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Genome Research
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https://doi.org/10.1007/978-3-...
Part of book or chapter of book . 2009 . Peer-reviewed
License: Springer TDM
Data sources: Crossref
Genome Research
Article . 2009 . Peer-reviewed
Data sources: Crossref
Genome Research
Article . 2009
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Incorporating nucleosomes into thermodynamic models of transcription regulation

Authors: Raveh-Sadka, T.; Levo, M.; Segal, E.;

Incorporating nucleosomes into thermodynamic models of transcription regulation

Abstract

Transcriptional control is central to many cellular processes, and, consequently, much effort has been devoted to understanding its underlying mechanisms. The organization of nucleosomes along promoter regions is important for this process, since most transcription factors cannot bind nucleosomal sequences and thus compete with nucleosomes for DNA access. This competition is governed by the relative concentrations of nucleosomes and transcription factors and by their respective sequence binding preferences. However, despite its importance, a mechanistic understanding of the quantitative effects that the competition between nucleosomes and factors has on transcription is still missing. Here we use a thermodynamic framework based on fundamental principles of statistical mechanics to explore theoretically the effect that different nucleosome organizations along promoters have on the activation dynamics of promoters in response to varying concentrations of the regulating factors. We show that even simple landscapes of nucleosome organization reproduce experimental results regarding the effect of nucleosomes as general repressors and as generators of obligate binding cooperativity between factors. Our modeling framework also allows us to characterize the effects that various sequence elements of promoters have on the induction threshold and on the shape of the promoter activation curves. Finally, we show that using only sequence preferences for nucleosomes and transcription factors, our model can also predict expression behavior of real promoter sequences, thereby underscoring the importance of the interplay between nucleosomes and factors in determining expression kinetics.

Related Organizations
Keywords

Binding Sites, Saccharomyces cerevisiae Proteins, Base Sequence, Models, Genetic, Transcription, Genetic, Acid Phosphatase, Nucleosomes, Gene Expression Regulation, Thermodynamics, Promoter Regions, Genetic, Protein Binding, Transcription Factors

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Powered by OpenAIRE graph
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
86
Top 10%
Top 10%
Top 1%
bronze