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Computers 'taught' to ID regulating gene sequences
Date:11/5/2012

erated a training set through experiments of their own. They began with a purified population of mouse melanocytes, which are the skin cells that produce the pigment melanin that gives color to skin and absorbs harmful UV rays from the sun. The researchers used a technique called ChIP-seq (pronounced "chip seek") to collect and sequence all of the pieces of DNA that were bound in those cells by special enhancer-binding proteins, generating a list of about 2,500 presumed melanocyte enhancer sequences.

Once the researchers had these two training sets for their computers, one specific to the brain and another to melanocytes, the computers were able to distinguish the features of the training sequences from the features of all other sequences in the genome, and create rules that defined one set from the other. Applying those rules to the whole genome, the computers were able to discover thousands of probable brain or melanocyte enhancer sequences that fit the features of the training sets.

In the brain study, the computers identified 40,000 probable brain enhancer sequences; for melanocytes, 7,500. Randomly testing a subset of each batch of sequences, the scientists found that more than 85 percent of the predicted enhancer sequences enhanced gene activity in the brain or in melanocytes, as expected, verifying the predictive power of their approach.

The researchers say that, in addition to identifying specific DNA sequences that control the genetic activity of a particular organ or cell type, these studies contribute to our understanding of enhancers in general and have validated an experimental approach that can be applied to many other biological questions as well.


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Contact: Catherine Kolf
ckolf@jhmi.edu
443-287-2251
Johns Hopkins Medicine
Source:Eurekalert  

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