Comparing motif enrichment in benign and cancerous prostate tissues

Abstract

Prostate cancer is one of the most common cancers in men. To better be able to treat cancers, they first need to be understood better. One avenue towards this understanding is to understand what differentiates cancer tissue from normal tissue and what differences there are between cancer types. One way to do this is to analyze different tissues at the epigenetic and chromatin level. This thesis used data that has been previously generated from different prostate tissues, including two prostate cancer types and benign prostatic hyperplasia, by using the technique assay for transposase-accessible chromatin using sequencing (ATAC-seq). The aim of this thesis was to try and find differences in motif enrichment between the tissue types. The data generated by using ATAC-seq indicates stronger signals in areas of the genome where the chromatin is more accessible and open. This openness can indicate binding sites for transcription factors. By utilizing the genomic position of these signal peaks, it is possible to see if any position and its corresponding sequence are more common in certain samples than in others. This can be achieved in different ways, but for this study, a tool called Hypergeometric Optimization of Motif EnRichment (HOMER) was used. The analysis results indicated several known and few possibly new motifs that were consistent across sample groups as well as motifs that seem to be more common in only one or two sample groups. Examples of consistent motifs found are Sp1, FOXA1, and CTCF. However, further analyses and validation of found sequences are needed to determine further significance.