Differential and Tissue-specific Expression of Novel Long Intergenic Noncoding RNAs in Equine Trophectoderm and Inner Cell Mass

Long noncoding RNAs (lncRNAs) are increasingly implicated as regulators of important events in early development, including maintenance of pluripotency, modification of epigenetic marks, and activation of transcription. Characterization of lncRNAs in equine blastocysts will provide new insight into how such transcripts may regulate developmental fates of the trophectoderm (TE) and inner cell mass (ICM). Additionally, it could help identify loci outside of protein coding genes that might contribute to variation in complex traits related to pregnancy and offspring health outcomes. The objective of this study was to identify novel long intergenic noncoding RNAs (lincRNAs) in TE and ICM cells from d8 expanded blastocysts using RNA sequencing. Transcripts from a publicly-available dataset were assembled ab initio and filtered for mapping quality and nucleotide length. Sequences determined to encode known or predicted proteins were eliminated from further analysis. A total of 17,826 uniquely mapped lincRNAs were identified in either lineage. Subsequent analysis revealed 706 transcripts that were found exclusively among all replicates (n=3) of TE, while 141 transcripts were unique to all replicates of ICM. Seventy-six transcripts found in all samples were differentially expressed; 27 were up-regulated in TE, and 52 were up-regulated in ICM. These results provide the first comprehensive list of lincRNAs in equine tissue, and suggest possible functional relevance of these novel transcripts in regulation of early embryonic development.