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Deep genomics
Date:1/13/2011

er again but with different antibodies. And we keep doing the experiment again and again and sending the data to the bioinformatics people."

As the data build up, the computer begins to look for groups of modifications that tend to occur together. For example, different sets of modifications might occur on genes that are repressed, paused, fluctuating or active.

In the end, the team found they were able to capture most of the complexity of the fruit fly's chromatin landscape with nine combinatorial states, that is, nine sets of DNA or protein modifications.

Beautiful chromosomes

Drosophila has a pretty simple genome, Elgin says, consisting of only four chromosomes.

The chromatin states can be visualized by drawing long, thin chromosomes and coloring them in bars that correspond to different chromatin states. But these vermicelli-like graphs are hard to read.

Another way to visualize the states is to fold the chromosomes into a geometric pattern that maintains the spatial proximity of nearby regions of the chromosome. This makes it easier to spot patches of uniform color that correspond to domains with the same chromatin state.

In these maps of the fruit fly's chromatin, differences are immediately evident.

The dark blue in the lower right corner of the left arm of the fruit fly's third chromosome (left middle) corresponds to heterochromatin, a tightly packed, usually silent form of DNA that forms around the structure called the centromere where the two arms of a chromosome are joined. (The centromere is the site where the chromosomes attach to the mitotic spindle during cell division.)

"The flecks of red mark transcription start sites," Elgin says, "spots where we find genes that are being actively expressed. They are usually flanked by states 2, 3 and 4 which we think are related to gene regulation. They include the enhancers, regions of DNA that facilitate the transcription of
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Contact: Diana Lutz
dlutz@wustl.edu
314-935-5272
Washington University in St. Louis
Source:Eurekalert  

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