Visualization and 3D Structure Determination of Defined Sequence Chromatin and Chromatin Remodeling Complexes

Horowitz-Scherer, Rachel A.; Woodcock, Christopher L.

doi:10.1016/s0076-6879(03)76003-0

Chromatin and Chromatin Remodeling Enzymes, Part B

2003

DOI: 10.1016/s0076-6879(03)76003-0

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Visualization and 3D Structure Determination of Defined Sequence Chromatin and Chromatin Remodeling Complexes

Rachel A. Horowitz-Scherer

Christopher L. Woodcock²

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Cited by 2 publications

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References 22 publications

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“…How the linker histones modify the path of the linker DNA is seen on cryo-electron microscopy images: a stem structure could be observed on mono- and oligonucleosomes ( , ). Our FRET distance measurements on reconstituted mononucleosomes at low ionic strength (5 mM NaCl) have already shown that the incorporation of H1 linker histone decreases the distance between the linker arms over their whole length (). This paper investigates further this effect in combination with the other compaction factors.…”

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confidence: 86%

Chromatin Compaction at the Mononucleosome Level

2006

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Using a previously described FRET technique, we measured the distance between the ends of DNA fragments on which nucleosomes were reconstituted from recombinant and native histones. This distance was analyzed in its dependence on the DNA fragment length, concentration of mono- and divalent counterions, presence of linker histone H1, and histone modifications. We found that the linker DNA arms do not cross under all conditions studied but diverge slightly as they leave the histone core surface. Histone H1 leads to a global approach of the linker DNA arms, confirming the notion of a "stem structure". Increasing salt concentration also leads to an approach of the linker DNAs. To study the effect of acetylation, we compared chemically acetylated recombinant histones with histones prepared from HeLa cells, characterizing the sites of acetylation by mass spectroscopy. Nucleosomes from chemically acetylated histones have few modifications in the core domain and form nucleosomes normally. Acetylating all histones or selectively only H3 causes an opening of the nucleosome structure, indicated by the larger distances between the linker DNA ends. Selective acetylation of H4 distances the linker ends for short fragments but causes them to approach each other for fragments longer than 180 bp.

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confidence: 86%

Chromatin Compaction at the Mononucleosome Level

2006

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Architecture of the SWI/SNF-Nucleosome Complex

Dechassa

Zhang

Horowitz-Scherer

et al. 2008

Molecular and Cellular Biology

131

161

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The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning ϳ50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.

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Visualization and 3D Structure Determination of Defined Sequence Chromatin and Chromatin Remodeling Complexes

Cited by 2 publications

References 22 publications

Chromatin Compaction at the Mononucleosome Level

Chromatin Compaction at the Mononucleosome Level

Architecture of the SWI/SNF-Nucleosome Complex

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