Investigation Of The Dynamic Chromatin Interactions During Human Cardiac Differentiation

The mammalian heart has littlemited potential for regeneration,and thus an in-depth understanding of heart development will provides new hope insights and theoretical basis for the future treatment of heart-related diseases.The c Cardiomyocytes that make up the heart have undergone differentiation from embryonic stem cells,mesoderm,and cardiac progenitor cells.This is a complex multi-step and multi-stage development process that relies on precise control of transcriptional regulatory networks,including a variety of cardiomyocyte development stage stage-specificities Participation participation and regulation of transcription factors,chromatin modification factors and signal transduction pathways.The t Tissue-specificity of enhancers plays a vital role in the developmental stage.The distal enhancers control the dynamic expression of heterologous genes in cardiomyocytes,and any the disruption of this controlperturbation of enhancer regulation may lead to a variety of congenital heart defects.Although there are several studies to that analyzed the dynamic changes of chromatin interaction at various stages of cardiomyocyte differentiation through Hi-C technology,there is still a lack of comprehensive analysis of specific gene transcription during the combinedexpression regulation regulated of by reenhancers and transcription factors during cardiomyocyte differentiation.In Tthis study,we integratesd the transcriptome,chromatin accessibility,and three-dimensional genomic data of cardiomyocyte differentiation,and analyzes analyzed the stage-specific transcriptional regulatory network mechanism during cardiomyocyte differentiation from the expression genes specific to each stage and interaction.First,based onwe collected a set of Hi-C data collected ifromn the SRA database,and the dynamic changes of chromatin interaction during cardiomyocyte differentiation were characterized.We found that the number of chromatin interactions gradually decreased,which may be important for cardiomyocyte differentiation.Influence,and through the Based on principal component analysis of the interaction data of each stage,we revealed the existence of specific interactionwidespread stage-specific interactions in each stage.Subsequently,this studywe identified topological associated domains(TADs)regions at various stages of cardiomyocyte differentiation.After counting Analysis of TAD data at various stages,we found that the length of TAD regions gradually increased and the number of TADs gradually decreased.This result confirmed the dynamics and specificity of TAD in the process of cardiomyocyte differentiation.Sex Our analysis revealed that it may be related to the gradual fusion of the borders of TADs that are close to each other during the differentiation process.In this study,the distribution of chromatin interaction within / between TADs at various stages was counted,and.it was We found that most chromatin interaction pairs are located in the same TAD,indicating suggesting that enhancers may are likelytend to play a regulatory role within the TAD.Stage-specific interaction may regulate gene expression,thusso further analysis of the relationship between chromatin interaction and gene expression is needed.This study We combined transcriptome and apparent setepigenetic data,including a total of four sets of expression profiling data and three sets of ATAC-seq data from the SRA database,to identify the specific interaction genes of each stage of cardiomyocyte differentiation and stage-specific expression genes.The result of ensemble f Function enrichment analysis found revealed that stage-specific interaction interacting genes are enriched stage-specific functions.The results show that P-Ppromoter-promoter interaction pairs play more functions at the genetic level,and Eenhancer-Ppromoter interaction pairs reflect the characteristics at this stage.In this study,we used the Fisher test and confirmed that genes with stage-specific interactions tend to be expressed specifically at this stage,.If and genes in such interactions with ATAC signal at one end of the region,the end of the promoter is more inclined likely to have ATAC signall,.this result is outstanding The regulation effect of chromatin interaction on gene expression was further deepened,and the regulation effect of chromatin changes on genes was further deepened.Based on the three-dimensional genome and transcriptome data of the four stages of cardiomyocyte development,this studywe constructed a stage-specific transcription factor-mediated transcriptional regulatory network and identified key regulatory subnetworks.The results of the n Network analysis revealed the relationship between transcription factors and enhancers to that regulate the specific expression of genes,which also explained the occurrence of interactions between enhancers and enhancers,promoters and promoters,and enriched by gene assembly functions.The analysis We also cidentifiedonfirmed the regulation and control of the nodes in the network at this stage.Finally,through the analysis of key nodes in the regulatory network,the target genes of enhancers and transcription factors were located,and some potential marker genes in the process of cardiomyocyte differentiation were identified,such as NANOG in ESC stage and TBX5 in CM stage.In summary,this study systematically investigatedexplored the important relationship pairs andthe potential regulatory mechanisms in the process of regulating differentiation by characterizing the chromatin interaction maps of cardiomyocytes at different stages of differentiation and combining transcriptome and apparent data.This study combined with Integrated gene expression and chromatin interactions,we gene function enrichment analysis confirmed the important functions of thealso analyzed the dynamic interactions and identified marker genes at various stages,.This integrative analysis proposed a new strategy for integrating transcriptome and three-dimensional genomic data,and provided a new perspective novel insights into the regulatory mechanisms during human on the differentiation of cardiomyocytes differentiation.