College of Animal Science, Yangtze University, Jingzhou, Hubei, China.
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
Reprod Domest Anim. 2022 Jan;57(1):111-122. doi: 10.1111/rda.14034. Epub 2021 Nov 8.
Long non-coding RNAs (lncRNAs) function through multiple tiers of molecular circuits and are vital to gamete maturation and early embryo development. However, in pig early embryos, identification and expression dynamics of lncRNAs remain less studied. Here, we systematically analysed the expression dynamics of lncRNAs based on our previously published single-cell RNA-seq data from pig mature oocytes (GSE160334), and single blastomeres biopsied from pig in vitro fertilized (IVF) and early parthenogenetically activated (PA) embryos (1- to 8-cell stages; GSE164812). With the progression of embryo development, the total number of expressed lncRNAs gradually decreased and showed great variation at each developmental stage for both IVF and PA groups. Consecutive stage pairwise comparison of MII oocytes, 1-cell zygotes, 2-cell, 4-cell and 8-cell IVF embryos identified 151, 245, 1119 and 188 differentially expressed (DE) lncRNAs, including 119, 80, 867, 77 up-regulated and 32, 165, 252, 111 down-regulated, while 289, 437, 895 and 495 DE lncRNAs (141, 89, 768, 97 up-regulated and 148, 348, 127, 398 down-regulated) were identified in PA embryos at the same stages. The DE lncRNAs identified within IVF embryos were much different from that identified within PA embryos, showing embryo type-specific manner. Further cross-comparison between PA and IVF embryos identified 184, 656, 2502 and 266 DE lncRNAs for the 1- to 8-cell embryo stages, respectively. Further GO and KEGG enrichment analysis of DE mRNAs targeted by DELs indicated that different signalling pathways were involved in maternal-only and bi-parental embryo development. Collectively, comparative profiling of lncRNA expression dynamics between pig IVF and PA embryos provides a valuable resource, to investigate further regulatory mechanisms of lncRNAs associated with ZGA and maternal RNA decay during early embryo development.
长链非编码 RNA（lncRNA）通过多个分子级联发挥作用，对配子成熟和早期胚胎发育至关重要。然而，在猪早期胚胎中，lncRNA 的鉴定和表达动态研究较少。在这里，我们基于之前发表的猪成熟卵母细胞（GSE160334）的单细胞 RNA-seq 数据以及猪体外受精（IVF）和早期孤雌激活（PA）胚胎（1-8 细胞阶段；GSE164812）中单个卵裂球活检的表达动态，系统地分析了 lncRNA 的表达动态。随着胚胎发育的进行，总表达的 lncRNA 数量逐渐减少，IVF 和 PA 组在每个发育阶段都表现出很大的差异。MII 卵母细胞、1 细胞受精卵、2 细胞、4 细胞和 8 细胞 IVF 胚胎的连续阶段两两比较，鉴定出 151、245、1119 和 188 个差异表达（DE）lncRNA，包括 119、80、867、77 个上调和 32、165、252、111 个下调，而在相同阶段的 PA 胚胎中鉴定出 289、437、895 和 495 个 DE lncRNA（141、89、768、97 个上调和 148、348、127、398 个下调）。在 IVF 胚胎中鉴定出的 DE lncRNA 与在 PA 胚胎中鉴定出的 DE lncRNA 大不相同，表现出胚胎类型特异性。PA 和 IVF 胚胎之间的进一步交叉比较在 1-8 细胞胚胎阶段分别鉴定出 184、656、2502 和 266 个 DE lncRNA。进一步对 DEL 靶向的 DEmRNA 的 GO 和 KEGG 富集分析表明，不同的信号通路参与了母系和双亲胚胎的发育。总之，猪 IVF 和 PA 胚胎之间 lncRNA 表达动态的比较分析提供了有价值的资源，可进一步研究与 ZGA 和早期胚胎发育过程中母体 RNA 降解相关的 lncRNA 调控机制。
