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'Goldilocks' rules may govern genes in our evolution

Our evolutionary history points out how a short list of neuro-developmental disorders may be due to the quantity of gene 'copy number variants' (CNVs) we carry. Particularly brain conditions such as autism spectrum disorders, ADHD, schizophrenia, intellectual disability, developmental delay, and epilepsy — may reflect an individual's quantity of CNV combinations.


There are over 20,000 genes in the human genome that contain codes to produce proteins in our body. Geneticists in the Molecular Evolution Laboratory at the Smurfit Institute of Genetics, University of Dublin, focused on those regions of our genome where duplicated or deleted codes are commonly found. These regions are called 'copy number variants' (CNVs) and are abundant in humans. They also occur in other organisms like the bacteria E. coli. But, approximately 4.8 to 9.5% of the human genome can be classified as CNVs.


CNVs are variations in the structure of a gene, specifically, a duplication or deletion of a base pair on the chromosome ladder.

 


CNVs are important in disease development and categorized in two main groups: short and long. The classification system is soley based on the length of the duplication.

Short repeats
are mostly two repeating nucleotides such as A-B-A-B-A-B... and so on. There are also tri-nucleotide repeats such as A-B-C-A-B-C-A-B-C-... and so on.

Long repeats are made up of entire genes repeating themselves. Not all CNVs result in noticeable differences between people — sometimes the genes within them function the same regardless of the number of repeats. However, variations in others are implicated in a variety of debilitating diseases and disorders. Disease CNVs are larger containing multiple genes. A major challenge is identifying which genes cause which problems.

A more fascinating question is how did CNVs come about in the first place? Most theories are still speculative. More importantly, there is still no conclusive evidence that relates a specific CNV to a specific disorder or disease outcome. However, there are two main molecular mechanisms that form CNVs: homologous based — or having the same relative position or structure on a gene — or non-homologous based.


"Our idea was that there must be some genes within these regions with 'Goldilocks' properties: too much or too little duplication, and things don't work properly. The number of copies must be just right."

Aoife McLysaght PhD, Principal Investigator, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland.


McLysaght's team looked back over human evolutionary history to discover over time, which genes do or do not tolerate increases or decreases in repeats. A key observation in the repeat process is the presence of  "Goldilocks genes" within disease-causing CNVs. "Goldilocks genes" may kick into action during early embryogenisis, so are particularly important.


The team found CNVs associated with disorders in development tend to vary less in number of gene copies than benign CNVs do. This pattern held true across different mammal species — from sheep to dogs to rabbits even gorillas.


This implies a wide variation in the number of gene copies may have evolved and persisted in benign CNVs because they do not seriously affect fetal physiology, nor end a pregnancy.

However, in disease and disorder-linked CNVs there is less gene variation but more quantity of CNVs, and these CNVs do get passed onto offspring.


"Our work demonstrates our evolutionary history is useful for understanding human disease ... allowing us to hone in on a short list of genes as candidates for a disease in question — some of which are seriously debilitating.

"Isolating specific genes linked to these disorders increases our understanding of how and why they develop, leading to better diagnostics, and potentially therapies further down the line."

Aoife McLysaght PhD, Professor, Molecular Evolution Lab, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Ireland


Abstract
Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in particular neurodevelopmental disorders. Pathogenic CNVs are typically very large and contain multiple genes, and understanding the cause of the pathogenicity remains a major challenge. Here we show that pathogenic CNVs are significantly enriched for genes involved in development and genes that have greater evolutionary copy number conservation across mammals, indicative of functional constraints. Conversely, genes found in benign CNV regions have more variable copy number. These evolutionary constraints are characteristic of genes in pathogenic CNVs and can only be explained by dosage sensitivity of those genes. These results implicate dosage sensitivity of individual genes as a common cause of CNV pathogenicity. These evolutionary metrics suggest a path to identifying disease genes in pathogenic CNVs.
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Feb 15, 2017   Fetal Timeline   Maternal Timeline   News   News Archive   



A relatively short list of genes are candidates for a suite of debilitating diseases
including autism spectrum disorders, schizophrenia, and epilepsy.
Image Credit: Trinity College Dublin, Ireland.

 


 


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