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Study of Twins Starts Unraveling Genetic, Environmental Contributors to Gene Regulation

NEW YORK (GenomeWeb) – In Nature Genetics, researchers from the University of Geneva Medical School, the Swiss Institute of Bioinformatics, and other international centers reported on findings from a massive effort to untangle genetic and environmental influences on gene activity.

Using samples collected from around 400 female twin pairs for the TwinsUK effort, the researchers did RNA sequencing on up to four tissue types per person. All told, they were able to assess messenger RNA patterns in 716 skin samples, 766 fat samples, 814 lymphoblastoid cell lines, and 384 blood samples from the twins.

The transcriptome data made it possible for the investigators to estimate and quantify allele-specific expression patterns at heterozygous SNPs transcribed in the four tissue types in individuals from the identical and non-identical twin pairs included in the study.

Together with information from discordant identical twins, the data allowed the researchers to begin picking apart environmental and genetic contributors to the thousands of allele-specific expression sites detected in the fat, skin, blood, and lymphoblastoid cell samples — an analysis that attributed anywhere from 38 percent to 49 percent of ASE variance to non-genetic factors.

Based on their findings, the study's authors presented a model for allelic expression imbalance that involves genetic regulators acting near a gene of interest, combined with more distant "trans" factors influenced by environmental inputs, which can tweak the extent of that so-called "cis" effect. 

"We have discovered that the genetic and environmental contexts of a mutation have a much greater influence on its expression in a given individual than we previously thought," the study's first author Alfonso Buil, a genetics and genomics researcher affiliated with the University of Geneva and the Swiss Institute of Bioinformatics, said in a statement. "Understanding the architecture of genetic expression constitutes an essential step in understanding the genetic bases of complex diseases."