Results 51 to 60 of about 64,059 (299)
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. [PDF]
PLoS Computational Biology, 2008 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.
Yair Field +7 more
doaj +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
Chemistry & Biology, 2010 In order to form a covalent complex with DNA inside human cells, cisplatin has to overcome the protective environment of a nucleosome, where DNA is complexed with histone proteins. Todd and Lippard (2010) expand our understanding of this process by describing the structure of a nucleosome containing a Pt-DNA adduct, which has important implications for
openaire +3 more sources
Nucleosome packaging and nucleosome positioning of genomic DNA [PDF]
Proceedings of the National Academy of Sciences, 1997 The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95% of bulk DNA sequences have an affinity for ...
J. Widom, P. T. Lowary
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Control of nucleosome movement: To space or not to space nucleosomes? [PDF]
Epigenetics, 2010 A key feature of ATP-dependent chromatin remodeling complexes is how they control the ability of the complex to translocate along DNA within the context of a nucleosome. Although these complexes generally initiate DNA translocation near the dyad axis of the nucleosome, the progression and eventual termination is regulated in quite distinct ways.
Blaine Bartholomew, Punit Prasad
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DNA Nanomechanics in the Nucleosome [PDF]
Structure, 2009 The sequence-dependent mechanics of DNA-histone binding are essential for nucleosome positioning and mobility. Here we reanalyze nucleosome crystal structures in terms of the well-characterized base-pair scale DNA elasticity, extracting the forces and torques acting on all bound DNA base pairs.
Ralf Everaers, Nils B. Becker
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Nucleosome destabilization by polyamines
Archives of Biochemistry and Biophysics, 2022 The roles and molecular interactions of polyamines (PAs) in the nucleus are not fully understood. Here their effect on nucleosome stability, a key regulatory factor in eukaryotic gene control, is reported, as measured in agarose embedded nuclei of H2B-GFP expressor HeLa cells.
Laszlo Imre +9 more
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Molecular Oncology, EarlyView.Loss of the frequently mutated chromatin remodeler ARID1A, a subunit of the SWI/SNF cBAF complex, results in less open chromatin, alternative splicing, and the failure to stop cells from progressing through the cell cycle after DNA damage in bladder (cancer) cells. Created in BioRender. Epigenetic regulators, such as the SWI/SNF complex, with important
Rebecca M. Schlösser +11 more
wiley +1 more source
Genomic sequence is highly predictive of local nucleosome depletion. [PDF]
PLoS Computational Biology, 2008 The regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome ...
Guo-Cheng Yuan, Jun S Liu
doaj +1 more source
Statistical mechanics of nucleosome ordering by chromatin structure-induced two-body interactions [PDF]
Phys. Rev. E 83, 050903 (2011), 2010 One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes ...
arxiv +1 more source