11.26.07

Review Highlights Recent Advances in Computational Epigenetics

Posted in news links at 9:57 am by Trevor

A nice review article by Bock et. al. in Bioinformatics sheds light on some of the recent advances (2006-2007) being made in computational epigenetics. Some highlights:

The article provides a succinct introduction to epigenetics research for bioinformaticians that are new to the field, including explanations of mitotic vs. meiotic epigenetic inheritance, mechanisms of epigenetic regulation, and common techniques for genome-wide mapping of the epigenome.
CHIP-on-chip analysis is explored from a bioinformatics perspective, providing technical details on how this data can be efficiently analyzed with freely available tools.
The review provides a handy list of epigenome mapping projects and their current state as of October 2007.
The review notes some of the ways in which the ENCODE project has helped to develop more refined techniques for bioinformatics analysis of epigenetic data, such as new methods for using epigenetic information in promoter prediction.
One key challenge in computational epigenetics is the issue of public data storage. Hundreds of gigabytes of data can be generated routinely, and the ability to easily share the data on publicly accessible servers will be an ongoing issue.
Using epigenetic data for promoter prediction is increasingly becoming less relevant, therefore work is now being focus on advanced questions of transcriptional control, such as inferring tissue-specific signals and reconstructing transcriptional networks.
The concept of CpG islands are being refined based on new insight using genome-wide computational studies to better predict the location of CpG islands and DNA methylation.
Recent work in cancer epigenetics has shown the potential benefits of combining computational and experimental approaches in deciphering how epigenetics shapes cancer progression.
The authors expect that future computational studies in epigenetics will increasingly take into account the proteins that read and write epigenetic information, and that reduced costs in epigenome mapping will enable many studies of epigenetic variation in human populations.

And finally: “In conclusion, exciting times are ahead for research in computational epigenetics!”

References:

Bock C, Lengauer T. 2007. Bioinformatics Advance Access published online on November 17, 2007.

doi:10.1093/bioinformatics/btm546

Tags: epigenetics, computational, methylation