Long Non-Coding RNAs Differentially Expressed in Swine Fetuses

Simple Summary Long non-coding RNAs (lncRNAs) are a type of RNA that does not produce proteins but plays crucial roles in diverse metabolic processes, including cellular development and differentiation, the regulation of protein production, the inactivation of genes and chromosomes, and gamete formation. Despite their recognized importance, there is a limited understanding of how these molecules function in pigs, particularly during fetal development. For this reason, we conducted this exploratory work, in which we aimed to identify and characterize potential novel lncRNAs in the initial fetal phase of pigs. We have not only identified potentially new lncRNAs but also identified that some of them have sex-specific expression. In the current study, hundreds of potential and already described lncRNAs were identified This allows for the expansion of our knowledge about genomics and transcriptomics in pigs, while also providing novel RNA sequences for the genomic databases of these species. This is particularly important as we are providing data for the international community regarding a research theme that is at its early stages. The potential novel lncRNAs identified in our study provide a basis for future research on their biological functions in a highly important livestock species.Abstract Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, especially during early fetal development. Therefore, we conducted this exploratory study aiming to identify, characterize, and investigate the differential expression of lncRNAs between male and female swine fetuses at 35 days of gestation. RNA-Seq libraries from 10 fetuses were prepared and sequenced using the Illumina platform. After sequencing, a data quality control was performed using Trimmomatic, alignment with HISAT2, and transcript assembly with StringTie. The differentially expressed lncRNAs were identified using the limma package of the R software (4.3.1). A total of 871 potentially novel lncRNAs were identified and characterized. Considering differential expression, eight lncRNAs were upregulated in male fetuses. One was mapped onto SSC12 and seven were located on the Y chromosome; among them, one lncRNA is potentially novel. These lncRNAs are involved in diverse functions, including the regulation of gene expression and the modulation of chromosomal structure. These discoveries enable future studies on lncRNAs in the fetal stage in pigs.