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
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Journal ArticleDOI
ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA
Claudia C. Carcamo,Matthew F. Poyton,Anand Ranjan,Giho Park,Robert K. Louder,Thuc Dzu,Carl Wu,Taekjip Ha +7 more
TL;DR: It is demonstrated that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA, which is well characterized for DNA binding proteins.
Journal ArticleDOI
Preferential Nucleosome Occupancy at High Values of DNA Helical Rise
Francesco Pedone,Daniele Santoni +1 more
TL;DR: Mean helical rise profiles obtained by using maps of positioned nucleosomes of the Drosophila melanogaster and Plasmodium falciparum genomes, as well as Homo sapiens chromosome 20, confirm that nucleosites are mainly located where the mean helicals rise reaches its largest values.
Posted ContentDOI
Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation
Sarina Y. Porcella,Natasha C. Koussa,Colin P. Tang,Colin P. Tang,Daphne N. Kramer,Priyanka Srivastava,Priyanka Srivastava,Duncan J. Smith +7 more
TL;DR: Although the initiation of both strands is widely thought to be mechanistically similar, it is determined that Ctf4, a hub that connects proteins to the replication fork, specifically recruits Pol α to the lagging strand but is not required for leading-strand initiation.
Dissertation
Chromatin Remodeling Around Nucleosome Free Regions Represses Non-Coding RNA By DNA Looping and Transcription Factor Dependent Targeting of Isw2
TL;DR: Chromatin Remodeling Around Nucleosome Free Regions Represses Non-Coding RNA By DNA Looping and Transcription Factor Dependent Targeting of Isw2.
Dissertation
Defining the chromatin structure of the human genome using size-selected nucleosome mapping
TL;DR: The work in this thesis examines genome-wide and local changes in the patterns of nucleosome positioning throughout the human genome to provide insight into the role of chromatin structure in the regulation of human neural cell differentiation.
References
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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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Journal ArticleDOI
Dynamic Regulation of Nucleosome Positioning in the Human Genome
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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
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Journal ArticleDOI
The DNA-encoded nucleosome organization of a eukaryotic genome
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TL;DR: The results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization ofucleosomes in vivo.