Genetic Variant Discovery and Functional Annotation in COPD Using ChIP-Sequencing Data

Abstract

Chronic Obstructive Pulmonary Disease (COPD) is a progressive respiratory disorder characterized by persistent airway inflammation, airflow limitation, and structural remodelling of lung tissue. Although environmental factors such as cigarette smoke are major contributors, genetic susceptibility plays a crucial role in disease development and progression. Genome- wide association studies (GWAS) have identified several COPD-associated loci; however, most variants reside in non-coding regions, indicating regulatory rather than protein-coding functions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) enables genome-wide identification of regulatory elements, including promoters, enhancers, and transcription factor binding sites. In this study, publicly available ChIP-seq datasets of COPD and healthy control samples were retrieved from the European Nucleotide Archive (ENA) under Project ID PRJNA1167187. Raw sequencing reads were assessed for quality using FastQC, aligned to the human reference genome using Bowtie2, and enriched genomic regions were identified using MACS2. Downstream analyses were conducted using R-based bioinformatics tools. To uncover regulatory mechanisms underlying COPD, motif discovery was performed using MEME-ChIP, revealing significantly enriched transcription factor binding motifs within disease-specific ChIP-seq peaks. These motifs suggest the involvement of transcriptional regulators associated with inflammatory responses, oxidative stress, and lung tissue remodelling. Integration of COPD-associated genetic variants with ChIP-seq peaks and motif information enabled functional annotation of regulatory variants with potential biological relevance. Overall, this integrative analysis highlights key regulatory motifs and transcriptional networks that may serve as novel biomarkers or therapeutic targets, demonstrating the relevance of regulatory genomics in advancing pharmaceutical research and biological understanding of complex diseases such as COPD.