A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
Reads0
Chats0
TLDR
Six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms are compiled, and new insights are reported.Abstract:
Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/.read more
Citations
More filters
Journal ArticleDOI
The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes
Christian J. Wippo,Lars Israel,Shinya Watanabe,Andreas Hochheimer,Craig L. Peterson,Philipp Korber +5 more
TL;DR: It is shown biochemically that RSC functions directly, can be sufficient, but mostly relies on other factors to properly position nucleosomes, and that nucleosome positioning specifically depends on the unique properties of the RSC complex.
Journal ArticleDOI
Histone variants at the transcription start-site.
TL;DR: It has traditionally been thought that transcription can only proceed once the nucleosomes at the TSS have been evicted, but new work suggests otherwise, and the focus of this review is to challenge this belief.
Journal ArticleDOI
Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes.
TL;DR: It is demonstrated that tRNA-mediated arrest is R-loop independent and proposed that replisome arrest and DNA damage are mechanistically separable.
Journal ArticleDOI
Evidence that the histone methyltransferase Dot1 mediates global genomic repair by methylating histone H3 on lysine 79.
Danielle Tatum,Shisheng Li +1 more
TL;DR: It is shown that Dot1 and H3K79 methylation are required for GGR in both nucleosomal core regions and internucleosomal linker DNA, but play no role in TCR.
Journal ArticleDOI
Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data
TL;DR: An improved nucleosome-positioning algorithm-iNPS- is described, which achieves significantly better performance than the widely used NPS package and achieves higher significance and lower false positive rates than previously published methods.
References
More filters
Journal ArticleDOI
Crystal structure of the nucleosome core particle at 2.8 Å resolution
TL;DR: The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it.
Journal ArticleDOI
Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome
Roger D. Kornberg,Yahli Lorch +1 more
TL;DR: The chromatin field needs much more information about structure beyond the nucleosome, and there is insufficient evidence that acetylation actually causes chromatin unfolding, and functional analysis in cell-free systems must be extended beyond theucleosome to the chromosomal context.
Journal ArticleDOI
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Dustin E. Schones,Kairong Cui,Suresh Cuddapah,Tae-Young Roh,Artem Barski,Zhibin Wang,Gang Wei,Keji Zhao +7 more
TL;DR: It is found that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding and the first nucleosomes downstream of a start site exhibits differential positioning in active and silent genes.
Journal ArticleDOI
The structure of DNA in the nucleosome core
TL;DR: Comparison of the 147-base-pair structure with two 146- base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.
Journal ArticleDOI
The DNA-encoded nucleosome organization of a eukaryotic genome
Noam Kaplan,Irene K. Moore,Yvonne N. Fondufe-Mittendorf,Andrea J. Gossett,Desiree Tillo,Yair Field,Emily M LeProust,Timothy P. Hughes,Jason D. Lieb,Jonathan Widom,Eran Segal +10 more
TL;DR: The results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization ofucleosomes in vivo.