Pyrosequencing positions nucleosomes precisely

Evidence that nucleosomes on the mouse mammary tumor virus promoter adopt specific translational positions.

We have previously demonstrated that an array of six nucleosomes are phased on the mouse mammary tumor virus (MMTV) long terminal repeat (1,2). In this study, we devised a new assay to measure the translational positions of specific nucleosomes on the MMTV promoter. Nucleosome core particles were purified and shown to contain A and B nucleosomal DNA by Taq polymerase primer extension with nucle...

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by deep-sequencing and high-density tiling arrays, and we discovered an array of well-positioned nucleosomes flanking sites occupied by the insulator binding protein CTCF across the huma...

A multi-layer method to study genome-scale positions of nucleosomes.

The basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamental nuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently reported. We have developed a new method, Multi-L...

Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing.

Playing Stochastic Games Precisely

We study stochastic two-player games where the goal of one player is to achieve precisely a given expected value of the objective function, while the goal of the opponent is the opposite. Potential applications for such games include controller synthesis problems where the optimisation objective is to maximise or minimise a given payoff function while respecting a strict upper or lower bound, r...