Fig 3. AML-1a specifically lacks 10 bp periodicity within the nucleosome-bound Ly49 regions.

(A) Schematic showing the significance of 10 bp periodicity within a nucleosome-bound stretch of DNA. Those factor binding sites that display 10 bp periodicity can be oriented in such a way as to always face out from the nucleosome surface and so still be accessible by transcription factors. Conversely, those factors without 10 bp periodicity are out of phase with the turn of the DNA helix, and so cannot adopt an outward-facing conformation. (B) 10 bp periodicity was determined by Fourier transform of the positional data for all 17 transcription factors pooled together across all nucleosome-bound regions of the Ly49 gene family (first column: ‘None’), or by removing one factor at a time and comparing how this removal affects the periodgram at 10 bp. Note that, because this is a leave-one-out analysis, an increase of 10 bp periodicity upon removing a factor indicates that the removed factor lacks 10 bp periodicity. (C) Individual periodgrams of all transcription factors indicated in (B).