Decoding the code code
A few weeks ago linkurl:I chided Nick Wade;http://www.the-scientist.com/blog/display/24083/ (lovingly!
A few weeks ago linkurl:I chided Nick Wade;http://www.the-scientist.com/blog/display/24083/ (lovingly! I?m a huge fan, after all) for invoking the ?code? word when describing a study on nucleosome positioning. It surprised me when my post spurred some comments on the nature of the __Nature__ press office, and their proclivity for hyping, but ?not overhyping,? the research papers within. Wade can be forgiven. I didn?t realize how pervasive the word code had been in __Nature__ until I saw the disturbingly assonant headline on the cover of the issue. -- ?The Chromatin Code Decoded.? And in all fairness, __Nature__ and their press office deserve some slack. They?re trying to generate interest in and sell their magazine, and I?ll be happy when science magazines like __Nature__ linkurl:(62,000);http://npg.nature.com/media/nature/pdf/nature.pdf sport more subscribers than __Cosmopolitan__ linkurl:(940,000).;http://www.cosmomediakit.com/r5/showkiosk.asp?listing_id=360478&category_id=27808&category_code=circ
Some of the skeptics of the linkurl:histone code hypothesis;http://www.the-scientist.com/article/display/23392/ have told me they get the sense that people love to use the word ?code? to describe their work because it?s marketable. While it?s not a completely unfounded observation, I understand the urge to see some sort of neat and readable codified message in life?s instructions. Few codes in nature will be quite as cut and dry as the genetic code. But when faced with the dizzying complexity of biological processes, it's natural for scientists to hope that some might follow a similarly simple set of rules.
Alas, this might not be one of those cases. In a linkurl:news and views;http://www.nature.com/nature/journal/v442/n7104/full/442750a.html that accompanied the nucleosome-positioning code article, Timothy Richmond at the ETH Zürich, Institut für Molekularbiologie und Biophysik, Switzerland, raises some interesting caveats about the ability of this new algorithm to predict nucleosome positioning strictly from DNA sequence. An interesting black box is the role of the linker histone H1, which acts to space nucleosomes in many eukaryotic genomes, but not in yeast (which the study largely worked with). Richmond points to some fascinating mouse work in which researchers deleted several copies of H1 and found that nucleosomes naturally packed much tighter. So, nucleosome spacing can?t be __completely__ directed by something encoded by the DNA sequence. It?s an interesting hypothesis, and one that?s captured my imagination, but it?s going to require some more testing in various eukaryotic genomes.
September 10, 2006
apparently it's more complicated than just an simple algorithm. In the research of mouse H1 deletion, the length of spacing DNA was changed drastically, but the compaction of chromatin and gene expression were almost the same as in natural condition. I simply believed that H1 can't dictate the whole bussiness of chromatin compaction, moreover, the nucleosome core DNA sequences should also involve in gene expression and regulation, otherwise there will be no meaning for remodelling factors.