A second code?
Nicholas Wade extols the virtues of chromatin organization and regulation in today?
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]
July 30, 2006
Papers like this (Sega et al.,) show how odd the translation from original artlce, to popular science writting can be. The NY times and several other major news sources reported these findings as "new code found within DNA that goes beyond genes" "hyper code within DNA" etc... and other slightly exagerated claims.\n\nI don't really know who to blame. The publishers of the original research wouldn't mind the extra publicity, if it leads to increased citations. The authors of the populat science piece need to jazz it up a bit to get more readers; and people love to read exciting things, even if they're not completely true.\n\n-Bill\nwww.ilikethings.com
August 1, 2006
The transition from original scientific paper in peer reviewed journal to popular press report also often goes through another filter -- the journal and/or university press release. This is usually where the problems start. Nature, for example, posts a clause at the head of its weekly press releases stating that all efforts are made not to over-hype (just hyping is bad enough!) the findings. And yet it frequently goes on to break its own rules by doing just that.\n\nSexy soundbites make a paper stand out, helping it gain the all important media attention its publishers -- not necessarily its authors -- crave. Whilst in fairness press releases are usually accurate, they are undoubtedly geared to extol the virtues of a study, whilst underplaying any weaknesses it might have.\n\nUnfortunately, it seems there is a snowball effect: a slight overstatement in a press release can gather momentum and end up on the printed page of a national newspaper as a poor representation of what the study's authors actually discovered, let alone the conclusions that can be drawn from their findings.
August 16, 2006
"A recent paper in Nature predicted these sequence-nucleosome interactions with about 50% accuracy. "\n\nThe link given above no longer works (it pointed to an 'advance publication'). The Abstract of "A genomic code for nucleosome positioning" can now be found at:\n\nhttp://www.nature.com/nature/journal/v442/n7104/abs/nature04979.html\n\nJohn Latter / Jorolat\nEvolution Research \nhttp://evomech.blogspot.com/