scholarly journals Extended and dynamic linker histone-DNA interactions control chromatosome compaction

2020 ◽  
Author(s):  
Sergei Rudnizky ◽  
Hadeel Khamis ◽  
Yuval Ginosar ◽  
Efrat Goren ◽  
Philippa Melamed ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Complex Dynamics ◽  
Linker Histone ◽  
Globular Domain ◽  
Entry And Exit ◽  
Nucleosome Core ◽  
Terminal Domain ◽  
Potential Regulatory Role ◽  
Rapid Binding

AbstractChromatosomes play a fundamental role in chromatin regulation, but a detailed understanding of their structure is lacking, partially due to their complex dynamics. Using single-molecule DNA unzipping with optical tweezers, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as ~ ±140 bp from the dyad. In addition to a symmetrical compaction of the nucleosome core governed by globular domain contacts at the dyad, the C-terminal domain compacts the nucleosome’s entry and exit. These interactions are dynamic, exhibiting rapid binding and dissociation, sensitive to phosphorylation of a specific residue, and crucial to determining the symmetry of the chromatosome’s core. Extensive unzipping of the linker DNA, which mimics its invasion by motor proteins, shifts H1 into an asymmetric, off-dyad configuration and triggers nucleosome decompaction, highlighting the plasticity of the chromatosome structure and its potential regulatory role.

scholarly journals N- and C-terminal Domains Determine Differential Nucleosomal Binding Geometry and Affinity of Linker Histone Isotypes H10 and H1c

2012 ◽  
Vol 287 (15) ◽  
pp. 11778-11787 ◽  
Author(s):  
Payal Vyas ◽  
David T. Brown
Keyword(s):  
Fluorescent Proteins ◽  
Dynamic Properties ◽  
Linker Histone ◽  
Chromatin Interaction ◽  
Globular Domain ◽  
Binding Characteristics ◽  
Domain Swap ◽  
Terminal Domain ◽  
Terminal Domains

Eukaryotic linker or H1 histones modulate DNA compaction and gene expression in vivo. In mammals, these proteins exist as multiple isotypes with distinct properties, suggesting a functional significance to the heterogeneity. Linker histones typically have a tripartite structure composed of a conserved central globular domain flanked by a highly variable short N-terminal domain and a longer highly basic C-terminal domain. We hypothesized that the variable terminal domains of individual subtypes contribute to their functional heterogeneity by influencing chromatin binding interactions. We developed a novel dual color fluorescence recovery after photobleaching assay system in which two H1 proteins fused to spectrally separable fluorescent proteins can be co-expressed and their independent binding kinetics simultaneously monitored in a single cell. This approach was combined with domain swap and point mutagenesis to determine the roles of the terminal domains in the differential binding characteristics of the linker histone isotypes, mouse H10 and H1c. Exchanging the N-terminal domains between H10 and H1c changed their overall binding affinity to that of the other variant. In contrast, switching the C-terminal domains altered the chromatin interaction surface of the globular domain. These results indicate that linker histone subtypes bind to chromatin in an intrinsically specific manner and that the highly variable terminal domains contribute to differences between subtypes. The methods developed in this study will have broad applications in studying dynamic properties of additional histone subtypes and other mobile proteins.

scholarly journals Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X

2016 ◽  
Vol 36 (21) ◽  
pp. 2681-2696 ◽  
Author(s):  
Mitsuru Okuwaki ◽  
Mayumi Abe ◽  
Miharu Hisaoka ◽  
Kyosuke Nagata
Keyword(s):  
Binding Site ◽  
Dynamic Behavior ◽  
Histone Variants ◽  
Linker Histone ◽  
Site Preference ◽  
Globular Domain ◽  
Linker Histones ◽  
Terminal Domain ◽  
Site Preferences ◽  
Linker Histone Variants

Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histonesin vivo. Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones.

scholarly journals DNA-sequence dependent positioning of the linker histone in a chromatosome: a single-pair FRET study

2020 ◽  
Author(s):  
Madhura De ◽  
Mehmet Ali Oeztuerk ◽  
Katalin Toth ◽  
Rebecca C. Wade
Keyword(s):  
Dna Sequence ◽  
Single Molecule ◽  
Binding Mode ◽  
Linker Histone ◽  
Single Pair ◽  
Globular Domain ◽  
Binding Modes ◽  
Single Molecule Fret ◽  
Fret Efficiency ◽  
Order Structures

The linker histone (LH) associates with the nucleosome with its globular domain (gH) binding in an on or off-dyad binding mode. The positioning of the LH may play a role in the compaction of higher-order structures of chromatin. Preference for different binding modes has been attributed to the LHs amino acid sequence. We here study the effect of the linker DNA (L-DNA) sequence on the positioning of a full-length LH, Xenopus laevis H1.0b, by employing single-molecule FRET spectroscopy. Chromatosomes were fluorescently labelled on one of the two 40bp long L-DNA arms, and on the gH. We varied 11bp of DNA flanking the core (non-palindromic Widom 601) of each chromatosome construct, making them either A-tract, purely GC, or mixed, with 64% AT. The gH consistently exhibited higher FRET efficiency with the L-DNA containing the A-tract, than that with the pure-GC stretch, even when the stretches were swapped. However, it did not exhibit higher FRET efficiency with the L-DNA containing 64% AT-rich mixed DNA, compared to the pure-GC stretch. We explain our observations with a FRET-distance restrained model that shows that the gH binds on-dyad and that two arginines mediate recognition of the A-tract via its characteristically narrow minor groove.

scholarly journals Common intermediates and kinetics, but different energetics, in the assembly of SNARE proteins

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Sylvain Zorman ◽  
Aleksander A Rebane ◽  
Lu Ma ◽  
Guangcan Yang ◽  
Matthew A Molski ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Energy Release ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Folding Energy ◽  
Single Molecule Level ◽  
Terminal Domain ◽  
Evolutionarily Conserved ◽  
Protein Receptors ◽  
And Function

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are evolutionarily conserved machines that couple their folding/assembly to membrane fusion. However, it is unclear how these processes are regulated and function. To determine these mechanisms, we characterized the folding energy and kinetics of four representative SNARE complexes at a single-molecule level using high-resolution optical tweezers. We found that all SNARE complexes assemble by the same step-wise zippering mechanism: slow N-terminal domain (NTD) association, a pause in a force-dependent half-zippered intermediate, and fast C-terminal domain (CTD) zippering. The energy release from CTD zippering differs for yeast (13 kBT) and neuronal SNARE complexes (27 kBT), and is concentrated at the C-terminal part of CTD zippering. Thus, SNARE complexes share a conserved zippering pathway and polarized energy release to efficiently drive membrane fusion, but generate different amounts of zippering energy to regulate fusion kinetics.

scholarly journals Optical tweezers in single-molecule biophysics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Carlos J. Bustamante ◽  
Yann R. Chemla ◽  
Shixin Liu ◽  
Michelle D. Wang
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Single Molecule Biophysics

Helical repeat of DNA in the nucleosome core particle

2000 ◽  
Vol 28 (4) ◽  
pp. 373-376 ◽  
Author(s):  
R. Negri ◽  
M. Buttinelli ◽  
G. Panetta ◽  
V. De Arcangelis ◽  
E. Di Mauro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Linker Histone ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Apparent Paradox ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
High Affinity Site ◽  
Hydroxyl Radical Cleavage ◽  
Radical Cleavage

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

Molecular Motors: Force and Movement Generated by Single Myosin II Molecules

Physiology ◽  
2002 ◽  
Vol 17 (5) ◽  
pp. 213-218 ◽  
Author(s):  
Caspar Rüegg ◽  
Claudia Veigel ◽  
Justin E. Molloy ◽  
Stephan Schmitz ◽  
John C. Sparrow ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Myosin Ii ◽  
Force Production ◽  
Myosin Isoforms ◽  
Single Molecule Level ◽  
Recent Developments ◽  
Muscle Myosin

Muscle myosin II is an ATP-driven, actin-based molecular motor. Recent developments in optical tweezers technology have made it possible to study movement and force production on the single-molecule level and to find out how different myosin isoforms may have adapted to their specific physiological roles.

Sign in / Sign up

Export Citation Format

Share Document