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Patterns in genome organization may partially explain how microbial cells work

ial patterns in the arrangement of most sequenced microbial genomes. They related the degree of organization in each genome they studied to various characteristics specific to each species.

"Bacterial chromosomes may have something like ZIP codes that fix groups of genes to certain locations within the cell where they are most needed," said Timothy E. Allen, a member of Palsson's team at UCSD who is currently an assistant professor of biomedical engineering at the University of Virginia. He said the surprising organization begs the question of what it means. The sequence order of bacterial genomes most likely affects the way in which the DNA is compressed, often more than 1,000-fold, to fit within the confines of the cell. "In some cases, it might suggest that a genome is arranged into relatively large physically distinct coils inside the cell, but nobody knows for certain," Allen said. "One of the take-home messages of our study is that we need to develop more ways to measure the location of specific genes within individual cells."

Palsson's team included Allen, recent Ph.D. graduate Nathan D. Price, and Ph.D. candidate Andrew R. Joyce. They downloaded the sequences of the 161 prokaryotic genomes from the CBS Genome Atlas Database and analyzed regions of each genome for the relative amount of four basic building blocks of DNA, the density of genes and expression level of those genes, and other factors.

To detect patterns in those features, they used wavelet analysis, a statistical technique used to identify patterns in geophysical data such as significant warming of the surface of the ocean off South America that causes El Niño climatic events. The wavelet analysis of bacterial genomes yielded "scalograms," maps colored to elucidate the strength of a variety of periodicities associated with chromosome position. Just as the wavelet analysis identified significant increases in sea surface temperatures; it also revealed nonrandom patterns in th
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Source:University of California - San Diego


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