rtain which of these genes CREB regulates by more traditional methods, evaluating one gene at a time, would be too labor-intensive, expensive, and take a very long time. Scientists have been working on short cuts, but all so far have limits. For example, in one recent technique, scientists mix the regulator protein of interest (let’s say, CREB) with the entire genome of a cell and let it bind. Then they fragment the genome into smaller pieces, 500 to 1,500 nucleotide bases long. Using antibodies that specifically recognize and bind to CREB, they then isolate the pieces that have CREB attached, and wash all the others away. Scientists can use traditional gene-sequencing methods to decipher the sequence of A, T, G, and C on these fragments and then locate their original positions on the genome, but it is a slow and somewhat expensive process. Other methods, such as matching the pieces to their compliments on microarrays, are limited by the size of genome they can analyze. Dunn’s team has come up with a technique to determine the positions of these 500-to-1,500-base-long pieces on an entire genome ?even one as large as the human genome ?relatively quickly and in very large numbers. After isolating the CREB-bound fragments, they release the CREB and then cut the DNA with a “restriction?enzyme that recognizes a particular nucleotide base sequence, CATG. Further manipulation of the cut ends allows them to isolate 20-base-long-fragments, or “tags,?in each direction from these cut sites. This gives the scientists a large number of very short DNA “tag?sequences, which all have the same start sequence of CATG plus 16 additional unknown bases. The scientists then “glue?together the tags into chains and sequence them. While small in length, the tags are large enough to allow computer searches to locate their specific positions on the complete genome in a manner that is analogous to a laser scanner reading barcodes on items in the grocery store. In this case the inventory isn’t
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Source:Brookhaven National Laboratory


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