Expression And Functions Of Transposable Elements During Goat Early Embryonic Development

During mammalian early embryonic development,the zygotic genes is involved in genome-wide epigenetic reprogramming,which initiates the expression pattern of totipotency in embryonic development.Mammalian transposable elements are a kind of sequences with autonomous transposition function,which have evolved into a large number of repeated sequences in eukaryotic genomes through long-term evolution.Conventional ideas hold that these transposable elements belong to the junk region of gene sequences.However,more and more evidences show that transposable elements play an important role in gene expression regulation,and some transposable elements have been found to be involved in various physiological and pathological processes.During the development of human pre-implantation embryos,the expression of different ERVs family display obviously stage-specific profile.A large number of ERVs and LINE-1 are specifically activated in mouse 2-cell stage.At present,the regulatory mechanism of zygotic genome activation has not been clarified.With the completion of genomic sequencing and functional gene annotation in various animals,the study on the regulatory functions of non-coding sequences in the genome during embryonic development is of great significance to the analysis of the regulatory mechanism of embryonic development.In this study,we first used bioinformatics to classify all transposable elements in the assembled genome of goat and built a more complete and detailed goat transposable elements library.Transposable elements were mapped to chromosomal positions and compared with cattle,humans and mice.The maximum likelihood trees of different transposable elements were constructed and the evolutionary relationship of each element is analyzed.Through the enrichment of transposable elements in goat genome,the transposable elements library which can be used for subsequent analysis and the important transposable elements in goat genome are preliminarily identified.Then,the gene expression patterns of goat pre-implantation embryos?zygote,2-cell,4-cell,8-cell and morula?were explored by single-cell RNA-seq,and the maternal genes and zygotic genes were obtained by classifying and annotating the gene patterns of embryos at different stages.Then the transposable elements library was mapped with the goat early embryonic transcriptome library to obtain the specific expression of transposable elements.Finally,the function of these elements in embryonic development was verified by knocking down the specific elements in vitro embryos.?1?The proportion of all scattered repeats in the goat genome is similar to that of cattle,accounting for 46.3%,RTE?BovB?belonging to the specific source of cattle and ruminants is about 8.8%;and SINEs <3%.It is less than the high proportion of bovine,human and mice;however,ERVs components are about 24%,which is significantly higher than other species.Transposable elements library we constructed is more complete and detailed than the transposable elements library of goat genome sequencing analysis,and the false positive rate is lower,evenly distributed throughout the chromosome,but chromosome 10 is relatively small;goat transposable elements are classified and composed.It is similar to cattle,but it differs greatly from human and mouse,the most abundant of which is ERV1;the maximum likelihood tree reflects that BovB?RTE?is no longer an source of important polymorphic site insertion or mutation,and BovB components are older than L1 components.?2?The transcriptome data of goat early embryos showed that transcripts expression was significantly higher than that of other stages in the 8-cell stages,which indicated that a large amount of transcripts were transcribed at 8-cell stage,and zygotic genome was activated,including typical ZGA genes,namely ZSCAN.Genes are also consistent with zygotic gene activation during early embryo development in goats;maternal genes are mainly involved in cell division,cell cycle,mitosis and G/2M transformation of mitotic cell cycle;zygotic genes are mainly involved in GTPase activation,transcription factor activity and transcription related.?3?ERV1,LINE1 and RTE elements were stage-specific expression in goat early embryos.ERV1?ERV₁₁₂471 and ERV₁₁₁2704 loci?which are maternal gene and zygote gene expression genes were specifically expressed during goat early embryonic development,respectively.The blastocyst rate in goat early embryos decreased significantly?blastocyst rate in control group was about 22%,and that in knockdown group was about 7%?.In summary,transposable elements are important parts of the mammalian genome,some of which are specifically expressed in early goat embryos and play an important role in embryonic development.This finding provides new insights into the role and mechanism of transposable elements in mammalian embryonic development and lays the foundation for further exploration of the regulatory mechanisms of embryonic development.