Background <p> <?tk 1?>Cervical cancer is the fourth most common cancer worldwide in females. This occurs primarily due to the infection of high-risk Human Papilloma Virus (HPV), although in advanced stages it requires support from host cellular factors. BRN3A is one such host cellular factors, whose expression remains high in cervical cancers and upregulates tumorigenic HPV gene expression. The effect of BRN3A on HPV-mediated cervical cancer and the underlying mechanism remains obscure.</p> Objective <p> <?tk 1?>To investigates the effect of BRN3A on cancer-promoting biological processes in HPV-positive uterine cervix cancer cells.</p> Methods <p> <?tk 1?>We have altered the expression of BRN3A through over-expression (OE) and knock-down (KD) constructs in cervical cancer cell line, SiHa, and did transcriptome profiling through next-generation RNA-sequencing, validation through RT-PCR and BRN3A binding study with in silico promoter study and ChIP PCR methods.</p> Results <p> <?tk 1?>This study revealed a substantial change in the expression of several genes associated with cancer-promoting biological processes including viral processes, immune response, cell-death, cell-proliferation, different signaling pathways, etc. Additionally, promoter analysis through in silico mode revealed that a total of 32.7% of genes possess BRN3A binding sites at their promoters. Physical interaction of BRN3A with <i>IFITM1</i>, <i>OAS3</i>, <i>ISG15</i>, <i>BCL2L1</i> and <i>HSP90AB1</i> genes was also confirmed.</p> Conclusions <p> <?tk 1?>The present study identified molecular targets of BRN3A and provided new insight into the pathogenesis of cervical cancer. According to our knowledge, this is the first report on the effect on eukaryotic transcriptomes after over-expression and knocking down BRN3A.</p>