Identification and expression analysis of lncRNA in seven organs of Rhinopithecus roxellana

Long noncoding RNA network for lncRNA-mRNA interactions throughout swine estrous cycle reveals developmental and hormonal regulations in reproductive tissues

The mechanism of estrous cycles of pigs should be explored because their reproductive traits are useful for manipulating productivity and solving problems such as infertility. These estrous cycles should be elucidated to understand the complex interactions between various reproductive tissues (including the ovary, oviduct, and endometrium) and the complex range of hormone secretions during estrous cycles. Long non-coding RNAs (lncRNAs) regulate target genes at transcriptional, post-transcriptional, and post-translational regulation levels in various species. However, unlike mRNAs, lncRNAs in pigs have not been sufficiently annotated, and understanding the protein level of coding genes has limitations in determining the mechanism of the reproductive traits of porcine. In this study, the lncRNAs of the porcine ovary, oviduct, and endometrium were investigated on days 0, 3, 6, 9, 12, 15, and 18 of the estrous cycle. In addition, the characteristics and functions of the identified lncRNAs were explored. 19,021 novel lncRNA transcripts were selected, and the comparison of the characteristics of the newly identified lncRNA and mRNA showed that similar to those of previous studies. Four lncRNA networks were chosen through network analysis. The cis-acting genes of lncRNAs included in each network were identified, and expression patterns were compared. The main lncRNAs (XLOC_021792, XLOC_017111, ENSSSCG00000050977, XLOC_000342, ENSSSCG00000050380, ENSSSCG00000045111, XLOC_008338, XLOC_004128, and ENSSSCG00000040267) were determined from the network by considering the cis-acting genes. Specific novel lncRNAs were discovered in the reproductive tissues during the swine estrous cycle, and their time-serial expression dynamics were confirmed. As the main lncRNAs are involved in the development of each reproductive tissue and hormone action, they can be utilized as potential biomarkers to help improve and develop the reproductive traits of pigs.

Identification and characterization of long non-coding RNAs in juvenile and adult skeletal muscle of largemouth bass (Micropterus salmoides)

Long non-coding RNAs (lncRNAs) are a class of transcriptional RNA molecules, which play critical roles in diverse biological processes. However, little is known about the overall expression pattern and roles of lncRNAs in skeletal muscle of largemouth bass (LMB). Here, we constructed two skeletal muscle RNA libraries to find lncRNAs that may involve in the regulation of skeletal muscle development between juvenile and adult LMB. A total of 16,147 lncRNAs and 4611 differentially expressed lncRNAs were identified. Among these identified lncRNAs, 10 lncRNAs were randomly selected to confirm their expression by real-time qPCR both in libraries, which were consistent with the RNA sequencing results. The target mRNAs of lncRNAs were predicted for GO enrichment analysis. Results showed that these targets associated with growth and development of muscle, such as skeletal muscle fiber development, myoblast proliferation and differentiation. Importantly, correlation analysis of lncRNA-miRNA-mRNA regulatory network revealed that several lncRNAs targeted miRNAs which are closely involved in the regulation of muscle development. It is the first time to identify a number of lncRNA that correlate with skeletal muscle development in LMB. Our results not only provide a comprehensive expression profile of muscle lncRNAs in this species, but also provide a theoretical basis for further elaborating genetic regulation mechanism of muscle growth and development, and pave the way for the future molecular assisted breeding in carnivorous fishes.