Using Allelic-Specific Expression Analysis To Decipher Bovine Zygote Genome Activation And Construction Of Bovine Early Embryo Development Multiomics Database

The early embryo development of domesticated animals is of great significance to the research of breeding technology and economic production.By producing embryos through in vitro fertilization or somatic cell cloning technology,high-quality offspring can be quickly and efficiently obtained through embryo transplantation,which is beneficial to the expansion and preservation of high-quality germplasm resources.Not only does it provide a time window for gene editing,but it is also a critical way to achieve the rapid propagation of superior breeds.However,embryos produced in vitro face the problem of developmental arrest.Research has found that most embryos are arrested during the Zygotic Genome Activation(ZGA)period,during which a large number of new genes are transcribed,replacing maternal substances to regulate early embryo development.ZGA can be divided into minor ZGA and major ZGA,and current research tends to focus on major ZGA while the study of minor ZGA is less explored.Research on mammalian early embryo development and ZGA has mainly focused on model animals such as mouse,with little attention paid to domestic animals.This lack of research has severely hindered our understanding of early embryo development in livestock.In this study,we collected multi-omics data on early embryo development in cattle and used allele-specific expression(ASE)analysis to investigate minor ZGA.Additionally,we constructed a comprehensive multi-omics database for early embryo development in cattle,which provides important theoretical support for further research on this topic.The main findings are as follows:1.This study has constructed a transcriptome atlas of the early development of hybrid embryos produced by in vitro fertilization of Yak sperm and Holstein oocytes.Using ASE analysis,this study identified that the minor ZGA in cows occurs during the 2-cell to 4-cell stages and accurately identified 383 minor ZGA genes,of which 296(77.3%)are maternalzygotic(MZ)genes.The accurate identification of MZ genes demonstrated the advantage of ASE analysis.Additionally,this study identified the activation of transposable elements during minor ZGA and found that the top five activated transposable elements during minor ZGA are all bovine-specific,suggesting that these species-specific transposable elements play an important role during minor ZGA and may lead to low conservation of minor ZGA between species.This study also compared the minor ZGA of humans,cows,and mouse and found poor conservation between species,with only ZSCAN4 and UBTFL1 being minor ZGA genes in all three species.Furthermore,this study used chromatin accessibility data to identify potential gene regulatory elements and transcription factors related to minor ZGA in the three species.The results showed that cows and humans share more transcription factors that regulate minor ZGA,indicating that the study of early embryo development in cows can benefit research on human assisted reproduction and infertility.2.Through the collection of multi-omics data on early-stage cattle embryos,this study has established a comprehensive database,known as the “Cattle Embryo DB”(http://animal.omics.pro/code/index.php/Cattle Embryo DB),which integrates transcriptomic and epigenomic data across all stages of early embryo development.This resource enables users to search for ZGA genes in cattle,along with associated epigenomic information within the respective genomic regions.The Cattle Embryo DB also provides search and visualization tools,such as UCSC Genome Browser and Wash U Epigenome Browser.This database represents a valuable tool for researchers seeking to explore new pathways and methodologies for investigating early mammalian embryo development.In summary,this study utilized multi-omics research methods,including genome resequencing,transcriptomics,and epigenomics data,combined with allele-specific expression analysis,to explore the activation of genes and transposable elements during the minor ZGA period of early bovine embryo development.Additionally,a comparative analysis of minor ZGA in different mammalian species was conducted.Furthermore,the construction of a multi-omics database for early bovine embryo development provides significant theoretical implications for a better understanding of the embryo development mechanism.