Long noncoding RNAs (lncRNAs) have various biological functions and have been extensively studied in recent years. However, the identification and characterization of bovine lncRNAs in skeletal muscle has been very limited compared with that of lncRNAs in other model organisms. In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as a shorter open reading frame and lower expression level than for mRNAs. Furthermore, the chromosomal locations and global expression patterns for these lncRNAs are also described in detail. More importantly, we detected the important interaction relationships of lncRNAs-miRNAs-mRNAs related to muscle development among 36 lncRNAs, 62 miRNAs and 12 mRNAs. Our results provide a global expression pattern of lncRNAs specific to bovine skeletal muscle and provide important targets for revealing the function of bovine muscle development by thoroughly studying the interaction relationships of lncRNAs-miRNAs-mRNAs.
miRNAs are a class of hairpin-derived RNAs, 21-24 nucleotides in length, which are involved in a range of biological processes. The bta-miR-2285 family has over 40 members spanning the entire bovine genome. We previously found that bta-miR-2285o-3p was highly expressed in yak heart and lung when compared with cattle, which prompted us to investigate its potential function in high-altitude adaptation of yaks. In this study, we detected wide-spread high expression of bta-miR-2285o-3p in yak tissues. Further experiments revealed that the protein tyrosine phosphatase receptor type M (PTPRM) gene was the host gene of bta-miR-2285o-3p and that two linked SNPs in bta-mir-2285o precursor affected the biogenesis of mature miRNA (bta-miR-2285o-3p). Functional analysis in vitro indicated that bta-miR-2285o-3p attenuated hypoxia-induced apoptosis by targeting very low-density lipoprotein receptor (VLDLR), phosphatase and tensin homolog (PTEN) and caspase-3. Expression level analysis in vivo revealed the high negative Pearson's correlation between bta-miR-2285o-3p and caspase3 in yak, highlighting the potential important roles of bta-miR-2285o-3p in yak high-altitude adaptation. Our study provides a typical model for deciphering the function of miRNAs in environmental adaptation.
Bamboo belongs to subfamily Bambusoideae of the grass family and is one of the most important non-timber forest resources in the world. The AP2/ERF superfamily is a group of plant specific transcription factors and plays important roles in the regulation of plant growth and responses to biotic and abiotic stress. By comprehensively analyzing the recently uncovered whole genome sequence and full length cDNA of moso bamboo (Phyllostachys edulis), 142 AP2/ERF transcription factors were identified and 53 among them are supported by full length cDNA. Compared with a recent report on the identification of 116 AP2/ERF transcription factors from the P. edulis genome, our study identified ~22% more AP2/ERF transcription factors. Phylogenetic analysis based on the sequence of the AP2/ERF domain assigned 23 genes to the AP2 family, 7 to the RAV family, 64 genes to the ERF subfamily, and 47 to the DREB subfamily, respectively. A soloist divergent from others was also found. The further multiple sequence alignment of the AP2/ERF domain, phylogenetic analysis and motif recognition were performed and revealed conserved residues, similarities and evolution relationship of members in each family or subfamily. The ortholog relationship and colinearity between P. edulis and O. sativa were analyzed. Additionally, 36 duplicates of orthologs in O. sativa genome were identified, which may originate from the whole genome duplication. Despite of the ortholog duplication, the gene numbers in groups A5, B3, and B6 are significantly lower than those in O. sativa and A. thaliana, and the A3 group is missing, suggesting potential gene loss of these groups during species divergence. This study provides more knowledge of AP/ERF genes in P. edulis.
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