28 November 2012
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
New Publication by Tanya Vavouri
Tanya Vavouri, Junior Group Leader at the IMPPC has just published her first paper for the IMPPC in Genome Biology. The paper, co-authored with Ben Lehner of the Genetic Systems group at the CRG, describes how the type of promoter in which transcription is initiated influences the chromatin of human genes.
Vavouri is interested in understanding the chromatin organization of genes, in other words the packaging of genes in the nucleus. This packaging, also referred to as ‘epigenetics’ affects in which cells in the human body, and when, genes become active. Since the 1980s it has been known that the control regions of many genes – called their promoters – are rich in CG sequences. More recently these CG-rich sequences, commonly referred to as ‘CpG islands’, were shown to affect chromatin. In this study, Vavouri and Lehner used genome-wide maps of chromatin marks for genes with or without CpG island promoters and found that genes with CpG island promoters have a characteristic series of transcription-associated chromatin modifications that is different to that observed in other human genes. This signature is complex, with the identity, levels, shape, positioning and ordering of chromatin modifications all differing depending on whether the gene has a CpG island promoter or not. This reveals that CpG islands do not just flag gene promoters, but they also have a greater influence on the chromatin organization of the gene itself.
As epigenetic modifications are intimately connected with transcription, this work suggests that there may be differences in how genes with different types of promoters are transcribed. Although the mechanisms are unclear, this work pins down some of the key players paving the way for how these differences arise to be described.
Tanya Vavouri's group is an example of a very new type of group in biological research. They carry out their work by analyzing previously published data, as in this paper. Vavouri explains that this way of working is relatively new in Biology and is changing the way much research is carried out. Recent technological advances allow huge amounts of high quality data to be generated by individual researcher groups, or large international consortia, this way providing computational biologists with excellent material to analyze. This means that researchers can now carry out research and discover new biology entirely from reanalyzing previously published data. This represents a way of doing biology that is developing rapidly and didn't even exist ten years ago. The IMPPC already has two computational biology groups working and plans to extend the Integrative Biology Program in the future.