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.
Supplementary Table 1 Information: 645 intact ERV sequences using LTRharvest and MGEScan-LTR methods. Tables containing all intact ERV sequences which were obtained by LTRharvest and MGEScan-LTR methods ( see Methods for details).
Supplementary Table 2 Information: LTR length and position of 645 potential complete ERV. Table containing information of LTR position in ERV. Each ERV has 5’LTR and 3’LTR. LTR_id: ERV number, chr: chromosome which ERV located, 5’LTR_start: the starting position of 5’LTR in chromosome, 5’LTR_end: the ending position of 5’LTR in chromosome, 3’LTR_start: the starting position of 3’LTR in chromosome, 3’LTR_end: the ending position of 3’LTR in chromosome, 5’LTR_length = 5’LTR_end - 5’LTR_start, 3’LTR_length = 3’LTR_end - 3’LTR_start, length: ERV overall length.
Supplementary Table 3 Information: The postion of RT domain of ERV sequence. Table illustrates the information of the RT domain of ERV sequence. Annotated methods: using different methods to annotated different ERVs. Structure name: RT domains which different ERVs contain. Start positions: RT domain starting position in chromosome. End positions: RT domain ending position in chromosome.
Supplementary Table 4 Information: Functional enrichment analysis of the upstream–downstream genes of ERVs within 10 kb. Table containing GO and KEGG information of different ERVs nearby genes, which can provide some indications for readers about different ERVs.
Supplementary Table 5 Information: Summary of RNA-seq data and reads mapped to Capra hircus reference genome. A table summarizing the raw data and clean data quality of our samples(see Methods for details of how gene reads were determined from RNA-seq data).
Supplementary Table 6 Information: FPKM scores for the lncRNAs and the mRNAs in IVF-2c and IVF-8c. The table containing all genes analysed using Cuffdiff ( see Methods for details).
Supplementary Table 7 Information: List of differentially expressed lncRNAs and mRNAs from IVF-2c and IVF-8c. Tables containing differentially expressed genes between IVF-2cell and IVF-8cell. The significance is determined by qvalue < 0.05.
Supplementary Table 8 Information: ERV-derived transcripts based on Blastall which was used to bidirectionally blast ERV library and RNA-seq library. Tables containing information of ERV-derived lncRNA and mRNA, including their ERVs and transcripts position in chromosome.
Supplementary Table 9 Information: Differentially expressed ERV-derived transcripts in goat IVF-2c and IVF-8c. Tables containing differentially expressed genes between IVF-2cell and IVF-8cell. The significance is determined by qvalue < 0.05.