Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat

Abstract

Pre-implantation development is a dynamic, complex and precisely regulated process that is critical for mammalian development. There is currently no description of the role of the long noncoding RNAs (lncRNAs) during the pre-implantation stages in the goat. The in vivo transcriptomes of oocytes (n = 3) and pre-implantation stages (n=19) at seven developmental stages in the goat were analyzed by RNA sequencing (RNA-Seq). The major zygotic gene activation (ZGA) event was found to occur between the 8- and 16-cell stages in the pre-implantation stages. We identified 5,160 differentially expressed lncRNAs (DELs) in developmental stage comparisons and functional analyses of the major and minor ZGAs. Fourteen lncRNA modules were found corresponding to specific pre-implantation developmental stages by weighted gene co-expression network analysis (WGCNA). A comprehensive analysis of the lncRNAs at each developmental transition of high correlation modules was done. We also identified lncRNA-mRNA networks and hub-lncRNAs for the high correlation modules at each stage. The extensive association of lncRNA target genes with other embryonic genes suggests an important regulatory role for lncRNAs in embryonic development. These data will facilitate further exploration of the role of lncRNAs in the developmental transformation in the pre-implantation stage.

Reproductive Seasonality Affects In Vitro Embryo Production Outcomes in Adult Goats

“…The blastocyst rate from the cleaved embryos was higher in the breeding (autumn: 73%) compared to the anestrus season (spring: 55%; OR: 2.18). This parameter is of utmost importance concerning the cytoplasmic competence since it specifically gives information about those embryos that were able to overcome the genome activation stage [ 25 ], which occurs in the 8–16 cells stage in goats [ 26 ]. Conversely, once cleaved, embryos had similar developmental competence to reach the blastocyst stage in plain bison [ 22 ] and in prepubertal goats [ 16 ].…”

Embryo development is impaired in goats that are treated for hydrometra and subsequently subjected to superovulation

“…According to Sirard and others,35 the developmental ability showed in the first week after fertilisation is inherent of certain oocytes, and it is influenced by the follicular status from which they came from. Embryos that blocked at maternal to zygotic transition period, which in goats occurs at 8–16 cells,16 may be associated to oocytes that fail to activate properly the embryonic genome 35 36. Second, it could be related to the occurrence of chromosomal abnormalities, which in bovine embryos is characterised as a delay in the early stage of embryonic development.…”

“…Inside the follicles, the oocyte stores specific gene products that will be first expressed by driving follicular growth up to ovulation 14. A healthy oocyte, equipped with entire maternal molecular machinery, must have the ability to be fertilised and sustain embryonic events15 until the maternal to zygotic transition, which occurs at 8–16 cells in goats 16. Activation of zygotic/embryonic genes is accompanied by gradual degradation of maternal RNAs and proteins and gene expression reprogramming, necessary for later developmental events 17.…”

The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species—Filling in the Picture With Epigenomic Analyses

“…Our understanding of ncRNAs during gametogenesis and embryo development in livestock species mainly comes from quantitative RT-PCR analyses (Tesfaye et al, 2009 ; Tscherner et al, 2014 ; Gilchrist et al, 2016 ; Berg and Pfeffer, 2018 ). However, comprehensive profiling of ncRNAs has been conducted in bovine (Gilchrist et al, 2016 ; Pasquariello et al, 2017 ; Cuthbert et al, 2019 ), porcine (Yang et al, 2012 ; Zhong et al, 2018 ), and caprine (Deng et al, 2018 ; Ling et al, 2019 ) with high-throughput sequencing-based technology. In cattle, miRNA abundance is elevated at 8-cell stage when the major EGA occurs.…”

“…Interestingly, many of the sncRNAs are mapped to annotated repetitive elements (e.g., SINEs and LINEs) in the pig genome, indicating the regulatory function of these elements during early embryo development (Yang et al, 2012 ). In goats, 5,160 differentially expressed lncRNAs were identified across developmental stages; the extensive association of lncRNA target genes with other key regulatory genes indicates that lncRNAs are indispensable in embryonic development (Ling et al, 2019 ). However, the functional characterization of sncRNAs during early embryo development and gametogenesis is still limited in livestock species, so how sncRNAs contribute to the overall epigenetic regulation that takes place during this time is unclear.…”