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

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

JOURNAL=Frontiers in Genetics

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1023041

DOI=10.3389/fgene.2022.1023041

ISSN=1664-8021

ABSTRACT=Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of mammalian early embryonic development. However, in pig, it is seldom investigated. Here, to annotate full-length RNA transcripts, we performed the annotation by a new developed computational pipeline, termed RNA-seq and small RNA-seq combined strategy (RSCS), using our previously obtained RNA-seq and small RNA-seq data in porcine oocyte and zygote. Evidenced by the length comparison and the frequency of the core promoter and the polyadenylation signal motifs, the transcripts appear to be full-length. Furthermore, taking advantages of our strategy, we identified a large number of endogenous retrovirus-associated lncRNAs (ERV-lncRNAs), and found some of them were highly expressed in porcine zygote, comparing to oocyte. By the knockdown strategy, two ERV-lncRNAs TCONS_00035465 and TCONS_00031520 were identified to play a potential role in early embryo development of pig, laying a foundation for future research.