Regensburg 2010 – scientific programme

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DY: Fachverband Dynamik und Statistische Physik

DY 2: Statistical Physics of Biological Systems I (joint session of BP + DY)

DY 2.9: Talk

Monday, March 22, 2010, 12:30–12:45, H45

Genome Folding at the 30 nm Scale — •Philipp M. Diesinger¹ and Dieter W. Heermann² — ¹Institute of Theoretical Physics, Heidelberg, Germany / MIT, Cambridge, USA — ²Institute of Theoretical Physics, Heidelberg

We present a Monte Carlo model for genome folding at the 30-nm scale with focus on linker-histone and nucleosome depletion effects. Depletion of linker histones and nucleosomes affects, massively, the flexibility and the extension of chromatin fibers. Increasing the amount of nucleosome skips can lead either to a collapse or to a swelling of chromatin fibers. We show that depletion effects may even contribute to chromatin compaction. Furthermore, we find that predictions from experimental data for the average nucleosome skip rate lie exactly in the regime of maximum chromatin compaction.

We determine the nucleosome pair distribution function of chromatin. We show that chromatin nanostructure might in principle be accessible by 2D high-resolution light microscopy: Our simulations show that even in the case of fibers with depletion effects and after a projection, the main dominant peaks can still be identified.

Furthremore, we compare our simulations with 5C data of a gene desert as well as FISH data and find that only fibers with random depletion of linker histones or nucleosomes can explain the probability of random chromatin contacts on small length scales that play an important role in gene regulation. Missing linker histones and nucleosomes might not just be randomly occuring simple unavoidable defects but instead they might even play a regulatory role in gene expression.