Cataloging DNA Methylation & Gene Expression in Children

Over the last few decades, the study of epigenetics has broadened our understanding of how the environment affects human development and disease. But, there’s still a lot we don’t know about this relationship. There have been several epigenome-wide association studies (EWAS) that have helped scientists identify altered methylation patterns. However, the challenge lies in interpreting the results obtained from these studies.

Now, a new study from the Barcelona Institute for Global Health (ISGlobal) hopes to assist researchers in their biological interpretation of EWAS. The work, featured in the online publication eLife, details a catalog of expression quantitative trait methylation (eQTM) in children’s blood. An eQTM represents a specific location on the genome where DNA methylation level regulates gene activity.

“Identifying associations between DNA methylation levels and gene expression might help us better interpret epigenome-wide association studies and understand the biological processes leading to disease,” said ISGlobal researcher Mariona Bustamante who co-led the first-time study with Carlos Ruiz-Arenas from the Universitat Pompeu Fabra (UFP). Before this investigation, scientists had only data available from adult subjects, not children.

The primary epigenetic tag found in differentiated cells is 5-methylcytosine (5-mC) or DNA methylation. This mechanism regulates the expression of genes by recruiting proteins to inhibit gene expression and transcription factor DNA binding. Environmental effects like diet, pollution, and exercise influence DNA methylation, allowing many organisms to adapt. However, as noted in prior studies, alterations in DNA methylation have been linked to conditions like cancer, metabolic & neurological disorders, autoimmune diseases, as well as aging.  

The current study referenced data from the Human Early Life Exposome (HELIX) project and examined blood samples from 832 children, ages 6-11yrs old, of European ancestry. DNA methylation and gene expression assessment was first conducted on each sample, followed by pairing each gene with the closest methylation site(s).

The results showed nearly 40,000 eQTMs, representing about 22,000 unique sites and roughly 9,000 individual genes – the majority tended to be close to their regulated gene and enriched for genetic variants. In addition, inverse associations between methylation and gene expression levels were seen in 58.8% of the cases, but there was only a small overlap with eQTMs compared to adult samples.

“This was expected, as it is known that DNA methylation and gene expression change with age,” said Ruiz-Arenas ” However, differences in study designs can also explain this.”

In addition to characterizing child blood eQTMs and reporting how they are altered by age and genetics, the study also provides a unique public resource, which can be found at https://helixomics.isglobal.org.

“Our results provide a catalogue of methylation-gene expression associations that could become a powerful tool to help researchers interpret epigenome-wide association studies in children,” notes Bustamante.

Source: C.Ruiz-Arenas, et al. Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood. eLife, March 18, 2022.

Reference:A New study Provides Valuable Information on DNA Methylation and Gene Expression in Children. Barcelona Institute for Global Health (ISGloba l), April