Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
A Translational Signature for Nucleosome Positioning In vivo
In vivo nucleosomes often occupy well-defined preferred positions on genomic DNA. An important question is to what extent, these preferred positions are directly encoded by the DNA sequence itself. We derive here from accurately mapped in vivo positions identified by partial micrococcal nuclease digestion a translational positioning signal that identifies the approximate midpoint of DNA bound by a histone octamer. This signal corresponds well to the averaged sequence organisation of cloned ?in vivo? octamer binding sequences and occurs in ~70% of sampled accurately mapped positions in yeast but differs substantially from the sequence organisation of octamer binding sites selected in vitro. In particular this signal is enriched in preferred microcccal nuclease cleavage sites relative to positioning sequences identified on the basis of limit micrococcal nuclease digestion to core nucleosomes. On the basis of these results we propose a modified sequence code for protein-induced DNA bending and hence for nucleosome positioning.
The translational signature comprises two components: a region of high sequence periodicity flanking the midpoint on one or both sides and a region of low average sequence periodicity spanning the midpoint itself. We suggest that in the latter position the DNA sequence could act as a torsional sink to facilitate octamer binding. Since the translational signature is associated with more than one nucleosome in an array and also occurs at a frequency greater than that of nucleosomes we infer that nucleosome positioning in yeast is neither completely statistical as proposed by Kornberg, but nor is it completely specified by the DNA sequence. We suggest that positioning of nucleosomes in an array in vivo requires an ?organiser?.
We further show that under more ?physiological? reconstitution conditions the same octamer-binding sequences identified ?in vivo? bind the octamer with a substantially higher affinity than a DNA sequence selected for octamer binding by salt dilution protocols. The change in the relative affinity for natural and selected sequences as determined by the different protocols can be up to 300-fold. The sequence associated with -1 nucleosome at the 5? end of the ADY2 array binds the octamer with a higher affinity than sequences associated with downstream nucleosomes and thus could act in part as an ?organiser?.
1Fondazione Istituto Pasteur-Fondazione