The Methods Of Epigenetic Feature Recognition And Applications In Early Embryonic Development And Radiation Damage

Background:Epigenetics refers to genetic changes in the function of genes that occur without altering the sequence of DNA.Epigenetic modifications include DNA methylation,histone modifications,and non-coding RNAs,which regulate cell differentiation,cellspecific gene expression,X chromosome inactivation,and genome stability.Histone modification of H3K4me3 plays an important role in regulating gene expression during mammalian embryonic development and shows extensive reprogramming across the genome.In addition,ionizing radiation causes DNA double-strand breaks in the process of radiation damage.Radiation-induced epigenetic changes such as DNA methylation,histone modification and non-coding RNA expression will occur in the process of DNA error repair.Radiation will damage cells through these changes.At present,the highthroughput sequencing technology for the study of epigenetic modification is increasingly improved,and the database involving various species is gradually established.These are foundation to develop algorithms,and also bring new opportunities for the research of epigenetic mechanisms in embryo development and radiation damage.Simultaneously,with the promotion and improvement of single-cell sequencing technology makes it possible to explore epigenetic regulation mechanisms from the single-cell resolution.Problems and Challenges:Facing the massive epigenetic sequencing data,it is necessary to develop corresponding analytical methods and tools for different biological problems.Numerous studies have focused on the dynamic changes of epigenetic modifications,and some invariant regulatory elements were also necessary for biological processes such as embryo development.However,there is still a lack of identification and annotation of the homeostasis regulatory elements in the process of epigenetic modifications.In addition,zygotic genomic activation is a complex and dynamic regulatory process during early embryonic development.The systematic identification and function mining of the genes and their epigenetic markers expressed in this process is a challenge in the research of early embryonic development.Currently,there are various different single-cell sequencing technology platforms,and it is necessary to integrate and analyze the sequencing data from these platforms.Objectives,contents,methods,results and conclusions:To investigate the role of homeostasis regulatory elements in epigenetic dynamics,we used publicly available Chip-Seq sequencing data to develop a method for the identification of a novel form of H3K4me3.This type of H3K4me3 constantly and steadily exists in all eight stages of mouse early embryo.We also propose a computational framework based on temporal RNA-seq data,and we named it as ZGA-Timer.ZGATimer can simultaneously detect the start time of ZGA and the key genes involved in the process.ZGA-Timer is superior to the existing mathematical statistical methods which is identifying ZGA genes by multiple changes.The ZGA-Timer framework provides a new method for further understanding the ZGA process.Further,we identified and investigated the function of stable H3K4me3 during early embryonic development in mice,and found that this stable H3K4me3 is more accessible and longer than normal H3K4me3.In addition,most of the stable H3K4me3 are located in the promoter region and enriched at the boundaries of chromatin architecture.Through analysis in detail,we demonstrate that stable H3K4me3 is associated with higher levels of gene expression and transcription initiation during embryonic development.We identified key genes for zygotic genomic activation using ZGA-Timer.And then,we analysis these combined with epigenetic modification data.The results exhibited that chromatin availability had a regulatory effect on these genes.Additionally,zygotic genome-activating genes were significantly enriched in housekeeping genes and cancer driver genes.We also analyzed the expression differences of essential genes in the process of radiation-induced cell deterioration and excavated the markers of chromatin accessibility.At the same time,we delineated the map of the dynamic changes of chromatin accessibility associated with essential genes.In order to integrate scATAC-seq and sRNA-seq data from multiple platforms,we developed a comprehensive analysis system for single-cell epigenome and transcriptome.And we named it as MAESTRO.MAESTRO provides data preprocessing,alignment,quality control,gene expression,chromatin accessibility analysis,clustering,differential analysis,cell type annotation and other functions.Innovation and significance of work:In order to investigate the epigenetic regulation mechanism of mammalian early embryo development and radiation damage,we have developed methods and tools for analyzing sequencing data.Among them,the innovation of the recognition method of stable H3K4me3 lies in its focus on the homeostasis regulatory elements,which makes up for the deficiency of the research on the homeostasis regulatory mechanism in the dynamic epigenetic changes.The ZGA-Timer framework is unique in that it models temporal RNA-seq data through pattern recognition and can accurately calculate the turn on time of zygotic genomic activation among multiple species.The biggest advantage of the MAESTRO system is that it in favor of data processing from raw sequencing data which comes from different various platforms.MAESTRO system models the gene regulatory potential using single-cell chromatin accessibility data,and the integrated analysis of scRNA-seq and scATAC-seq is superior to existing methods.