Results 41 to 50 of about 71,049 (222)
DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
Nucleic Acids Research, 2018 While nucleosomes are highly stable structures as fundamental units of chromatin, they also slide along the DNA, either spontaneously or by active remodelers.
G. Brandani +3 more
semanticscholar +1 more source
eLife, 2016 We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict ...
Max A Horlbeck +10 more
doaj +1 more source
Ubiquitous nucleosome unwrapping in the yeast genome [PDF]
, 2013 Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of DNA-binding factors to their target sites and thus may provide a dominant pathway for effecting rapid and robust access to ...
arxiv +1 more source
Genes & Development, 2018 Here, Rawal et al. analyzed Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC and uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and repositioning the +1 ...
Yashpal Rawal +6 more
semanticscholar +1 more source
Nonspecific transcription factor-DNA binding influences nucleosome occupancy in yeast [PDF]
Biophysical Journal, Volume 101, Issue 10, 2465-2475 (2011), 2011 Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of nonspecific transcription factor (TF)-DNA binding free energy
arxiv +1 more source
A core viral protein binds host nucleosomes to sequester immune danger signals
Nature, 2016 Viral proteins mimic host protein structure and function to redirect cellular processes and subvert innate defenses. Small basic proteins compact and regulate both viral and cellular DNA genomes.
Daphne C. Avgousti +16 more
semanticscholar +1 more source
Making better CRISPR libraries
eLife, 2016 A new algorithm improves the performance of CRISPR-based genetic screens in mammals.
Shiyou Zhu, Wensheng Wei
doaj +1 more source
, 2007 We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a significant density of two-level nucleosome switching regions where, as a function of the chemical potential, the ...
arxiv +1 more source
DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
eLife, 2017 Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic
David B. Lyons, Daniel Zilberman
semanticscholar +1 more source
Ctf4 organizes sister replisomes and Pol α into a replication factory
eLife, 2019 The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol α-primase.
Zuanning Yuan +8 more
doaj +1 more source