| Background:Epigenetics is the study of reversible,heritable phenotypes that do not involve changes in nuclear DNA sequences.Epigenetics is a branch of genetics with stable genetic characteristics.Generally speaking,chemical modification includes DNA and RNA methylation,histone modification and so on.Similar to DNA methylation,N~6-methyladenosine(m~6A),as the most common post transcriptional RNA modification in the whole transcriptome,has attracted a lot of attention recently.m~6A modification can be methylated by the m~6A"writer",which is composed of the core catalytic component(METTL3/METTL14/WTAP)and the other regulator,and is demethylated by the m~6A"eraser"(FTO and ALKBH5).The function of m~6A is performed directly with the m~6A"reader"(mainly include proteins containing YTH domains).Materials and Methods:We selected 4 pairs of gastric cancer tissues and corresponding paracancerous tissues,and constructed a transcriptome m~6A modification map of gastric cancer for the first time with the help of MeRIP-seq and other experimental techniques,and revealed the common and differential regulatory functions of RNA m~6A methylation modification between gastric cancer and normal paracancerous tissues.Results:1.By using the MeRIP-seq technique,we tested m~6A date from 4 pairs of tissues.We found that there were differences in the m~6A methylation modification patterns between gastric cancer and normal gastric tissues.There were 5814 and 4093 m~6A peaks,while separately corresponding 4259 and 3174 transcripts in gastric cancer and normal gastric tissues.However,1039 m~6A peaks(only 12%of all peaks in tumor and normal groups)and 1637 associated m~6A modifying genes(also only 28%of all m~6A modifying genes in tumor and normal groups)were detected in gastric cancer and normal gastric tissues.2.The classical sequence of m~6A methylation is conserved in gastric cancer and normal adjacent tissues.We found that m~6A peak was abundant near CDS and stop codon,followed by start codon and 3'UTR,and had the same motif,i.e.RRACH(R:A/G,H:A/C/U)3.We found 272 differentially m~6A methylated sites(FC>2,P<0.05),including 188hyper-methylated sites and 84 hypo-methylated sites.Then we analyzed the genes containing 272 different methylated sites by bioinformatics.The results showed that abnormal m~6A methylation genes were involved in many tumor formation related pathways,including cancer pathway,basal cell carcinoma pathway,Wnt signaling pathway,HTLV-I infection,erbB signaling pathway.Various pathways may be related to each other,thus forming a complex signal regulatory network,which is involved in the tumorigenesis and development of gastric cancer.These differentially methylated genes and their signal regulatory pathways may be new targets of gastric cancer treatment.4.By RNA-seq,we detected 20348 mRNAs in gastric cancer and normal adjacent tissues,and then found 3069 differentially expressed mRNAs(FC>2,P<0.05),of which 2032 were up-regulated and 1037 were down regulated.And then we do the bioinformatics analysis of these differentially expressed genes.5.Combined with the results of m~6A-seq and RNA-seq,we analyzed the relationship between the differentially m~6A methylated gene and its mRNA expression level.We found that hyper-methylated genes tended to be up-expressed,while hypo-methylated genes tended to be down-expressed.Conclusion:This study presented the first m~6A transcriptome map of human gastric cancer.It provided a potential link between abnormal m~6A RNA modifications and cancer-related gene expressions.It can provide some light on further studies regarding m~6A modifications in gastric cancer. |
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