Epigenomics is the study of chemical modifications to DNA and histones that influence gene expression without altering the underlying genetic code. These modifications, such as DNA methylation and histone modifications, act as molecular switches, determining which genes are turned on or off in different cells and conditions. Unlike genetic mutations, epigenetic changes are reversible and influenced by multiple factors, including environment, lifestyle, and diseases.
Over the past decades, advancements in high-throughput sequencing and single-cell technologies have also revolutionized epigenomic research. Techniques like Nanopore sequencing, whole-genome bisulfite sequencing (WGBS), ATAC-seq, and ChIP-seq provide unprecedented insights into DNA methylation, chromatin accessibility, and histone modifications at a genome-wide scale. Epigenetic microarrays, on the other hand, offer a scalable and cost-effective solution, enabling the analysis of thousands of samples at a fraction of the cost of other methods. The rise of spatial transcriptomics has further enabled researchers to explore other omics in single-cell space including epigenetics, driving new discoveries in developmental biology, cancer, and neurological disorders.
Studies of epigenomics changing the world
Epigenetic Clocks and Aging [1], [2], [3]. Studies by Steve Horvath and others have shown that DNA methylation patterns can predict biological age which is not always the same as the chronological age. This has implications for aging research, longevity interventions, and disease risk prediction.
Epigenomics in Neurodegenerative Disorders [1], [2]. Research has linked altered DNA methylation patterns to neurodegenerative diseases, shedding light on disease mechanisms and identifying potential biomarkers for early diagnosis and treatment.
Developmental Epigenomics [1], [2]. Studies show that prenatal and early-life environmental factors (e.g., nutrition, stress, toxins) influence lifelong health through epigenetic modifications, affecting conditions like obesity, diabetes, and cardiovascular disease.
Epigenetics in Regenerative Medicine [1], [2], [3]. Epigenomic studies help improve stem cell therapies by identifying the optimal epigenetic states for cell differentiation, enhancing regenerative treatments for conditions like spinal cord injury and organ repair.
Applications of epigenomics Across Disciplines
Epigenomics is widely applied across various fields of research and medicine, providing critical insights into gene regulation and disease mechanisms. Key applications include: cancer research and therapy, environmental and lifestyle effects, neurodegenerative disorders, developmental biology and inherited traits, immunology and infectious diseases.
At VUGENE
We specialize in cutting-edge epigenomic analysis across various biological contexts, including cancer, neurodegenerative disorders, aging, and environmental impact. Our advanced analysis methods enable the generation of meaningful and deep insights into gene regulation and disease mechanisms. Our expertise includes:
- Epigenetic microarrays (EPIC arrays)
A cost-effective and high-throughput method to assess DNA methylation across the genome. - Whole-genome epigenomics (WGBS, EM-seq)
Comprehensive sequencing-based approaches to profile DNA methylation and modifications at single-base resolution. - Nanopore sequencing
A real-time, long-read technology that enables DNA and DNA modification identification with high accuracy. - ChIP-seq & ATAC-seq
Powerful tools for studying chromatin accessibility and histone modifications, providing insights into gene regulation mechanisms. - Single-cell epigenomics
Dissecting cellular heterogeneity to uncover unique epigenetic signatures at the single-cell level.
Key Considerations in Epigenomic Analysis
A robust epigenomic analysis requires careful attention to several critical factors:
- Batch Effects
Unwanted technical variations as a result of study’s imperfection can obscure biological signals, resulting in misleading conclusions. - Confounders
Variables such as age, sex assigned at birth, lifestyle factors, and medication use must be properly accounted for in statistical models and when building predictive models to prevent biased results. - Data Integration
Combining multi-omics data, including transcriptomics and genomics, to achieve a comprehensive understanding of gene regulation at multiple omics levels.
Interested In Learning More
Epigenomics is revolutionizing our understanding of gene regulation and its role in interaction with the environment and health. We use our expertise and machine learning models to develop novel and rigorous analyses for high-quality epigenomic insights in research or clinical applications.
Contact us to discuss how VUGENE can support your research.
Written by: Miglė Gabrielaitė, PhD
Cover image credits: Olena / Adobe Stock