Analysis Of Variation In Cancer Genome Based On Epigenomic Data

Genomic variations in cells,which can alter normal expression of genes,plays the most important role in canceration.As there are many functional sequences in non-coding region responsible for regulating gene expression,variations on them do make significant difference to gene expression.In fact,recent research,especially GWAS,reveals that diseases-related risk SNVs are usually located in non-coding regions.Despite quantities of sequencing data generated with the rapid development of next-generation sequencing technology,corresponding methods for analyzing needs improvement and the relationship between variations in non-coding region and cell canceration remains unclear yet.In this paper,we tried to develop a process of analyzing how variations on non-coding region affect genes and applied it to the research of cancer cells based on DNase-seq data.Methods for identifying variants in regulation regions and evaluate their effect are shown as follows: Firstly,identify open chromatin regions based on corresponding sequencing data(DNase-seq);Secondly,find out transcription factor binding sites located in open chromatin regions making use of transcription factor motifs;Thirdly,get genomic variations(Single Nucleotide Polymorphisms)in the DNA sequences of TFBS which may affect the binding of TF;Fourthly,evaluate and quantify the influence made to the TF binding process by these SNPs according to the sequence specificity of TFBS(Position Probability Matrix).DNase-seq data of 66 cell lines are all analyzed and thousands of peaks are identified for each sample.168 kinds of TFs are recognized from these conserved regions.And to verify their binding sites,expression data of genes which code the 168 kinds of TFs above is acquired for 8 cell lines chosen from the 66 ones.Based on position probability matrices of motifs,a method of evaluating the influence that SNPs in TFBS make on transcription factor binding process is developed.It quantifies the influence by calculating the ratio of probability that two nucleotide of SNPs may arise in a particular position of a TFBS motif,and the probability value can be obtained from the corresponding position probability matrix.This method is then applied to the SNP analysis of HepG2,K562,MCF-7 and M059 J cells.Hundreds of SNPs for each cell are found to make influence on TF binding and all correlated to genes downstream.Finally,networks among SNP,TFBS and regulated genes are constructed.The result shows that open chromatin regions among different cell lines in same kind are highly conserved(r>0.75(Lymphocyte)),and quite similar between cancer cells and lymphocyte(r>0.5).Besides,it's shown that open chromatin regions prefer locating a little far from transcription start sites(more than 10,000 bp away),suggesting the richness of distal regulation regions.Statistical result of SNPs shows no enrichment in TFBS and SNPs are mainly transitions.Functions of genes highly affected by SNPs located in TFBS via TF binding process are mostly correlated with canceration and apoptosis.Relevant TFs include Sox2,Klf9,Pax5,NFY and more,which are related to cell differentiation and growth.The gene ontology enrichment analysis shows that influenced genes(top 100)are involved in aspects of vital activities of cells such as regulatory of cell death and material transport in cells.In a word,our research explored the procedure of analyzing SNPs on non-coding regions in cancer genome and developed a method for evaluating the effect of these SNPs on genes downstream.This paper provided a viable procedure for non-coding DNA variations and made sense to understand the mechanism of cancer and overcome it.