Genetics: Computational Approaches to the Role of Epigenetic Marks in Transcription Regulation

A closer alliance between computational and experimental researchers is needed to make progress towards one of biology’s most challenging goals, understanding how epigenetic marks contribute to regulation of gene expression. This emerged from a recent workshop organised by the European Science Foundation (ESF), “Computational Approaches to the Role of Epigenetic Marks in Transcription Regulation”. Epigenetics studies features of the DNA and chromatin that are stably inherited through cell division but that are beyond the DNA sequence itself. It has been well established that epigenetic features influence the transcription process whereby the DNA sequences of genes are translated into the RNA and protein products that determine structure and function. Just as crucially, it is believed that epigenetics also allows changes to these gene expression patterns to be remembered, so that different organs and tissues can emerge during embryonic development, and retain their identity and function for the rest of the organism’s lifetime. Changes in gene expression can result from modifying chromatin, which is the structure comprising proteins and DNA that is the repository for genetic information. Marks are imposed that serve as templates for modification of the chromatin, altering the ability of genes to be accessed by the DNA transcription machinery. The result is that some genes are suppressed and others are silenced altogether. One of the key questions discussed at the ESF workshop concerned how these changes are “remembered” during cell division through replication of the epigenetic marks, and yet how in some cases these can be reversed, allowing a cell to be reprogrammed so that it can take on a different role or function. The ability of cells...