Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis.

Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.

spFRET reveals changes in nucleosome breathing by neighboring nucleosomes.

Chromatin, the structure in which DNA is compacted in eukaryotic cells, plays a key role in regulating DNA accessibility. FRET experiments on single nucleosomes, the basic units in chromatin, have revealed a dynamic nucleosome where spontaneous DNA unwrapping from the ends provides access to the nucleosomal DNA. Here we investigated how this DNA breathing is affected by extension of the linker DNA and by the presence of a neighboring nucleosome. We found that both electrostatic interactions between the entering and exiting linker DNA and nucleosome-nucleosome interactions increase unwrapping. Interactions between neighboring nucleosomes are more likely in dinucleosomes spaced by 55 bp of linker DNA than in dinucleosomes spaced by 50 bp of linker DNA. Such increased unwrapping may not only increase the accessibility of nucleosomal DNA in chromatin fibers, it may also be key to folding of nucleosomes into higher order structures.

Engineering mononucleosomes for single-pair FRET experiments.

In DNA nanotechnology, DNA is used as a structural material, rather than as an information carrier. The structural organization of the DNA itself determines accessibility to its underlying information content in vivo. Nucleosomes form the basic level of DNA compaction in eukaryotic nuclei. Nucleosomes sterically hinder enzymes that must bind the nucleosomal DNA, and hence play an important role in gene regulation. In order to understand how accessibility to nucleosomal DNA is regulated, it is necessary to resolve the molecular mechanisms underlying conformational changes in the nucleosome. Exploiting bottom-up control, we designed and constructed nucleosomes with fluorescent labels at strategically chosen locations to study nucleosome structure and dynamics in molecular detail with single-pair Fluorescence Resonance Energy Transfer (spFRET) microscopy. Using widefield total internal reflection fluorescence (TIRF) microscopy on immobilized molecules, we observed and quantified DNA breathing dynamics on individual nucleosomes. Alternatively, fluorescence microscopy on freely diffusing molecules in a confocal detection volume allows a fast characterization of nucleosome conformational distributions.

Single-pair FRET experiments on nucleosome conformational dynamics.

Nucleosomes, the basic units of DNA compaction in eukaryotes, play a crucial role in regulating all processes involving DNA, including transcription, replication and repair. Nucleosomes modulate DNA accessibility through conformational dynamics like DNA breathing - the transient unwrapping of DNA from the nucleosome, repositioning of nucleosomes along the DNA, or partial dissociation. Single molecule techniques, in particular single-pair Fluorescence Resonance Energy Transfer (spFRET), have resolved such conformational dynamics in individual nucleosomes. Here, we review the results of FRET experiments on single nucleosomes, including fluorescence correlation spectroscopy (FCS), confocal single molecule microscopy on freely diffusing nucleosomes and widefield total internal reflection fluorescence (TIRF) microscopy on immobilized nucleosomes. The combined spFRET studies on single nucleosomes reveal a very dynamic organization of the nucleosome, that has been shown to be modulated by post-translational modifications of the histones and by DNA sequence.

A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation.

Lysine acetylation of histones defines the epigenetic status of human embryonic stem cells and orchestrates DNA replication, chromosome condensation, transcription, telomeric silencing, and DNA repair. A detailed mechanistic explanation of these phenomena is impeded by the limited availability of homogeneously acetylated histones. We report a general method for the production of homogeneously and site-specifically acetylated recombinant histones by genetically encoding acetyl-lysine. We reconstitute histone octamers, nucleosomes, and nucleosomal arrays bearing defined acetylated lysine residues. With these designer nucleosomes, we demonstrate that, in contrast to the prevailing dogma, acetylation of H3 K56 does not directly affect the compaction of chromatin and has modest effects on remodeling by SWI/SNF and RSC. Single-molecule FRET experiments reveal that H3 K56 acetylation increases DNA breathing 7-fold. Our results provide a molecular and mechanistic underpinning for cellular phenomena that have been linked with K56 acetylation.