Identification and functional predication of long non-coding rnas in rainbow trout and cattle

The simplest definition of a long noncoding RNA (lncRNA) is an RNA transcript larger than 200 nucleotides that does not encode for a functional protein product. This definition distinguishes lncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs) and other short RNAs. They have emerged as a new class of regulatory transcripts in recent years. Recent advances in sequencing technologies have opened a new horizon for the identification and annotation of this class of RNAs in many species. With the increasing evidence supporting important roles of lincRNAs in diverse processes, a systematic catalog of these RNA transcripts and their expression across tissues in rainbow trout is warranted. Here we report the systematic identification and characterization of lincRNAs in 15 major tissue types of rainbow trout. We analyzed the known genomic features of the identified lincRNAs including transcript length, exon number and spatiotemporal expression specificity. We also used weighted gene co-expression network to assign functionalities to the lincRNAs, which revealed that lincRNAs are expressed in a strong tissue-specific manner, and many of them are highly associated with biological processes specific to that tissue.;Reproductive phases in rainbow trout is crucial as the energy expenditure to address the synthesis and release of oocytes is taxing. Skeletal muscle during reproductive phase act as an endogenous source to address the energy demand, compromising muscle quality. Reduced muscle quality in turn results in reduced fillet and egg quality. Reproduction in female fish starts with the release of steroid hormone estrogen initiating synthesis of vitellogenin in liver. Estrogen (E2) is a steroid hormone that negatively affects muscle growth and protein homeostasis in rainbow trout but the mechanisms associated with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of normal and E2 treated rainbow trout. A total of 226 lncRNAs and 253 mRNAs were identified. We identified crucial pathways, including several signal transduction pathways, hormone response, oxidative response and protein, carbon and fatty acid metabolism pathways. Subsequently, functional lncRNA-mRNA co-expression network was constructed, which consisted of 681 co-expression relationship between 164 lncRNAs and 201 mRNAs. Moreover, an lncRNA-pathway network was constructed. A total of 65 key lncRNAs were identified, which regulate 20 significantly enriched pathways. Finally, the function of a novel lncRNA (lnc-OM9822) was predicted, which may be activated by estrogen receptor alpha (ER1) and involve in the estrogen-signaling pathway. Overall, our analysis not only effectively provides insights into the mRNA and lncRNA association with the effect of E2 on skeletal muscle in rainbow trout, but also provides further insights into understanding the molecular mechanism of lncRNAs.;We also performed ab initio assembly of more than 80 million RNA-Seq reads from bovine oocytes, and identified 1,535 transcribed lncRNAs from 1,183 loci. In addition, by comparing with previous studies and NONCODE database, we found 115 (7.6%) of our lincRNAs overlap with previously reported bovine lncRNAs in NONCODE database and 565 reported in previous studies. Furthermore, we calculated the tissue specificity score for each oocyte lincRNA. The results indicate that the majority of oocyte lincRNAs (80%) are tissue-specific. Finally, the predicted function of oocyte specific lincRNAs suggested the involvement of bovine oocyte lincRNAs in oogenesis through regulating their neighboring protein-coding genes

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

Non-protein coding RNAs (ncRNAs) have emerged as a vast and heterogeneous portion of eukaryotic transcriptomes. Several ncRNA families, either short (200 nt), have been described and implicated in a variety of biological processes, from translation to gene expression regulation and nuclear trafficking. Most probably, other families are still to be discovered. Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes. Indeed, primary sequence alone is often insufficient to infer ncRNA functionality, whereas secondary structure and local conservation of portions of the transcript could provide useful information for both the prediction and the functional annotation of ncRNAs. Here we present an overview of computational methods and bioinformatics resources currently available for studying ncRNA genes, introducing the common themes as well as the different approaches required for long and short ncRNA identification and annotation