A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
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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
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Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo.
TL;DR: It is demonstrated that both the nucleolytic processing and the ligation of Okazaki fragments can be uncoupled from DNA replication and delayed until after synthesis of the majority of the genome is complete.
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Distal chromatin structure influences local nucleosome positions and gene expression
TL;DR: This study shows that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called ‘antinucleosomal elements’ like poly(dA:dT) tracts being key determinants of nucleosomes positions.
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Comparative analysis of methods for genome-wide nucleosome cartography
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Preferential repair of DNA double-strand break at the active gene in vivo.
TL;DR: This study reports for the first time that DNA double-strand break (DSB) repair is also coupled to transcription, and reveals that DSB repair at the active gene is faster than that at the inactive gene, thus supporting transcription-coupled D SB repair in living cells.
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Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data
TL;DR: This work uses Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA.
References
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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.
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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.