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Taking into account nucleosomes for predicting gene expression

Teif, VB and Erdel, F and Beshnova, DA and Vainshtein, Y and Mallm, JP and Rippe, K (2013) 'Taking into account nucleosomes for predicting gene expression.' Methods, 62 (1). 26 - 38. ISSN 1046-2023

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Abstract

The eukaryotic genome is organized in a chain of nucleosomes that consist of 145-147. bp of DNA wrapped around a histone octamer protein core. Binding of transcription factors (TF) to nucleosomal DNA is frequently impeded, which makes it a challenging task to calculate TF occupancy at a given regulatory genomic site for predicting gene expression. Here, we review methods to calculate TF binding to DNA in the presence of nucleosomes. The main theoretical problems are (i) the computation speed that is becoming a bottleneck when partial unwrapping of DNA from the nucleosome is considered, (ii) the perturbation of the binding equilibrium by the activity of ATP-dependent chromatin remodelers, which translocate nucleosomes along the DNA, and (iii) the model parameterization from high-throughput sequencing data and fluorescence microscopy experiments in living cells. We discuss strategies that address these issues to efficiently compute transcription factor binding in chromatin. © 2013 Elsevier Inc.

Item Type: Article
Uncontrolled Keywords: Gene regulation function TF-nucleosome interference Protein binding map Combinatorial binding Chromatin
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Life Sciences, School of
Depositing User: Elements
Date Deposited: 11 Oct 2017 13:05
Last Modified: 14 Oct 2019 23:17
URI: http://repository.essex.ac.uk/id/eprint/20476

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