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The rumen epithelium of Tibetan sheep plays a critical role in energy metabolism and immune defense; however, its post-transcriptional regulatory mechanisms under high-altitude hypoxia stress remain unclear. In this study, we employed integrated mRNA and miRNA transcriptome sequencing to analyze the adaptive strategies of the rumen epithelium in Tibetan sheep at different altitudes. A total of 2183 differentially expressed genes (DEGs) and 135 differentially expressed miRNAs (DEmiRNAs) were identified. Functional enrichment analysis revealed that DEGs and their target genes were significantly enriched in immune-related pathways such as the NF-κB signaling pathway and cytokine-cytokine receptor interaction, as well as metabolic pathways including oxidative phosphorylation and branched-chain amino acid degradation. Integrated network analysis highlighted key regulatory pairs, including oar-miR-370-3p targeting PCK2 and IL1R2, and novel-miR-781 regulating PIK3R5, suggesting coordinated modulation between mitochondrial homeostasis and immune responses. Specifically, the upregulation of immune genes (CCL19, MADCAM1) and heat shock proteins at TS4500m indicates enhanced mucosal immunity and stress tolerance, while altered expression of metabolic genes reflects a shift in energy substrate utilization. These findings elucidate a complex mRNA-miRNA regulatory network that enables Tibetan sheep to maintain rumen epithelial integrity and energy balance under extreme high-altitude conditions, providing novel insights into the molecular basis of hypoxia adaptation in ruminants.
Pubmed ID: 42278085
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Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
View all literature mentionsCentral online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsThe Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome
View all literature mentionsThe National Natural Science Foundation of China (NSFC) is an organization directly affiliated to the State Council for the management of the National Natural Science Fund. # In accordance with the guiding principles, policies and plans for the development of science and technology in China and by adopting the operating mechanisms for the National Natural Science Fund which conform to the socialism market economic system, NSFC supports basic research and some of applied research, identifies and fosters talented researchers in the realm of science and technology, accelerates the progress of science and technology, and promotes the socioeconomic development in China by giving full play the guidance and coordinating role of the National Natural Science Fund from the central government. # NSFC is in charge of the management of the National Natural Science Fund. It compiles and promulgates the annual Guide to Programs for basic research and some of applied research, handles applications of research projects, and organizes peer review and select the best projects to support. It endeavors to create an academic environment conducive to innovation. # NSFC cooperates with the Ministry of Science and Technology to formulate the principles, policies and plans for the development of basic research in China. When entrusted, it provides consultation and undertakes related assignments on major issues for the development of high technology and applied research in China. # NSFC gives help and support to other Chinese foundations in natural sciences. # NSFC establishes contacts with governmental departments in charge of science and technology, science foundations and related academic organizations in other countries and carries out international cooperation and exchange. # NSFC is responsible for the administration, supervision and guidance of the subordinated bodies. # NSFC undertakes other tasks entrusted by the State Council and the State Leading Group for Science and Technology and Education.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsDatabase of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.
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