Methods for Investigating DNA Accessibility with Single Nucleosomes

2016 ◽  
pp. 379-415 ◽  
Author(s):  
M.D. Gibson ◽  
M. Brehove ◽  
Y. Luo ◽  
J. North ◽  
M.G. Poirier
Keyword(s):  
Dna Accessibility

scholarly journals Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Laxmi N. Mishra ◽  
Sharon Pepenella ◽  
Ryan Rogge ◽  
Jeffrey C. Hansen ◽  
Jeffrey J. Hayes
Keyword(s):  
Dna Accessibility ◽  
Nucleosome Arrays

scholarly journals Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Xingqi Chen ◽  
Ulrike M. Litzenburger ◽  
Yuning Wei ◽  
Alicia N. Schep ◽  
Edward L. LaGory ◽  
...  
Keyword(s):  
Single Cell ◽  
Environmental Regulation ◽  
Dna Accessibility

DNA STAINABILITY DEPENDS ON DNA QUANTITY AND DNA ACCESSIBILITY TO DYES

1991 ◽  
Vol 73 (2-3) ◽  
pp. 34a-34a
Author(s):  
Philippe Vago ◽  
Bernard Lamy
Keyword(s):  
Dna Accessibility

scholarly journals Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET

2020 ◽  
Vol 48 (3) ◽  
pp. 1551-1571 ◽  
Author(s):  
Kathrin Lehmann ◽  
Suren Felekyan ◽  
Ralf Kühnemuth ◽  
Mykola Dimura ◽  
Katalin Tóth ◽  
...  
Keyword(s):  
Single Molecule ◽  
Histone H3 ◽  
Time Range ◽  
Histone H2a ◽  
Histone Tails ◽  
Dna Accessibility ◽  
Single Molecule Fret ◽  
Multiple Interaction ◽  
Nucleosome Disassembly ◽  
Dynamic Transitions

Abstract Chromatin compaction and gene accessibility are orchestrated by assembly and disassembly of nucleosomes. Although the disassembly process was widely studied, little is known about the structure and dynamics of the disordered histone tails, which play a pivotal role for nucleosome integrity. This is a gap filling experimental FRET study from the perspective of the histone H3 N-terminal tail (H3NtT) of reconstituted mononucleosomes. By systematic variation of the labeling positions we monitored the motions of the H3NtT relative to the dyad axis and linker DNA. Single-molecule FRET unveiled that H3NtTs do not diffuse freely but follow the DNA motions with multiple interaction modes with certain permitted dynamic transitions in the μs to ms time range. We also demonstrate that the H3NtT can allosterically sense charge-modifying mutations within the histone core (helix α3 of histone H2A (R81E/R88E)) resulting in increased dynamic transitions and lower rate constants. Those results complement our earlier model on the NaCl induced nucleosome disassembly as changes in H3NtT configurations coincide with two major steps: unwrapping of one linker DNA and weakening of the internal DNA - histone interactions on the other side. This emphasizes the contribution of the H3NtT to the fine-tuned equilibrium between overall nucleosome stability and DNA accessibility.

scholarly journals Distinct modes of DNA accessibility in plant chromatin

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Huan Shu ◽  
Thomas Wildhaber ◽  
Alexey Siretskiy ◽  
Wilhelm Gruissem ◽  
Lars Hennig
Keyword(s):  
Dna Accessibility

Enhanced DNA Accessibility and Increased DNA Damage Induced by the Absence of Poly(ADP-ribose) Hydrolysis

Biochemistry ◽  
2010 ◽  
Vol 49 (34) ◽  
pp. 7360-7366 ◽  
Author(s):  
Yiran Zhou ◽  
Xiaoxing Feng ◽  
David W. Koh
Keyword(s):  
Dna Damage ◽  
Dna Accessibility

scholarly journals A base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding

2021 ◽  
Author(s):  
Aldo Hernandez-Corchado ◽  
Hamed S Najafabadi
Keyword(s):  
Binding Site ◽  
Cytosine Methylation ◽  
Binding Activity ◽  
Cpg Methylation ◽  
In Vivo Models ◽  
Cpg Dinucleotides ◽  
Dna Accessibility ◽  
Dna Binding Activity

Methylation of the cytosine base at CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of the majority of transcription factors (TFs). Recent in vitro studies of TF-DNA interactions have revealed a more complex picture, suggesting a heterogeneous cytosine methylation impact that varies across TFs, with over a third of TFs preferring methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences, however, is challenging, as the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. As a result, the in vivo methylation preferences of most TFs remain uncharacterized. Here, we introduce Joint Accessibility-Methylation-Sequence (JAMS) models for inferring the effect of CpG methylation on TF binding in vivo. JAMS creates quantitative models that connect the strength of the binding signal observed in ChIP-seq to the DNA accessibility of the binding site, regional methylation level, DNA sequence, and base-resolution cytosine methylation. Furthermore, by jointly modeling both the control and pull-down signal in a ChIP-seq experiment, JAMS isolates the TF-specific effects from background effects, revealing how methylation of specific CpGs within the binding site alters the TF binding affinity in vivo. We show that JAMS can quantitatively model the TF binding strength and learn the accessibility-methylation-sequence determinants of TF binding. JAMS models are reproducible and generalizable across cell lines, and can faithfully recapitulate cell type-specific TF binding. Systematic application of JAMS to 2368 ChIP-seq experiments generated high-confidence models for 260 TFs, revealing that 45% of TFs are inhibited by methylation of their potential binding sites in vivo. In contrast, only 6% prefer to bind to methylated sites, including 11 novel methyl-binding TFs. Comparison of these in vivo models to in vitro data confirmed high precision of the methyl-preferences inferred by JAMS. Finally, among the CpG-binding proteins from the ZF-KRAB family of TFs, we observed a disproportionately high preference for methylated sequences (24%), highlighting the role of CpG methylation in determining the genome-wide binding profiles of the TFs from this family.

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