New long-non coding RNAs related to fat deposition based on pig model

Abstract

Abstract Obesity has been a problem in the last decades since the development of certain technologies has led to a faster pace of life, resulting in nutritional changes. Domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied next-generation sequencing to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), including long non-coding RNAs in Złotnicka White pigs (n=16). Moreover, besides commonly used functional analysis, we applied the Freiburg RNA tool to predict DE lncRNA targets based on calculation hybridisation energy. And in addition, DE lncRNAs were recognized based on information available in databases. The obtained results show that close to 230 gene expressions were found to be dependent on fat content, including 8 lncRNAs. The most interesting was that among identified DE lncRNAs was transcript corresponding to human MALAT1, which was previously considered in the obesity-related context. Moreover, it was determined that in ENSSSCG00000048394, ENSSSCG00000047210, ENSSSCG00000047442 and ENSSSCG00000041577 lncRNAs are contained repeat insertion domains of LncRNAs (RIDLs) considered as important gene expression regulatory elements, and ENSSSCG00000041577 seems to be the host for mir1247(NR_031649.1). The analysis of energy hybridisation between DE lncRNAs and DEGs using the Freiburg IntaRNAv2 tool, including isoforms expressed in AT, showed that ENSSSCG00000047210 lncRNA interacted with the highest number of DEGs and ENSSSCG00000047210 expression was only correlated with positive fat-related DEGs. The functional analysis showed that down-regulated DEGs involved in ECM proteoglycan pathways could be under the control of both positive and negative fat-related lncRNAs. The present study, using pigs as an animal model, expands current knowledge of possible gene expression regulation by lncRNAs in fat tissue and indicates for MALAT1 role in the fat deposition determination, whose function is still often questioned or doubtful.