There's so much more to the human genome than just instructions for making proteins, for example, many non-coding regions help control the expression of those protein-coding genes. Regulating protein expression is crucial - not all genes are expressed in all cells at the same time. Some genes are only active during development, others might only be expressed in certain tissues, while others are turned on exclusively in specific tissues. Researchers have now learned more about the parts of the human genome that have a regulatory function, and they've made the data publicly accessible at eqtlgen.org.
Reporting in Nature Genetics, an international team of scientists analyzed the genomic data of over 30,000 people to identify sequences that help control the activity of genes that other research has linked to disease. The study authors are hopeful that this study will advance precision medicine, and can help match patients to the right treatment.
“Our discovery provides researchers an entirely new perspective on their genes of interest, and will help prioritize genes that may be more relevant for therapeutic intervention. It could also lead us to better markers for tracking disease progression and the efficacy of medicines,” noted co-senior study author Professor Lude Franke of the University Medical Centre Groningen.
Advanced genetic and computational tools have enabled researchers to find even small associations between certain diseases and small variations in the sequence of DNA. Some of those small sequence changes or genetic variants occur in protein-coding genes, but the impact of those variants may be very small, or might only be understood in the context of changes in other parts of the genome. Other variants appear in regulatory regions, and they influence the activity of genes and affect how much of a protein is produced.
Expression quantitative trait loci (eQTLs) are features in the genome that influence gene expression; they can affect how much of an mRNA transcript is produced. Variants in eQTLs may help us understand how certain genes are involved in disease, or how to treat certain diseases.
This study has revealed new eQTLs after assessing genetic data from 31,684 people.
“Thanks to the statistical power of this large dataset, we were able to uncover new regulatory regions on the human genome,” said co-senior study author Associate Professor Joseph Powell, Director of the Garvan-Weizmann Centre for Cellular Genomics. “Instead of just cataloguing the regulatory gene locations that were adjacent [called cis-eQTLs], we were able to reveal genes that modulated the activity of more distant genes [called trans-eQTLs].”
This study determined that about 88 percent of genes had a cis-eQTL influence, and 37 percent had a trans-eQTL influence. Many of these distant influences had a biological impact that could be predicted - though those predictions were not tested.
“While it’s clear that genetic variants are almost always a root cause of disease, the mechanism by which they influence disease is far less clear. For instance, while a specific condition may be linked to hundreds of genetic variants, the vast majority contribute to disease by regulating gene activity,” said Powell.
If we can determine which genes are most affected by this regulation, we may be able to find new drug targets, Powell added. “What we’ve discovered is an entirely new level of genomic information, providing a deeper understanding of biology and disease.”
Sources: Garvan Institute of Medical Research, Nature Genetics