How DNA Methylation Shapes Our Earliest Development
The delicate chemical dance that begins at conception may be subtly different for the millions of children born through assisted reproductive technology.
In July 1978, Louise Joy Brown made history as the first "test-tube baby," marking a revolutionary breakthrough in reproductive medicine. Since then, over 8 million children have been born worldwide through assisted reproductive technology (ART), with these procedures now accounting for approximately 1-6% of all births in developed countries. While the overwhelming majority of ART-conceived children are healthy, decades of research have revealed subtle increases in certain health risks, particularly for imprinting disorders—rare conditions involving improper gene regulation. At the heart of this mystery lies DNA methylation, an essential epigenetic process that ART may inadvertently disrupt during the vulnerable early stages of embryonic development.
In our cellular orchestra, most genes play both copies—one inherited from each parent. However, genomic imprinting creates an exception to this rule. Through this unique process, approximately 100-150 human genes are "stamped" with their parental origin during egg and sperm formation, resulting in monoallelic expression where only one copy is active while the other remains silent.
For some genes, only the paternal copy is expressed; for others, only the maternal copy functions. This precise regulation is crucial for normal growth and neurodevelopment.
Genomic imprinting represents a classic example of epigenetics—molecular modifications that regulate gene activity without changing the DNA sequence itself.
These specialized DNA regions, known as differentially methylated regions, maintain parent-specific methylation patterns.
"The disruption of imprinting processes during gametogenesis and the expression of imprinted genes causes significant developmental defects and diseases in humans referred to as genomic imprinting disorders," scientists noted in a 2023 review 6 .
The connection between ART and epigenetic disruptions largely comes down to developmental timing. ART procedures—including ovarian stimulation, in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and embryo culture—occur precisely when the early embryo undergoes massive epigenetic reprogramming.
The newly formed embryo actively removes most methylation marks from both parental genomes.
Despite this global erasure, methylation at imprinted regions is specially protected to maintain parental-specific expression.
The embryo then establishes new methylation patterns appropriate for development.
This carefully orchestrated process may be vulnerable to external influences during ART. "ART involves the manipulation and culturing of embryos during a period that coincides with extensive epigenetic remodeling," explained researchers in a 2022 study 5 .
Environmental factors in the ART laboratory—including culture media composition, oxygen concentration, and even temperature stability—may potentially introduce errors in these delicate epigenetic patterns.
In 2014, a landmark systematic review and meta-analysis examined the relationship between ART and epigenetic disturbances, analyzing data from 18 studies comparing ART-conceived and spontaneously conceived children 1 . The findings were noteworthy:
Higher odds of imprinting disorders in IVF/ICSI children
Statistically significant methylation differences at several imprinted genes
Substantial heterogeneity between studies in protocols and methods
A 2022 study in Nature Communications analyzed cord blood DNA methylation in 962 ART-conceived and 983 naturally conceived newborns 5 . Using advanced Illumina EPIC arrays examining over 770,000 CpG sites, they discovered:
Parental influence was ruled out as the methylation patterns were not explained by parental subfertility or the parents' own methylation profiles.
| Disorder | Key Features | Imprinted Region | Association with ART |
|---|---|---|---|
| Beckwith-Wiedemann syndrome | Overgrowth, abdominal wall defects, macroglossia | 11p15.5 | Well-established increased risk |
| Angelman syndrome | Developmental delay, speech impairment, seizures, happy demeanor | 15q11-q13 | Some reported associations |
| Prader-Willi syndrome | Neonatal hypotonia, feeding difficulties, hyperphagia and obesity in childhood | 15q11-q13 | Some reported associations |
| Silver-Russell syndrome | Intrauterine growth restriction, poor growth after birth, body asymmetry | 11p15.5, chromosome 7 | Limited evidence |
To better understand how ART affects the fetal epigenome, let's examine the Norwegian Mother, Father and Child Cohort Study in detail, published in Nature Communications in 2022 5 . This research represents one of the most comprehensive epigenetic investigations of ART effects to date.
962 ART-conceived and 983 naturally conceived newborns with parental samples
Illumina EPIC array analyzing 770,586 CpG sites
Sophisticated models controlling for confounders
Distinguished ART effects from subfertility influences
ART-conceived newborns showed slightly but significantly lower methylation across the genome, with 74% of CpGs being hypomethylated compared to naturally conceived infants.
A clear separation emerged between ART and non-ART groups when examining the 607 significantly different CpGs, suggesting a consistent ART-associated methylation pattern.
Fresh embryo transfers showed more pronounced epigenetic differences (800 significant CpGs) compared to frozen embryo transfers (only 3 significant CpGs).
Differentially methylated genes included those involved in neurodevelopment, growth regulation, and immune function.
| Gene | Number of Significant CpGs | Known Gene Function | Potential Health Relevance |
|---|---|---|---|
| HLA-DQB2 | 11 | Immune response regulation | Autoimmune conditions, immune function |
| BRCA1 | 10 | DNA repair, tumor suppression | Cancer risk, genome maintenance |
| NBR2 | 10 | Located near BRCA1, non-coding RNA | Cancer-associated genomic region |
| Multiple genes | 8 or fewer | Neurodevelopment, growth, metabolism | Various developmental processes |
Understanding how scientists detect these subtle epigenetic changes helps appreciate the technical sophistication behind these findings. Here are essential tools enabling this research:
| Research Tool | Specific Example | Function in Research |
|---|---|---|
| Methylation arrays | Illumina Infinium MethylationEPIC BeadChip | Simultaneously measures methylation at 850,000+ CpG sites across the genome |
| Bisulfite conversion reagents | Sodium bisulfite treatment | Chemically converts unmethylated cytosines to uracils while leaving methylated cytosines unchanged |
| Bioinformatics pipelines | Custom R and Python scripts | Statistical analysis of methylation data, controlling for cell type composition and other confounders |
| Tissue-specific reagents | Cord blood, placental, buccal cell collection kits | Enable examination of methylation patterns in different tissues relevant to development |
| Control materials | Reference DNA standards with known methylation patterns | Quality control and standardization across experiments and laboratories |
While the increased relative risk of imprinting disorders with ART demands scientific attention, it's crucial to contextualize these findings. The absolute risk remains low. Even with a 3.67-fold increased odds, imprinting disorders affect only approximately 1-2% of ART-conceived children 1 3 .
Higher odds compared to spontaneous conception
Of ART-conceived children affected by imprinting disorders
Remaining 98% unaffected
The growing understanding of ART's epigenetic impact has spurred research into novel interventions. Scientists are exploring epigenetic-based therapies that could potentially prevent or correct imprinting disruptions 6 :
Compounds that inhibit specific enzymes involved in epigenetic regulation, such as histone deacetylases (HDACs) or EHMT2/G9a.
Short nucleic acid strands designed to target and modulate the expression of specific imprinted genes.
Using modified CRISPR-Cas systems to precisely alter methylation patterns at specific genomic locations without changing the underlying DNA sequence.
The journey to understand ART's epigenetic impact reflects a larger narrative in modern medicine: how technological breakthroughs can simultaneously solve profound challenges while introducing new complexities. The evidence strongly suggests that ART procedures can subtly influence the epigenetic landscape of early embryonic development, particularly at delicately regulated imprinted genes.
However, these findings represent the beginning, not the end, of scientific inquiry. As one research team concluded, "More controlled studies, using standardized methodologies, in larger, better clinically defined populations are needed" 1 . What remains clear is that for millions of families worldwide, ART has fulfilled the fundamental human desire to build a family—a benefit that continues to drive research toward optimizing these technologies for both short-term success and long-term health.