EPIGENOMICS
Regulatory Genome Architecture & Epigenetic Profiling
At Nucleome, we explore the regulatory architecture that governs gene expression beyond the DNA sequence. Our epigenomics solutions provide high-resolution insights into DNA methylation, histone modifications, and chromatin dynamics, enabling a deeper understanding of gene regulation in health, disease, and development.
From genome-wide methylation profiling to targeted epigenetic assays, we translate complex epigenomic landscapes into actionable, biologically meaningful insights.
Partner with Nucleome to uncover epigenetic regulation with precision, depth, and impact—from basic research to clinical and translational applications.
Why Epigenomics Matters
Epigenetic modifications regulate gene activity without altering the DNA sequence, playing a crucial role in development, cellular differentiation, and disease progression. Epigenomics enables:
- Identification of DNA methylation patterns associated with gene regulation.
- Reconstruction of metagenome-assembled genomes (MAGs) for genome-level insights.
- Discovery of functional pathways and metabolic potential.
- Detection of antimicrobial resistance (AMR) genes and resistomes.
- Understanding of microbiome-host and microbiome-environment interactions.
At Nucleome, we go beyond profiling to deliver integrated and interpretable epigenetic insights that link regulation with function.
Next-Generation Epigenomics Ecosystem
At Nucleome, our epigenomics ecosystem integrates advanced sequencing approaches to comprehensively profile DNA methylation, histone modifications, and chromatin accessibility at high resolution. By combining genome-wide and targeted strategies, we enable precise mapping of epigenetic marks that regulate gene expression across diverse biological systems.
Our workflows include bisulfite sequencing–based methods for base-resolution DNA methylation profiling, chromatin immunoprecipitation sequencing (ChIP-seq) for mapping histone modifications and transcription factor binding, and
targeted epigenetic
assays for focused analysis of regulatory regions and biomarkers. These approaches provide detailed insights into promoters, enhancers, CpG islands, and other regulatory elements.This integrated framework enables identification of differential methylation patterns, chromatin states, and regulatory networks, linking epigenetic variation to gene expression, phenotype, and disease mechanisms. By combining epigenomic data with other omics layers, we deliver high-resolution, functionally relevant insights for research, clinical, and translational applications.
Bioinformatics & Data Analysis
At Nucleome, we implement robust and scalable bioinformatics pipelines to transform epigenomic sequencing data into high-resolution, regulatory insights. Our workflows begin with stringent quality control, alignment, and signal processing, enabling accurate detection of epigenetic marks across the genome.
We perform comprehensive analyses including DNA methylation calling at single-base resolution, differential methylation analysis (DMRs), and peak detection for histone modifications and transcription factor binding sites. These analyses are complemented by chromatin state annotation and identification of regulatory elements such as promoters, enhancers, and CpG islands.
Advanced downstream interpretation includes integration with gene expression data, pathway and gene ontology (GO) enrichment, and regulatory network modeling to link epigenetic modifications with functional outcomes.
By integrating epigenomic data with genomics, transcriptomics, and clinical metadata, we deliver multi-dimensional insights into gene regulation, disease mechanisms, and biomarker discovery, supporting both research and translational applications.
Our Key Solutions
Whole Genome Bisulfite Sequencing (WGBS)
Genome-wide, base-resolution profiling of DNA methylation patterns using bisulfite conversion, enabling comprehensive coverage of CpG and non-CpG sites.
Why it should be done:
Provides a complete view of the methylome, essential for studying gene regulation, epigenetic alterations, and disease-associated methylation changes.
Reduced Representation Bisulfite Sequencing (RRBS)
Targeted bisulfite sequencing focused on
CpG-rich regions
, including promoters and CpG islands, offering efficient methylation profiling.
Why it should be done:
Cost-effective approach for analyzing
regulatory regions
, ideal for differential methylation studies and large cohort comparisons.
ChIP-Seq (Chromatin Immunoprecipitation Sequencing)
Genome-wide mapping of histone modifications and transcription factor binding sites, providing insights into chromatin organization and regulation.
Why it should be done:
Enables identification of regulatory elements and chromatin states, critical for understanding transcriptional control and epigenetic mechanisms.
Targeted Methylation Panels
Focused analysis of selected genomic regions or biomarkers using high-sensitivity targeted approaches for methylation detection.
Why it should be done:
Ideal for clinical validation, biomarker discovery, and translational research, offering high precision in specific regions of interest.