| In recent years,it was reported that the chromatin three-dimensional(3D)structure has allelic effect,i.e.maternal chromatin and paternal chromatin showing differences in some genomic locations.However,the relationship between allelic chromatin 3D structure and allelic gene expression is not clear.Somatic cell nuclear transfer(SCNT)refers to the technology of transfering the differentiated somatic cell nuclei to enucleated oocytes to develop new embryos and eventually new animal individual.However,the role of chromatin 3D structure and its allelic effects in this process remain unclear.To solve the above problems,we first participated in the development of Hi-C data processing software Hi CHap,including processing Hi-C data in the traditional way(without distinguishing parental chromosomes)and analyzing allele-specific chromatin 3D structures using genetic variatiants.In this dissertation,the maternal and paternal chromatin interactions derived from Hi-C and phased genetic variants is called haplotype-resolved HiC.For diploid cells,few softwares support the processing of haplotype-resolved Hi-C data,and these available softwares ignore the systematic bias caused by single nucleotide polymorphism(SNP)density during the processing of haplotype-resolved Hi-C data.The software Hi CHap can reduce this systematic bias to a certain extent,enabling it to construct allele-specific chromatin interaction matrices using phased SNPs and also keep the traditional Hi-C data processing.Specifically,the effect of SNP density on the bias of haplotype-resolved chromatin interaction was comprehensively evaluated,paving the way for proposing the bias correction method and corresponding allele-specific analysis of chromatin 3D structure.In addition,we investigated the relationship between allele-specific chromatin 3D structure and allele-specific histone modification,and revealed the potential roles of allele-specific structure in regulating biological processes.Secondly,we used Hi CHap software to study the chromatin 3D structures for mouse Cumulus Cells,f ESCs and nt ESCs,and then investigated the potential roles of chromatin3 D structures in SCNT reprogramming by integrating Hi-C data and other omics data.Specifically,the in situ Hi-C technique was used to generate the high-throughput chromatin interactions for CCs,f ESCs and nt ESCs.Hi-C data of the three different cell lines were analyzed by Hi CHap software and corresponding chromatin 3D structures were obtained respectively.Then,the chromatin 3D structures of these three cell types were compared in three different layers: chromatin compartment,TADs,and chromatin loop.The results reveal that nt ESCs and f ESCs show very similar chromatin 3D structure generally,indicating that nt ESCs exhibit the successful chromatin 3D rearrangement in promoting the interactions between genes and regulatory elements in overall.However,nt ESCs and f ESCs also show some structural differences in some chromatin regions,in which many genes related to cell differentiation and organ development are abnormally expressed in nt ESCs.These results imply that the locally abnormal chromatin 3D structures in nt ESCs hinder the cell differentiation potential.Our collaborators verified the above findings through related experiments.In addition,we also found the association between H3K9me3-marked chromatin region and incomplete TAD reconstruction in nt ESCs,suggesting that the local abnormalities of chromatin 3D structures were associated with the intensity of H3K9me3 histone modification signals.Next,we analyzed the allele-specific chromatin 3D structures during nuclear transfer reprogramming,and found that the allele-specific chromain 3D structures were closely related to allele-specific gene expressions during the SCNT reprogramming.To sum up,first of all,this dissertation carries out corresponding data characteristics analysis and comprehensive evaluation on the independently developed Hi-C data processing software Hi CHap,and further optimizes the software performance.Secondly,this paper uses Hi CHap software to further analyze the relationship between the dynamic changes of chromatin 3D structure and genome function in SCNT reprogramming,as well as the relationship between allele-specific chromatin 3D structure and allele expression.The potential role of chromatin 3D structure in regulating nuclear transfer cell fate is explained,and it provides ideas for solving corresponding biological problems. |
