Tracing of Porcine lncRNA MALAT1 Shaped by Tissue Localisation and Adipogenesis

Background: The long non-coding RNA MALAT1 is known to regulate various cellular processes; however, its role in porcine adipose tissue remains largely unexplored. Methods: In this study, we examined MALAT1 in pigs differing in fat-deposition traits by combining promoter sequencing, in silico analysis of transcription factor binding site analysis, expression profiling, and in vitro adipogenesis assays. Results: We identified three novel polymorphisms in the MALAT1 promoter regions. Several SNPs were predicted to alter binding sites for transcription factors related to metabolism and immunity, such as NFAT5, NFATC1, and BCL6B. One variant, rs329590882, differed significantly in frequency between breeds and may influence MALAT1 regulation. During adipocyte differentiation, expression of the MALAT1 isoform ENSSSCT00000080860 increased as adipogenesis progressed. Notably, this isoform was more highly expressed in lean-type Pietrain pigs than in the fatty Złotnicka Spotted (ZS) breed, suggesting that its function may not be directly related to fat accumulation. Additionally, we identified novel exon-exon junctions in MALAT1, including a junction associated with the ENSSSCT00000077869 isoform. Conclusions: These findings provide new insights into the potential role of MALAT1 in porcine adipose tissue development and immunometabolic regulation and highlight the need for improved annotation of porcine lncRNAs.