Identification And Functional Analysis Of Arabidopsis Thaliana Histone Modification Binding Site Based On High-throughput Sequencing

Histone modification is an epigenetic regulation of post-translational modification such as methylation,acetylation,ubiquitination,and phosphorylation under the action of related enzymes.Recent studies have revealed that it plays an important role in important biological processes such as transcriptional activation/inhibition,gene silencing,and chromatin structural regulation.With the rapid development of high-throughput Sequencing technologies,especially Ch IPSeq,this technology is increasingly being used to explore protein and DNA interaction mechanisms.In recent years,more than 20 functions of Arabidopsis histone modification have been discussed in related research.For example,studies have found that acetylation/deacetylation of histones is involved in transcriptional activation/inhibition,while histone phosphorylation plays an important role in mitosis,apoptosis,and DNA damage repair.However,due to the complex regulation mechanism of histone modification,the regulation in cells is often combined by a variety of histone modifications or antagonism to play a regulatory role,which brings great difficulties to the study of related histone modification regulatory mechanisms.At the same time,compared with the research in humans,the amount of histone modification data in Arabidopsis in public databases is relatively small,and there is a lack of a comprehensive database for query and functional analysis.This has made it difficult for researchers to obtain valuable reference information from published data.In addition,we found that there are some common problems in the Sequencing data of Arabidopsis thaliana histone modifications in many public databases: 1 Many Ch IP Sequencing results have poor data quality,and many data lack further bioinformatics analysis 2 In different Ch IP experiments There are large differences in the results of homologous histone modifications,which do not provide a reliable and reliable reference for future related studies.3 There is no further annotation and functional analysis of the identified histone binding sites.To address these issues and to provide a more systematic and comprehensive analysis of the Arabidopsis histone modification regulatory mechanism,we downloaded more than 300 wild-type Arabidopsis Ch IP-Seq samples from NCBI's GEO database.After removing low-quality Sequencing and samples that failed to identify binding sites,we obtained a total of 140 histone-modified samples involving 24 histone modifications and 4 tissue types for further analysis.At the same time,in order to solve the problem of different analysis standards of histone modification in different studies,we combined the research of histone modification in the past five years and reconstructed a set of rigorous and credible analysis procedures for the identification and annotation of histone modification sites.Finally,we found that the results of different samples in the same histone modification varied widely,with the proportion of conserved binding sites accounting for less than 50%.Such a difference clearly does not provide a rigorous and reliable reference binding site for sub Sequent studies,and it is also important to provide a high-confidence histone modification result.In view of this situation,we have identified relatively conserved binding sites in these samples on the one hand,and we have also identified binding sites that are differentially expressed due to tissue specificity for related research references.After obtaining the positional information of these binding sites,we annotate this positional information to explore the interrelationship between them and the gene functional elements to reveal the potential regulatory functions of these histone modifications.Based on our annotation of these conserved histone modification binding sites,these binding sites tend to fall near the promoter and transcription initiation sites,suggesting that these binding sites may play an important role in transcriptional regulation.Finally,we also performed enrichment analysis of genes near these binding sites and found that genes near different histone modification binding sites have this similarity in many biological functions.This also confirms the argument that multiple histone modifications are often combined to regulate gene expression.In summary,in order to explore the Sequence characteristics and potential regulatory mechanisms of conserved binding sites in Arabidopsis histone modifications,we constructed a rigorous and credible analytical procedure to obtain conserved site positions of 24 histones and their Information on the enrichment of nearby genes.Our analysis will provide a conservative and credible reference for the future research of Arabidopsis histone modification,and lay a solid foundation for the future construction of Arabidopsis histone modification database.We hope that through our research,we can provide new ideas and directions for the study of related plant histone modification functions.