A new technique developed by scientists from Salk Institute to rapidly map regions of DNA targeted by regulatory proteins could provide insight into what makes some plants drought tolerant or disease resistant. Revealing this landscape of protein-binding zones on DNA, called the "cistrome," shows how plants control where and when genes are expressed. Previous methods to map the cistrome in plant cells were difficult and slow, but the new approach offers a sweeping view of this critical aspect of genetic regulation.

The cistrome was mapped using a system that the researchers created, where they could add a tagged transcription factor to a library of DNA, let it bind and then isolate all the DNA-protein pairs. The method, called DNA affinity purification sequencing (DAP-seq), vastly expands how much more information scientists can understand about transcription factors and their binding sites. To test DAP-seq, the researchers mapped 529 transcription factors bound to the genome of Arabidopsis thaliana and identified 2.7 million binding sites.

They repeated the experiments using DNA containing or not containing cytosine methylation, and the binding patterns of about three-quarters of the transcription factors that they tested changed. The results show not only how regulatory proteins alter gene expression, but also the roles the epigenomic methylation marks may play in this regulation.

For more details, read the news release at the Salk Institute website.

Figure: From left: Ronan O’Malley, Anna Bartlett, Joe Ecker and Carol Huang