title: Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2'-deoxycytidine.
abstract: DNA methylation in gene promoters leads to gene silencing and is the therapeutic target of methylation inhibitors such as 5-Aza-2'-deoxycytidine (5-Aza-CdR). By analyzing the time series RNA-seq data (days 5, 9, 13, 17) obtained from human bladder cells exposed to 5-Aza-CdR with 0.1 uM concentration, we showed that 5-Aza-CdR can affect isoform switching and differential exon usage (i.e., exon-skipping), in addition to its effects on gene expression. We identified more than 2,000 genes with significant expression changes after 5-Aza-CdR treatment. Interestingly, 29 exon-skipping events induced by treatment were identified and validated experimentally. Particularly, exon-skipping event in Enhancer of Zeste Homologue 2 (EZH2) along with expression changes showed significant down regulation on Day 5 and Day 9 but returned to normal level on Day 13 and Day 17. EZH2 is a component of the multi-subunit polycomb repressive complex PRC2, and the down-regulation of exon-skipping event may lead to the regain of functional EZH2 which was consistent with our previous finding that demethylation may cause regain of PRC2 in demethylated regions. In summary, our study identified pervasive transcriptome changes of bladder cancer cells after treatment with 5-Aza-CdR, and provided valuable insights into the therapeutic effects of 5-Aza-CdR in current clinical trials.
authors.affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.|Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Xiao-Lei
authors.initials: XL
authors.lastname: Ding
authors.affiliation: Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Gangning
authors.initials: G
authors.lastname: Liang
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D001374:Azacitidine / Q000008:administration & dosage / Q000031:analogs & derivatives*; D045744:Cell Line, Tumor; D019175:DNA Methylation / Q000235:genetics*; D000077209:Decitabine; D000071221:Enhancer of Zeste Homolog 2 Protein / Q000096:biosynthesis* / Q000235:genetics; D005091:Exons / Q000187:drug effects; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics; D020033:Protein Isoforms / Q000187:drug effects / Q000235:genetics*; D017423:Sequence Analysis, RNA; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D020033:Protein Isoforms; D000077209:Decitabine; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D001374:Azacitidine