Systematic Analysis And Database Construction Of Alternative Transcription Start Sites In Multiple Cancers

Alternative Transcription Start Site(ATSS)is an important transcriptional regulatory mechanism that can generate mRNA isoforms with different 5’UTR,or mRNA with different first exons,thereby influencing biological processes and being associated with diseases.Recent studies have highlighted the important roles of ATSS in human.However,the landscape of differential cancer-related ATSSs and their related factors have not been fully investigated.Firstly,this study systematically identified ATSS with significant differences in usage rates between cancer and paracancerous tissues based on TCGA(The Cancer Genome Atlas,TCGA)pan-cancer data,abbreviated as differential ATSS.Secondly,this study integrated relevant databases such as eRic and JASPAR to analyze the factors related to differential ATSS.Finally,this study built a database and conduct in-depth analysis of the differential ATSS.This study first selected RNA-seq paired data for a total of 18 cancer types with primary cancer and normal samples from the TCGA database.Secondly,a bioinformatics analysis process was constructed,identified 14,076 differential ATSSs from 18 cancer types.In addition,the factors significantly related to differential ATSS were identified through correlation analysis,including enhancer,DNA methylation and transcription factor(TF).3,119 ATSSeRNA(eRNA was used to characterize the activity of enhancer),960 ATSS-DNA methylation and 62,373 ATSS-TF data pairs significantly related with differential ATSS were identified.Finally,by integrating these data,a differential transcription start site database: Pancan-ATSS(http://gong＿lab.hzau.edu.cn/Pancan-ATSS#!/)was constructed.This database can be used for searching,browsing,and downloading data of differential ATSS.The construction of this database provides important data resources for analyzing the role and potential mechanisms of ATSS in cancer.For the identified differential ATSS,this study screened potential important ATSSs that appeared in 10 or more types of cancer and were significantly correlated with patient prognosis,resulting in 21 important ATSS.According to the number of relevant literature and the screening of Kaplan-Meier curve,this study obtained the differential ATSSs chr5:138337956-138338355 and chr10:62049211-62049483 that are significantly related to prognosis in lung adenocarcinoma and bladder urothelium cancer,respectively.They correspond to the genes CDC25C(Cell Division Cycle 25C)and ARID5B(AT-Rich Interaction Domain 5B),which have been confirmed to play a role in a variety of cancers.Among them,high expression of ARID5 B is associated with poor prognosis in hepatocellular carcinoma.High expression of CDC25 C is associated with poor prognosis in lung adenocarcinoma.CDC25 C has only one differential ATSS in lung adenocarcinoma,and the increased use of this candidate ATSS is significantly correlated with a good prognosis.Therefore,it is speculated that other ATSS of this gene plays a more important role.ARID5 B has two different ATSS in bladder urothelium carcinoma.The increase in the use rate of this candidate ATSS is significantly related to the poor prognosis,so it is speculated that the corresponding transcript of this ATSS may play an important role in cancer.This study also analyzed the influencing factors related to ATSS.The differential ATSS chr5:138337956-13838355 was significantly correlated with one eRNA 5:138939407-138945407 and multiple transcription factors.By searching the hTFtarget database,it can be confirmed that transcription factors such as GATA2,an important regulatory factor for hematopoietic and urogenital development,and SPI1,a key regulatory factor for signal communication in the immune system,may have binding sites in the CDC25 C promoter region of the gene.The difference ATSS chr10: 62049211-62049483 was significantly correlated with one eRNA ENSR00000012237 and multiple transcription factors.There is literature confirming that this eRNA may regulate the gene ARID5 B.By searching the h TFtarget database,it was also confirmed that transcription factor YY1,which regulates cell proliferation,migration,cycle,and differentiation,as well as transcription factor TCF3,which plays a key role in the maintenance and hematopoietic development of stem cells,may have binding sites in the ARID5 B promoter region of the gene.The above results confirm that the database can indeed provide certain clues and theoretical support for screening important ATSSs and their related factors in cancer.In summary,this study conducted a series of analyses on ATSSs in pan-cancer,including identifying differential ATSSs and their related factors,constructing a differential ATSS database,and mining potentially important differential ATSS,in order to provide new ideas for the treatment and prevention of cancer.