While I am (generally) aware of the controversy about the "genomic code", my understanding of the issue has become much clearer after reading the correspondences between both sides published in the 17(8), August 2010 issue of Nature Structural & Molecular Biology [NSMB]:
- "Nucleosome sequence preferences influence in vivo nucleosome organization" (pp918 - 920) by Kaplan … and Segal
- "Evidence against a genomic code for nucleosome positioning" Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization” (pp920 - 923) by Zhang … and Struhl
- "A preoccupied position on nucleosomes" (p923) by Pugh
It should be noted that early work by Drew & Travers (JMB85) and Satchwell et al. (JMB86) provided evidence that the rotational positioning of DNA about the histone octamer is regulated by DNA sequence-dependent bending preferences. Goodsell & Dickerson quantified the Satchwell trinucleotide model by assigning a set of roll angles to predict DNA bending from base sequence. This bending model, along with five others, was implemented by SCHNArP for building approximate 3D DNA structures (with fixed values for slide, twist etc other parameters). However, this functionality is dropped out from 3DNA, simply because of the arbitrariness/subtleties in picking up the parameters.