network that affects the difference between intramuscular fat (IMF) and subcutaneous fat (SCF) deposition, and to screen key circRNAs and their regulatory genes. In this experiment, we identified 265 differentially expressed circRNAs, of which 187 up-regulated circRNA and 78 down-regulated circRNA in IMF. Subsequently, we annotated the function of DEcircRNA's host genes, and found that DEcircRNA's host genes were mainly involved in GO terms (including cellular response to fatty acids, lysophosphatidic acid acyltransferase activity, R-SMAD binding, etc.) and signaling pathways (fatty acid biosynthesis, Citrate cycle, TGF- β Signal pathway) related to adipogenesis, differentiation and lipid metabolism. By constructing a circRNA-miRNA network, we screened out DEcircRNA that can competitively bind to more miRNAs as key circRNAs (circRNA_06424 and circRNA_08840). Through the functional annotation of indirect target genes and protein network analysis, we found that circRNA_06424 affects the expression of PPARD, MMP9, UBA7 and other indirect target genes by competitively binding to miRNAs such as ssc-miR-339-5p, ssc-miR-744 and ssc-miR-328, and participates in PPAR signaling pathway, Wnt signaling pathway, unsaturated fatty acid and other signaling pathways, resulting in the difference of fat deposition between IMF and SCF. This study provide a theoretical basis for further research investigating the differences of lipid metabolism in different adipose tissues, providing potential therapeutic targets for ectopic fat deposition and lipid metabolism diseases.