Identification and characterization of ERV transcripts in goat embryos

Abstract

Endogenous retroviruses (ERVs), which are abundant in mammalian genomes, can modulate the expression of nearby genes, and their expression is dynamic and stage-specific during early embryonic development in mice and humans. However, the functions and mechanisms of ERV elements in regulating embryonic development remain unclear. Here, we utilized several methods to determine the contribution of ERVs to the makeup and regulation of transcripts during embryonic genome activation (EGA). We constructed an ERV library and embryo RNA-seq library (IVF_2c and IVF_8c) of goat to serve as our research basis. The GO and KEGG analysis of nearby ERV genes revealed that some ERV elements may be associated with embryonic development. RNA-seq results were consistent with the features of EGA. To obtain the transcripts derived from the ERV sequences, we blasted the ERV sequences with embryonic transcripts and identified three lncRNAs and one mRNA that were highly expressed in IVF-8c rather than in IVF-2c (q-value <0.05). Then, we validated the expression patterns of nine ERV-related transcripts during early developmental stages and knocked down three high-expression transcripts in EGA. The knockdown of lncRNA TCONS_00460156 or mRNA HSD17B11 significantly decreased the developmental rate of IVF embryos. Our findings suggested that some transcripts from ERVs are essential for the early embryonic development of goat, and analyzing the ERV expression profile during goat EGA may help elucidate the molecular mechanisms of ERV in regulating embryonic development.Reproduction (2019) 157 111-122

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

“…The major ZGA in goat development was found in our present experiments to occur in the 8- to 16- cell stages. This was in contrast to the recent findings by Deng et al (2018), which reported that the 8-cell stage goat stopped developing in in vitro developmental block cultures and showed that ZGA occurred in the 4- and 8-cell stages in vitro . However, other studies had shown that the timing of ZGA onset in pre-implantation cells was different between in vitro and in vivo (Misirlioglu et al, 2006; Graf et al, 2014).…”

“…Previous studies had reported that ZGA-related genes begin to be expressed in the 8-cell to 16-cell stage of goats (Ma et al, 2014; Deng et al, 2018). Recent study of the developmental block of cultured of goat in vitro suggested that cell development stops at the 8-cell stage, and further verification by RNA-seq has indicated that it occurs between the 4- and 8-cell stage (Deng et al, 2018).…”

LncRNA affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification and the downstream gene SIN3A

“…Wang et al (2016) indicated that lincGET is essential for correct ZGA processes and further promotes the cleavage of two-cell embryos via regulating transcription and RNA alternative splicing in mice. In the goat embryos, the knockdown of the lncRNA TCONS_00460156 significantly decreases the developmental rate (Deng et al, 2019). Deng et al (2021) showed that lnc_3712 impedes nuclear reprogramming via repressing KDM5B, and the microinjection of siRNA against lnc_137 causes development arrests (Deng et al, 2018).…”

The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development

“…The expression of retrotransposons is a vital event for genome reprogramming during early embryonic development (Bui et al, 2009). Some studies have also provided substantial evidence for the extensive role of TEs in regulating gene expression during early embryonic development (Kigami et al, 2003;Macfarlan et al, 2012;Percharde et al, 2018;Deng et al, 2019). Many TEs have been found, but the regulatory effects of most of these TEs have not been studied in depth.…”