Study On The Relationship Between DNA 6mA Methylation And Nucleosome Positioning

DNA methylation,which is one of the significant epigenetic modifications and involved in many important biological processes,is closely associated with nucleosome positioning.DNA N6-methyladenine,also called 6m A,is widely distributed in prokaryotes and plays crucial roles in DNA mismatch repair,chromosome replication,cell defense,cell-cycle regulation,transcription,and virulence.However,due to its low content in eukaryotes,6m A is difficult to detect,and has not been taken seriously until recently.The presence of 6m A modifications in eukaryotic genomes,such as Chlamydomonas reinhardtii,Caenorhabditis elegans,Mus Musculus,Drosophila melanogaster,and Xenopus lavias,was revealed lately and draw attention of researchers.But the relationship between the function of 6m A and nucleosome positioning remains unclear.I this dissertation,we analyzed the 6m A data from C.reinhardtii,C.elegans and H.sapiens by bioinformatics and statistical methods,and discussed their relationship to nucleosome positioning and regulation of gene expression,based on the data of nucleosome positioning,enhancer and Hi-C.The relationship between 6m A and nucleosome positioning in C.reinhardtii was analyzed,which revealed that 6m A distributes regularly in the genome of C.reinhardtii and is mutually exclusive with nucleosomes in C.reinhardtii.Genome-wide analysis of 6m A showed that 6m A is enriched in 5'UTR(5'Untranslated Region)in C.reinhardtii,and positively correlated with gene expression,which suggested that DNA 6m A in the 5'UTR might be related to specific functions such as gene expression.Moreover,Analysis about 6m A modifications near the TSS(transcriptional start sites)and nucleosome positioning revealed that both 6m A and nucleosomes promote gene expression to some extent,and there is mutual exclusion between 6m A and nucleosomes in C.reinhardtii.Based on the CAGT clustering algorithm and functional area analysis,we also found that the pattern of 6m A and nucleosome positioning are possibly related to different functional regions.The relationship between 6m A and nucleosome positioning in C.elegans genome was also analyzed,which suggested that 6m A is enriched around TSS,promote gene expression and is mutually exclusive with nucleosomes.The genome of C.elegans was considered as nonmethylated due to the lack of 5m C.But recent studies have negated the previous understanding and founded that the 6m A modifications are widespread in the genome,and likely to play important roles in epigenetic processes.Based on the third generation sequencing(SMRT)data of C.elegans,make use of CAGT clustering,Meth SMRT and other biological information analysis methods,we found that 6m A is enriched in the initial transcription site(TSS),and have a positive correlation with gene expression.We also found the absence of nucleosomes at the 6m A sites,of which the obviousness increased with the distance between 6m A and TSS.At the same time,the mutex relationship between 6m A and nucleosome exist different mode,in different mode,the + 1,+ 2 nucleosome around the 6m A have level exists obvious difference,which has nothing to do with 6m A relative to the location of the TSS.3D genome structure data was employed to analyze 6m A in the genome of H.sapiens,which revealed a complicated relationship between nucleosomes and 6m A,and significant enrichment of 6m A near the border of the topological associated domains(TAD)in human genome.The distribution of 6m A in human genome was analyzed and the characteristics of 6m A were discussed.Then,the relationship between 6m A and nucleosomes was studied by analyzing the distribution of both around TSS and TTS(transcription termination site).Also,the distribution of 6m A in TAD was analyzed in the 3D genome,based on the conformational data of chromatins.The biological function of 6m A in lymphocyte was discussed too.The results showed that 6m A is enriched in mitochondrias,and absent in the sex chromosomes,which may be related to the levels of adenine in different chromosomes.In the functional areas,6m A is concentrated in genes,enhancers and exon regions,which promote gene expression to some extent.The 6m A modifications not only regulate gene expression,but also have a specific relationship with the nucleosomes.According to the distribution of nucleosomes and 6m A,although 6m A exclude nucleosomes near TSS,there is a high occupancy of nucleosomes at 6m A sites overall,which indicates that 6m A generally tends to modify the DNA wrapping nucleaosomes,and the exclusion in promoters might be influenced by transcriptional regulation.The analyses of the conformational data of chromatins showed that 6m A is enriched on the left side of TAD,and also in the strong boundaryies,which indicates that 6m A may be involved in the formation of the chromatin conformation.In summary,the 6m A modifications show a certain enrichment in TSS to promote gene expression,have a specific correlation with nucleosome positioning which might be influenced by the regions they are positioning in.6m A modifications may be related to cell development,which leads to their different functions and distributions in different species.Our research provides data and informational supports for better understanding the relationship between 6m A and nucleosome positioning.