Frontiers in Genetics (Oct 2022)

Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq

  • Xu Yang,
  • Jingzhang Ji,
  • Hongdi Cui,
  • Qi Zhao,
  • Chunming Ding,
  • Chang Xu

DOI
https://doi.org/10.3389/fgene.2022.1023041
Journal volume & issue
Vol. 13

Abstract

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Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of early embryonic development in mammals. However, they are seldom investigated in pigs. Here, to annotate full-length RNA transcripts, we performed annotation using a newly developed computational pipeline—an RNA-seq and small RNA-seq combined strategy—using our previously obtained RNA-seq and small RNA-seq data from porcine oocytes and zygotes. As evidenced by the length comparison, the frequency of the core promoter, and the polyadenylation signal motifs, the transcripts appear to be full-length. Furthermore, our strategy allowed the identification of a large number of endogenous retrovirus-associated lncRNAs (ERV-lncRNAs) and found that some of them were highly expressed in porcine zygotes, as compared to oocytes. Through the knockdown strategy, two ERV-lncRNAs (TCONS_00035465 and TCONS_00031520) were identified as playing potential roles in the early embryo development of pigs, laying a foundation for future research.

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