Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
By Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal. PLoS Comput. Biol., 2008
500 citations recorded by the source corpus.
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of ∼380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/d19d4a7498607f6caf083e4569569ee969ce628f
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Lin F. Yang
- T. Rando
- Desiree Tillo
- Eran Meshorer
- Gil Ast
- Anshul B Kundaje
- Schraga Schwartz
- A. Brunet
In Plant Science
Citations in the corpus
- Chromatin organization marks exon-intron structure (2009, background): “The splicing code and the chromatin code overlap In a recent study, all 1,024 possible pentamers were scored on the basis of their empirically observed tendency to be covered by a nucleosom”
- DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale (2013, background): “nucleosome binding sites (22,23), and its average is compared with previously published OH-cleavage data derived from ORChID2 (19).”
- H3K4me3 breadth is linked to cell identity and transcriptional consistency (2014, background): “In addition, increased chromatin accessibility at promoters may facilitate transcriptional consistency, in part by minimizing transcriptional bursting (Field et al., 2008).”
- G+C content dominates intrinsic nucleosome occupancy (2009, methodology): “In order to further benchmark our model, we compared the performance of the 14 feature model with published models[2,8,22-26,29,31,32] on other in vitro and in vivo nucleosome occupancy data sets, using Pearson correlation between predicted and actual data.”