(540d) Effect of Local Sequence On the Genomic Positioning of Nucleosomes

DNA encodes the genetic information necessary for most living organisms. While cellular functions require this information be accessible, the genome (human genome ~ 2 meters in length) must also be highly compacted in order to fit within the nucleus of the cell (~10 μm). In eukaryotes, the compact form of the genome is the chromosome. At the lowest level of organization, the chromosome consists of the nucleosome in which approximately 147 base-pairs of DNA are wrapped around a core histone protein complex. Adjacent nucleosomes are then separated by short nucleosome-free linker regions of DNA.

The mechanism of nucleosome positioning on the genome is not well understood with competing viewpoints being presented in the literature^1,2.  It is known that certain sequence motifs have a higher affinity for nucleosome formation both in vitro and in vivo compared to others^3,4. However, whether this local affinity, or lack thereof, dominates nucleosome positioning in vivo and thus constitutes a “code” for nucleosome positioning is unclear; recent data suggests that the location of nucleosomes on the genome is largely statistical in nature with sequence preference playing a minor role⁵. These emerging viewpoints have been formulated in the context of experimental data; molecular models capable of describing nucleosome positioning are not yet available.

In this work, we employ a coarse grain model for DNA^6,7 and the histone protein complex in combination with a novel molecular simulation technique to study the effect of dinucleotide base steps on the preferred orientation of DNA wrapped around the histone complex.  Recently, this coarse-grain model was used to determine the work required to bend different DNA sequences to the curvature required by nucleosomes⁸.  We study sequences known to show high affinity for nucleosome formation as well as sequences that do not. We examine the orientational preference of these sequences and identify those motifs that enhance the stability of the nucleosome structure. In addition, to address the question of whether sequence alone, in the absence of DNA binding factors, can drive the positioning of nucleosomes, we determine the free energy surface associated with the position of a histone complex along a strand of DNA with a region in which nucleosome formation is not observed in vivo (e.g. a protein binding site) and an adjacent region that favors nucleosome formation.

GSF and DMH are supported by an NHCRI training grant to the Genomic Sciences Training Program, T32HC002760.

¹Kaplan et al., Nature Structural & Molecular Biology 17, 918 (2010).

²Zhang et al., Nature Structural & Molecular Biology 17, 920 (2010).

³Segal et al., Nature 442, 772 (2006).

⁴Kaplan et al., Nature 458, 362 (2009).

⁵Zhang et al., Nature Structural & Molecular Biology 16, 847 (2009).

⁶Knotts, et al., Journal of Chemical Physics 126, 084901 (2007).

⁷Sambriski et al., Biophysical Journal 96, 1675 (2009).

⁸Ortiz et al., Physical Review Letters, in press.