A second code?

Nicholas Wade extols the virtues of chromatin organization and regulation in today?s linkurl:__Science Times__;http://www.nytimes.com/2006/07/25/science/25dna.html hitting on a topic that I always love reading and writing about. Here he talks about DNA directed nucleosome positioning. Certain DNA sequences, perhaps because of their relative bendability, might be more or less amenable to histone wrapping making some regulatory sequences more or less accessible. A linkurl:recent paper;http://www.nature.com/nature/journal/v442/n7104/abs/nature04979.html in __Nature__ predicted these sequence-nucleosome interactions with about 50% accuracy. Wade?s billing it as a ?second code,? a ?nucleosome code? which hearkens to the linkurl:controversial histone code hypothesis,;http://www.the-scientist.com/article/display/23393 stating that modifications to histones might provide epigenetic control of gene regulation. The wording is a slight but forgivable misstep, and to his credit the piece is pretty carefully worded overall. The words that the authors on the Nature paper use are ?nucleosome positioning code.? What?s ?encoded? here (if the results stand up to scrutiny and replication) is directed by the DNA sequence, not by the nucleosomes as Wade notes. As a ?code? it?s arguably pretty arbitrary, though. Key dinucleotides, TT, AA, or TA appear spaced about 10 bp apart through much of the nucleosome. The wiggle room noticeable in the authors 50% success rate is likely to ramp up considerably as the model is applied to more complex eukaryotes (the current study is largely in yeast). Nevertheless, this should provide another way to interrogate chromatin in a more quantitative fashion. [Note added 8/18: Thanks for the note about the broken link. It should be working now]

A second code?

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