The first 'layer' (my scare quotes) is in the sequence of bases (G, A, T and C) in the double helix.
Leiden Schiessel and his research group "have simulated the folding of DNA strands with randomly assigned mechanical cues." And the simulation suggests "that these mechanical cues actually do determine how the DNA molecule is folded into so-called nucleosomes." The original research:Since the mid 1980s, it has been hypothesized that there is a second layer of information on top of the genetic code consisting of DNA mechanical properties. DNA molecules are much longer than the cells that contain them, and these molecules need to be wrapped up tightly to fit inside a single cell.This need for compression introduces also an opportunity: the regulation of transcription through a differentiated fashion of DNA packaging.The way in which DNA is folded determines how the letters are read out, and therefore which proteins are actually made. In each organ, only relevant parts of the genetic information are read.This has been referred to as the “nucleosome positioning code”. The theory suggests that mechanical cues within the DNA structures determine how preferentially DNA folds.
Eslami-Mossallam B, Schram RD, Tompitak M, van Noort J, Schiessel H, Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach, PLoS ONE 11(6): e0156905. doi:10.1371/journal.pone.0156905