Nucleosome position affects transcriptional regulation, models for position are required for understanding of TR. - Roland Krause

75-90% of the DNA is associated with nucleosomes, play an important regulatory role. - Oliver Hofmann

Use a recently published model to produce the affinity landscape, showing the suitability of nucleosome occupancy. - Roland Krause

Genomic nuceosome affinity landscape based on a thermodynamical model - Oliver Hofmann

The model is probably published here (http://www.ncbi.nlm.nih.gov/pubmed...) - Roland Krause

Can interactions between nucleosomes introduced into the model? - Roland Krause

Two kinds of interactions: direct or bridged by transcription factors or other proteins. - Roland Krause

Additional interactions are important for chromatin organization. DNA bending proteins, TF, histone modifications, etc. - Oliver Hofmann

First approach focuses on direct interaction, including the distance between the nucleosomes. - Roland Krause

Trying to capture interactions between adjacent nucleosomes (cooperative effects) - Oliver Hofmann

What types of functions can represent cooperativity types? - Roland Krause

Notable features include a right shifted main peak, followed by exponential decay. - Roland Krause

Tested Exponential, Stepped Exp, S-ES, Stepping-Off and Stepping-On - Roland Krause

Sampled 5000 configurations and compared it to the linker length preference. - Roland Krause

Can the model properly learned? - Roland Krause

Repeat with data samples, add noise and try to fit different models to the sampled occupancy landscape - Oliver Hofmann

Used synthetic data, including experimental noise, then forgot the algorithm to generate the data and used the previously described models. - Roland Krause

Exponential function shows a good correlation in five-fold cross-validation, with the model incorporating the interaction outperforming the ones without. - Roland Krause

Are the interactions relevant in vivo and in vitro? - Roland Krause

For an in vitro validation the Exp, Step functions work better than the no cooperativity model - Oliver Hofmann

Short linker lengths are favored. - Roland Krause

Interactions are also important using in vivo data, data from several chromosomes and different organisms (yeast and C. elegans) show similar results. - Roland Krause

The interesting part -- biological basis for this preference? - Oliver Hofmann

The in vitro system consists of nucleosomes and DNA only. - Roland Krause

shorter length may allow for interaction of nucleosomes, energetically favoring their shift from otherwise better binding positions - Oliver Hofmann

Hypothesis: electrostatic interaction between nucleosomes, which has been described previously but not shown in the data. - Roland Krause

# Surprised that the very model was not presented in the talk. - Roland Krause

# Wonder whether there is a difference between promoters, other nucleosome covered regions (or other genomic subsets); with the role nucleosome displacement plays in regulation I'd expect some shift - Oliver Hofmann

Blog notes: http://www.fiamh.info/article... - Oliver Hofmann

Q: When you started motivating the model, there was a peak at 10 but the sample data did not have that.[?] A: These are effects of histone H1, which are not modeled. There are a lot of question marks about the role of H1 in yeast. The interaction that we modeled are global and can occur anywhere on the DNA. More complex model would incorporate additional local effects, e.g. other factors. - Roland Krause

Q. Have you finished the model for the higher eukaryotes: A The model is independent of the organism. There might be differences, although this is debated. Differnces between yeast and human are known. - Roland Krause