Molecular basis of gene insulation

A lot of attention in research has been focused on mapping all the gene promoters and regulatory elements in the genome, yet little is known about which regulatory element is connected with which promoter. We spoke to Dr Maria Cristina Gambetta about her research into how gene expression patterns arise and how they become specific.

Our gene promoters are controlled by regulatory elements, that can either activate or silence a particular gene. Regulatory elements can be located at a relatively long distance from their target genes in the genome, as Dr Maria Cristina Gambetta, Assistant Professor in the Center for Integrative Genomics at the University of Lausanne, explains. “As a consequence, regulatory elements have the potential to connect to the wrong promoter during development, leading to its misregulation,” she outlines. “The challenge is to identify which regulatory element is connected to which promoter, and how they specifically connect,” she says. “Over the past decade or so new technologies have been developed that allow us to look at how the genome is folded in three dimensions, allowing us to assess how regulatory elements are wired to their target genes in 3-D.”

Genome folding

The wider relevance of this genome folding is still a matter of debate, as most studies so far have been conducted on mammalian cell cultures, which don’t reflect the overall complexity of gene expression patterns. After experimentally perturbing 3-D genome folding, cells need to survive for long enough for researchers to assess whether genome mis-folding causes mis-wiring of regulatory elements to the wrong promoters. Dr Gambetta is therefore using the classical model of the fruit fly – Drosophila melanogaster – in her research. “Human cells with misfolded genomes just die too quickly, that’s where the fly is useful,” she says. The aim in this research is to test the relevance of this 3-D genome folding to establishing connections between genes and their regulatory elements. “We test this by making flies with mutations in genes that encode for proteins that – we hypothesise – help fold the genome in three dimensions,” explains Dr Gambetta.

A gene that would normally encode for a protein is knocked out in these mutant flies, then researchers check whether this particular protein was indeed required for genome folding. Using genomics technologies researchers in the lab found that specific proteins are important for forming 3-D

In wildtype fly embryos, chromosomes are folded into domains containing genes and their regulatory elements. In mutant fly embryos, domain boundaries are blurry, and genes are expressed in imprecise patterns.

physical boundaries between genomic domains. Dr Gambetta also looks at the expression patterns of developmental genes in mutant flies lacking these 3-D physical boundaries. “Developmental genes are expressed in embryos, and are important to specify cell identity,” she outlines. “We were able to see that the expression patterns of certain developmental genes in our mutants changed in a way that we would have predicted if the genes were being misregulated by known regulatory elements from which they are normally protected by a 3-D physical boundary.”

This research is largely fundamental in nature, with Dr Gambetta investigating how 3-D, physical boundaries in the genome function to prevent regulatory cross-talk between genes and regulatory elements on either side of a boundary. Using Drosophila allows Dr Gambetta to test this concept in a very well-controlled, biological model, while also allowing the researchers to understand how gene expression patterns can be altered in developmental time, as well as spatially within the embryo. “We’re working with proteins that, if you remove them from a human cell, the cell will die within a few hours. The organism also dies in a fly, but only after going through at least a little bit of development first,” she explains. The fruit fly provides researchers with a handle to study the importance of genome folding to gene expression patterns. “We’re interested in how these gene expression patterns are made, and how they are specific,” says Dr Gambetta.

Molecular basis of gene insulation

Financed by the Swiss National Science Foundation grant to MCG #184715 and the University of Lausanne. Prof. Maria Cristina Gambetta Center for Integrative Genomics (CIG) University of Lausanne Unil-Sorge district Genopode building CH-1015 Lausanne Switzerland T: +41 21 692 3985 E: mariacristina.gambetta@unil.ch W: http://gambettalab.org

Maria Cristina Gambetta is an Assistant Professor in the Centre for Integrative Genomics at the University of Lausanne. She leads an independent research group and is investigating the molecular basis of gene regulation specificity, while she also supervises junior researchers at trainee, Masters, Ph.D and Postdoctoral levels.