Epigenetics is a growing area of research, important to our understanding of development, aging, disease, and other biological processes. In this blog post, we discuss common forms of epigenetic modifications. We then discuss different omics tools available to epigenomics researchers, as well as examples of those tools advancing human health, development, and disease research.
What Is Epigenomics?
Epigenomics is the study of epigenetic changes in cells. These environmentally influenced changes don’t alter the DNA sequence. Instead, they impact cell function by turning genes on or off.
Many of these changes occur naturally. They are part of the regulatory processes that facilitate cell growth and development. However, inappropriate epigenetic changes are implicated in many disorders and diseases.
Epigenetic changes include factors like:
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DNA methylation, which involves small chemical groups binding to a DNA, often in the promoter regions of genes. This represses gene expression by recruiting factors that lead to the compaction of chromatin, thus blocking transcription factors and making the gene less accessible for transcription. Mammals have DNA methylation in CpG (cytosine followed by guanine). Other organisms (like plants) can have DNA cytosine methylation in other contexts, such as CHH and CHG regions (H=C,T,A). DNA methylation, along with several other epigenetic changes, is explored in more detail in the video at the end of this section.
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Histone modification or variation, which in turn changes chromatin structure and influences gene expression. Deletion of an allele of the histone-modifying CREB binding protein, for example, can lead to Rubinstein-Taybi syndrome.
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Chromatin remodeling, which modifies the position of nucleosomes. This changes gene expression by hiding or exposing regions of the genome for transcription.
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Non-coding RNA (sncRNA and lncRNA), which performs regulatory functions in gene expression. Abnormal non-coding RNA behaviors can contribute to cancer, cardiovascular or immunological disorders, viral infections, and many other diseases.
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Genomic imprinting, a normally occurring process in which only one allele is expressed in an individual. Imprinting errors caused by epigenetic factors can lead to serious disorders. Prader-Willi syndrome, for example, is caused by maternal-only imprinting in a specific genetic region, or deletion or defects in the same region of the paternally inherited chromosome. This disorder is characterized by obesity, cognitive delays, behavioral problems, and often infertility. A better understanding of epigenetic changes in this region has allowed researchers to delineate methylation differences between this and Angelman syndrome, which has changes in the same genetic region.
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X-chromosome inactivation in females, which ensures that one of the two X chromosomes is deactivated in each cell. If both X chromosomes are active in a cell, that cell will produce double the amount of protein of a standard cell. Genetic mosaicism is also possible when X inactivation is inconsistent throughout the body.
Why Do We Study Epigenetics?
Epigenetic mutations are reversible. This makes these factors targets for therapeutic intervention. Inherited disorders, metabolic disorders, cancers, and degenerative diseases have all been linked to epigenetic modifications.
Epigenomic changes also provide major insights into biological processes and the role of the environment in development and disease. The more we uncover about the epigenome, the more we understand regulatory mechanisms of many biological processes.
Tools for Epigenetic Research
Whole-genome bisulfite sequencing
Whole-genome bisulfite sequencing (WGBS) measures the methylation status of the nucleotide cytosine across the genome. This tool helps researchers identify CpG islands (areas of the genome with a higher than average occurrence of CG dinucleotides). Because these islands are common in gene promoters, they are a prime candidate for methylation to inhibit expression of the downstream gene.
WGBS also helps to identify changes in CHH and CHG regions (H=C,T,A). CHH regions are implicated in methylation patterns in plants and are associated with silencing transposable elements. CHG regions are also found in plants, and are involved in gene silencing and chromatin structure.
WGBS has been used in recent studies on cardiovascular disease, including this one in which circulating cell-free DNA (ccfDNA) was explored as an additional marker for acute coronary syndrome (ACS). WGBS data from ACS patients was used to categorize methylation patterns with sub-types of the disease. These researchers proved that 254 differentially methylated regions could successfully stratify ACS patients without the need for other cardiac biomarkers.
Reduced representation bisulfite sequencing
Reduced representation bisulfite sequencing (RRBS) offers a more limited view of methylation. Where WGBS looks at the whole genome, RRBS focuses on CpG regions of the most relevance to the specific research study. This is a cost-effective option for projects where the location of epigenetic changes is suspected.
In 2023, RRBS was used to profile epigenetic changes in mucosal tissue of surgical and non-surgical Crohn’s disease (CD) patients. Both of these groups had DNA methylation signatures, distinct from each other and from healthy mucosal tissue. DNA methylation was reported in CD-implicated genes identified in previous GWAS projects, as well as different methylation signatures at different stages of the disease. These results are a step toward more precise diagnosis and categorizing of disease state in CD patients.
ATAC-Seq
The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a tool for investigating chromatin accessibility throughout the genome. ATAC-seq investigates accessible chromatin regions and provides insights into gene regulation and expression. ATAC-seq is commonly utilized in developmental biology and to study epigenetic dysregulation.
A 2024 Nature Communications publication used ATAC-Seq to profile motor neurons of 380 ALS patients. This research indicated that chromatin accessibility in ALS is heavily impacted by several factors, including sex and ancestry. Once these factors were accounted for, they were able to use this data to identify ALS signals and to predict ALS disease progression rates. These results indicate that ALS-related epigenetic changes in motor neurons are an important source of information to monitor disease progression.
ChIP-Seq
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is used to study protein–DNA interactions. This technology has been applied to understanding histone modifications, mapping chromatin states, and identifying epigenetic therapeutic targets.
For example, a 2024 study used both ChIP-Seq and ATAC-Seq to investigate iron deficiency during fetal and neonatal development. We know that iron deficiency in this period leads to long-term neurodevelopmental impairment. ChIP-Seq was conducted on rats suffering neonatal ID with and without prenatal choline supplementation.
Both ChiP-Seq and ATAC-Seq uncovered significant epigenetic changes in the ID-deficient groups. Prenatal choline supplementation can limit these negative effects. Further research is needed to uncover the iron-dependent epigenetic mechanisms that lead to long-term effects of neonatal ID.
Small RNA sequencing
Small RNA sequencing looks at only sncRNA, a component of gene expression regulation. sncRNAs include:
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microRNAs (miRNAs)
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Piwi-interacting RNAs (piRNAs)
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Small interfering RNAs (siRNAs)
Small RNA sequencing quantifies the amount of small RNA populations in a sample. When those quantities deviate from normal, we gain information about how sncRNA impacts regulatory function and contributes to epigenetic changes.
Both siRNAs and miRNAs are known to exert crucial regulatory functions by both pre- and post-transcriptional gene silencing — the RNAi Pathway. In contrast, piRNAs direct methylation and silencing of transposons in the germline. Small RNAs regulate gene expression by stimulating mRNA degradation or by inducing changes in heterochromatin structure causing loss of gene expression.
This technique is a high-sensitivity, whole genome option that focuses on post-transcription factors, making it a powerful tool for better understanding regulatory networks. A study from researchers in several Chinese hospitals investigated the role of sncRNA in chondrocyte senescence. Although we know chondrocyte senescence is a factor in age-induced osteoarthritis, sncRNA's role in this process is less clear. Using small RNA sequencing on human hip joint cartilage, researchers identified over 500 differentially expressed RNAs in senescent chondrocytes. These results suggest that some sncRNAs may be successful therapeutic targets in treating osteoarthritis.
Microarray
Microarrays have been developed to profile methylation status and histone modifications. Illumina’s Infinium MethylationEPIC Array is a popular option. Version 2.0 targets approximately 930,000 significant methylation sites at single nucleotide resolution.
This tool is a valuable option in disease research. In a recent publication out of NYU, scientists used this array to investigate triple negative breast cancers. TNBCs are a diverse group of cancers associated with poor prognosis. No targeted treatments have proven successful for these cancers. This study analyzed 44 cases of TNBC and was able to classify these patients into clinically relevant groups. These results point to DNA methylation profiling as an alternative way to categorize patients by risk and to choose more effective therapies.
Epigenetic research has revolutionized our understanding of gene regulation and its role in development, disease, and environmental adaptation. Epigenetic research tools provide powerful methods to explore the complex layers of gene expression regulation.
As these tools evolve, they deepen our insights into fundamental biological processes and open the door to novel therapeutic approaches, such as precision medicine and epigenetic drugs. The future of epigenetic research holds immense potential for addressing some of the most pressing challenges in health and disease, making it an exciting frontier in modern biology.
