Protocol for Analyzing Epigenetic Regulation Mechanisms in Breast Cancer

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2024 Jul 27

PMID 39068369

Authors

Sri Lakshmi Bhavani Pagolu

Nita Parekh

Affiliations

Soon will be listed here.

Abstract

DNA methylation and gene expression are two critical aspects of the epigenetic landscape that contribute significantly to cancer pathogenesis. Analysis of aberrant genome-wide methylation patterns can provide insights into how these affect the cancer transcriptome and possible clinical implications for cancer diagnosis and treatment. The role of tumor suppressors and oncogenes is well known in tumorigenesis. Epigenetic alterations can significantly impact the expression and function of these critical genes, contributing to the initiation and progression of cancer. This protocol chapter presents a unified workflow to explore the role of DNA methylation in gene expression regulation in breast cancer by identifying differentially expressed genes whose promoter or gene body regions are differentially methylated using various Bioconductor packages in R environment. Functional enrichment analysis of these genes can help in understanding the mechanisms leading to tumorigenesis due to epigenetic alterations.

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