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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Does DNA sequence matter for nucleosome positioning in vivo?

Nucleosome formation is a first step towards packaging genomic DNA into chromosomes. Nucleosomes are formed by wrapping 147 base pairs of DNA in a superhelix around a spool of eight histone proteins. It is reasonable to assume that formation of single nucleosomes in vitro is primarily determined by DNA sequence: it costs less elastic energy to wrap a flexible DNA polymer around the histone octamer, and more if the polymer is rigid. However, it is unclear to which extent this effect is important in living cells, which have evolved chromatin remodeling enzymes to actively reposition nucleosomes. In addition, nucleosome positioning on genome-length DNA sequences is strongly affected by steric exclusion - multiple nucleosomes have to form simultaneously without overlap, creating regular arrays. At the same time, our recent analysis of the changes in chromatin structure that accompany addition of glucose to starved yeast cells (in collaboration with James Broach) reveals that correlation between nucleosome positioning and transcriptional response is fairly weak. At most promoters we observe stereotypical chromatin structure which does not depend on glucose levels and which could in principle be determined by the DNA sequence alone. Currently available bioinformatics methods for predicting nucleosome positions are trained on in vivo data sets and are thus unable to distinguish between extrinsic and intrinsic nucleosome positioning signals. Furthermore, in most cases no attempt is made to explicitly de-convolute DNA sequence specificity from steric exclusion. In order to see the relative importance of these contributions to nucleosome positioning in vivo, we have developed a model based on a large collection of DNA sequences from nucleosomes reconstituted in vitro by salt dialysis (data provided by Frank Pugh). We have used these data to infer the free energy of nucleosome formation at each position along the genome. Our method uses an exact result from the statistical mechanics of classical 1D particles of finite size, enabling us to infer the free energy landscape while automatically taking steric exclusion into account. We will discuss the degree to which in vitro nucleosome occupancy profiles are predictive of in vivo nucleosome positions, and will estimate how many nucleosomes are sequence-specific and how many are positioned through other means. Our physical approach to nucleosome energetics is applicable to multiple organisms and genomic regions.

George Locke
Alexandre V. Morozov

Department of Physics & Astronomy
and BioMaPS Institute for Quantitative Biology
136 Frelinghuysen Rd
Piscataway, NJ 08854-8019
morozov@physics.rutgers.edu