Investigation of RNA editing on cancer transcriptome

• Main Authors: Chung-Tang Hsu, 許眾棠
• Other Authors: I-Fang Chung
• Format: Others
• Language: zh-TW
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/ahtmr6

碩士 === 國立陽明大學 === 生物醫學資訊研究所 === 107 === One of the post-transcriptional modification is RNA edting. It can cause sequence form alternative nucleotide composition without mutation in DNA. RNA editing may affect the original function of gene. For example, A-to-I RNA editing is the most common event of RNA editing especially in mammalian. When base substitution occurs on mature transcripts, it might change codons of protein coding regions (CDS) or miRNA bind sites on 3’ untranslated regions (3’UTR). The aim of the study is to discover potential A-to-I RNA editing sites which may play a role in cancer progression. We downloaded RNA sequencing and DNA sequencing (whole exome sequencing and whole genome sequencing) data of breast invasive carcinoma (BRCA) from The Cancer Genome Atlas (TCGA). To identify potential A-to-I editing sites, variant calling was first performed with Genome Analysis Toolkit (GATK) to obtain variant sites in RNA which were further compared with the same sites in DNA sequencing results for confirmation of wild type DNA sequence. We then categorized RNA-seq variant sites into two main groups with different RNA and DNA read coverages. After that, we annotated each site with the variant effect predictor (VEP) and summarized it based on different regions to look into editing site distribution and probable affected functions. We identified some novel events on cancer-related miRNA and gene interaction , which are worthful for further experimental validation in the future.