title: Comprehensive Expression Profiling and Functional Network Analysis of p53-Regulated MicroRNAs in HepG2 Cells Treated with Doxorubicin.
abstract: Acting as a sequence-specific transcription factor, p53 tumor suppressor involves in a variety of biological processes after being activated by cellular stresses such as DNA damage. In recent years, microRNAs (miRNAs) have been confirmed to be regulated by p53 in several cancer types. However, it is still unclear how miRNAs orchestrate their regulation and function in p53 network after p53 activation in hepatocellular carcinoma (HCC). In this study, we used small RNA sequencing and systematic bioinformatic analysis to characterize the regulatory networks of differentially expressed miRNAs after the p53 activation in HepG2. Here, 33 miRNAs significantly regulated by p53 (12 up-regulated and 21 down-regulated) were detected between the doxorubicin-treated and untreated HepG2 cells in two biological replicates for small RNA sequencing and 8 miRNAs have been reported previously to be associated with HCC. Gene ontology (GO) and KEGG pathway enrichment analysis showed that 87.9% (29 out of 33) and 90.9% (30 out of 33) p53-regulated miRNAs were involved in p53-related biological processes and pathways with significantly low p-value, respectively. Remarkably, 18 out of 33 p53-regulated miRNAs were identified to contain p53 binding sites around their transcription start sites (TSSs). Finally, comprehensive p53-miRNA regulatory networks were constructed and analyzed. These observations provide a new insight into p53-miRNA co-regulatory network in the context of HCC.
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Wenrong
authors.initials: W
authors.lastname: Liu
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Ruofan
authors.initials: R
authors.lastname: Ding
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Lili
authors.initials: L
authors.lastname: Xiong
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Rongkun
authors.initials: R
authors.lastname: Dou
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Yiming
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan, P.R. China.
authors.forename: Zhiyun
authors.initials: Z
authors.lastname: Guo
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002877:Chromosomes, Human / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology; D004249:DNA Damage; D004317:Doxorubicin / Q000494:pharmacology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects; D056945:Hep G2 Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009711:Nucleotides / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D009711:Nucleotides; D016159:Tumor Suppressor Protein p53; D004317:Doxorubicin