Exploration Of Epigenomic Landscape Changes During Mycobacterium Tuberculosis Infection

Mycobacterium tuberculosis(Mtb)the causal bacteria of Tuberculosis is one of the biggest global health threat.It leads to perishment of millions of human life in each successive decade.As a major pathogen since last centuries and come to notice after famous Physician Robert Koch found it.Alveolar macrophages as a major Antigen presenting cells(APC’s)functions as the first lines of innate immune defense against an invading Mtb through aerosol droplets inside lungs.After undergoing severe immune response,some Mtb survived and leads to intracellular persistent bacterial infection(PBI)in the host cells.In the complex immune interaction between Mtb and host cells,numerious ways by Mtb inhibit host defense systems.There are many unknowns in host-Mtb interaction.We tried to solve this complex issue by finding answer to a major question:how does Mtb regulate the epigenetic modification of host cells.Epigenetic modification which includes histone methylation,histone acetylation,and genomic DNA methylation plays a key role to regulate gene expression and determination of the phenotype without changing the genotype.With the advancements in epigenomics,researcher found the genome does not just function in a sequential fashion but is folded in three-dimensional(3D)space.Thereby,allowing genomic elements located very remotely to the contact regulate each other and influence the phenotype of the genes.The three-dimensional(3D)structure of the genome plays a major role in DNA replication,repair of DNA damage,and gene transcription regulation.The ENCODE(ENCyclopedia Of DNA Elements)project unveiled millions of regulatory elements in the human genome,whose target genes desperately need to be elucidated.A potential approach to identifying these target genes of regulatory elements is by applying long-range chromatin interactions or 3D genomic architecture.Due to the importance of 3D genomics,NIH initiated the 4D Nucleome(4DN)program and pledged to study the 3D genome architecture and its dynamics(the 4th dimension).Although,Hi-C technique seems promising to uncover the landscape of 3D genomes.Several significant limitations,including sophisticated and laborious experimental procedures,high costs,high random ligated DNA noise and lack of straightforward noise evaluation remarkably limit its broad application.In present study,we aim to develop a method based on simple enzyme digestion and ligation steps,designated Digestion-Ligation-Only Hi-C(DLO Hi-C),to delineate the 3D genome landscape.This method efficiently removes the noise DNA in a cost-effective step by purifying specific linker-ligated DNA fragments instead of biotin-labeling and pull-down steps.Notably,we have introduced an early quality-control step to quickly evaluate the ratio of random ligation noise before sequencing,which can greatly reduce the experimental period and costs.In order to investigate the epigenetic modification and chromatin spatial organization change during Mtb infection,we choose THP-1 cells(a human monocytic cell line which can differentiate into macrophage-like cells)as the differentiation and infection model.By combine with ATAC-seq and ChIP-seq,we adopted DLO Hi-C,to find out the dynamic of histones modification(H3K4me1,H3K4me3,H3K9me3,H3K27ac,and H3K27me3),chromatin open-close region,and genome three-dimensional(3D)structure during monocyte differentiation and Mtb infection.By multi-omics analysis,we found 186 differential genes,these genes enable us investigate the host-pathogen interaction from a different perspective,which is very important for the prevention and cure of tuberculosis.