Related Experiment Video
Updated: Jul 20, 2026
05:58
In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
Published on: September 6, 2024
Trinucleosome compaction studied by fluorescence energy transfer and scanning force microscopy
Malte Bussiek1, Katalin Tóth, Nathalie Schwarz
1Division of Biophysics and Macromolecules, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, TP3, D-69120 Heidelberg, Germany.
Biochemistry
|September 7, 2006
Summary
Increasing salt concentration and linker histone H1 compact trinucleosomes, reducing DNA end-to-end distances. Histone acetylation generally decompacts structures, except for selective histone H4 acetylation which causes compaction.
Area of Science:
- Molecular Biology
- Biophysics
- Chromatin Structure
Background:
- Nucleosomes are the fundamental units of DNA packaging in eukaryotes.
- Linker histone H1 and histone acetylation are known to modulate chromatin structure and function.
Purpose of the Study:
- To investigate the impact of salt concentration, linker histone H1, and histone acetylation on trinucleosome structure.
- To determine how these factors influence DNA accessibility and internucleosomal organization.
Main Methods:
- Reconstitution of trinucleosomes on defined DNA sequences.
- Fluorescence resonance energy transfer (FRET) measurements in solution.
- Scanning force microscopy (SFM) in liquid.
Main Results:
- Increasing salt concentration and H1 histone incorporation reduced the distance between DNA ends, indicating compaction.
- H1 histone decreased internucleosomal center-to-center distances to a minimum of ~20 nm and narrowed angular distribution.
- Acetylation of all histones led to decompaction (increased DNA end-to-end distance and internucleosomal distances).
- Selective acetylation of histone H4 resulted in compaction, as measured by FRET.
Conclusions:
- Salt concentration and linker histone H1 play crucial roles in compacting trinucleosome structures.
- Histone acetylation has differential effects on chromatin compaction, with H4 acetylation promoting a more compact state.
Related Concept Videos
01:17Studying the Cytoskeleton
The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...
01:01Euchromatin
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
01:32Chromatin Packaging
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
02:21Chromatin Packaging
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...