Reprogramming gene expression with small molecules

A small molecule stabilises a secondary structure in replicating DNA
A small molecule (white) stabilises a secondary structure (pink) in replicating DNA

When cells divide, they must accurately copy their genetic material (DNA) and also ensure that their pattern of gene expression is maintained – genes that were ‘on’ before the cell divides need to remain on in the daughter cell, and genes that were ‘off’ need to remain off. These patterns of gene expression are determined by epigenetic signals, and it is possible to alter these signals to reprogram gene expression. New work by Julian Sale’s group in the LMB’s PNAC Division, in collaboration with Shankar Balasubramanian’s group in the University of Cambridge Department of Chemistry, has shown that small molecules, which target an unusual DNA secondary structure known as a G-quadruplex, can be used to cause localised changes in epigenetic signals and gene expression, which remain even after the small molecule is removed.

Epigenetic signals that determine the pattern of gene expression in a cell often come in the form of modifications to histone proteins, around which the DNA is wrapped. In order for the information carried by histone modifications to remain close to the DNA sequence with which it is associated, the replication of DNA needs to be coupled with the recycling of histone proteins. If the DNA is folded up into a secondary structure and there is a problem unfolding this structure, DNA replication can be delayed. Previous work from Julian’s group has shown that, under certain circumstances, this can disrupt the recycling of histone proteins, creating patches of the genome in which the parental histone modifications are lost, thus altering histone information and therefore gene expression.

Guillaume Guilbaud from Julian’s group and Pierre Murat from Shankar’s group designed and synthesised small molecules to bind and stabilise a G-quadruplex secondary structure found in the BU-1 gene and studied their effects on gene expression. Stabilising the secondary structure disrupted DNA replication resulting in epigenetic changes to the locus and reduced BU-1 expression. These changes in gene expression persisted even after the small molecule was removed, showing that the molecule caused a change in the cell’s epigenetic signature which was then passed on to daughter cells. Moreover, Guillaume and Pierre were able to demonstrate that there were two stages to the change in gene expression: first active histone modifications around BU-1’s G-quadruplex motif were lost, and secondly the region was methylated, converting it to inactive DNA.

There has been much interest in epigenetic therapies which seek to reprogram cells’ gene expression. However, such techniques target the machinery which regulates histone modifications, leading to genome-wide epigenetic changes and the risk of extensive undesired effects. This work suggests a new approach for epigenetic therapy, by targeting discrete DNA sequences, which has the potential to be more selective and could be theoretically used to reprogram only a subset of genes rather than the entire genome. In the future, this approach could be used to control the aberrant expression of disease-causing genes, such as in cancer cells.

This work was funded by the MRC, Wellcome Trust, Cancer Research UK and the European Research Council.

Further references

Paper in Nature Chemistry
Julian’s group page
Shankar Balasubramanian’s group page