The structure of the nucleosome core particle of chromatin in chicken erythrocytes visualized by using atomic force microscopy

Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure

As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.

DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging

Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

Genome Reorganization during Erythroid Differentiation

Hematopoiesis is a convenient model to study how chromatin dynamics plays a decisive role in regulation of cell fate. During erythropoiesis a population of stem and progenitor cells becomes increasingly lineage restricted, giving rise to terminally differentiated progeny. The concerted action of transcription factors and epigenetic modifiers leads to a silencing of the multipotent transcriptome and activation of the transcriptional program that controls terminal differentiation. This article reviews some aspects of the biology of red blood cells production with the focus on the extensive chromatin reorganization during differentiation.

Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

Recent experiments showing scaling of the intrachromosomal contact probability, P(s)∼s(-1) with the genomic distance s, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of P(s) varies across organisms, requiring an explanation. We illustrate dynamical arrest in a highly confined space as a discriminating marker for genome organization, by modeling chromosomes inside a nucleus as a homopolymer confined to a sphere of varying sizes. Brownian dynamics simulations show that the chain dynamics slows down as the polymer volume fraction (ϕ) inside the confinement approaches a critical value ϕ(c). The universal value of ϕ(c)(∞)≈0.44 for a sufficiently long polymer (N≫1) allows us to discuss genome dynamics using ϕ as the sole parameter. Our study shows that the onset of glassy dynamics is the reason for the segregated chromosome organization in humans (N≈3×10(9), ϕ≳ϕ(c)(∞)), whereas chromosomes of budding yeast (N≈10(8), ϕ<ϕ(c)(∞)) are equilibrated with no clear signature of such organization.

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.

Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications

The yeast Cyc8p-Tup1p protein complex is a general transcriptional corepressor of genes involved in many different physiological processes. Herein, we present the crystal structure of the Tup1p N-terminal domain (residues 1-92), essential for Tup1p self-assembly and interaction with Cyc8p. This domain tetramerizes to form a novel antiparallel four-helix bundle. Coiled coil interactions near the helical ends hold each dimer together, whereas interdimeric association involves only two sets of two residues located toward the chain centers. A mutagenesis study confirmed that the nonpolar residues responsible for the association of the protomers as dimers are also required for transcriptional repression. An additional structural study demonstrated that the domain containing an Leu(62) → Arg mutation that had been shown not to bind Cyc8p exhibits an altered structure, distinct from the wild type. This altered structure explains why the mutant cannot bind Cyc8p. The data presented herein highlight the importance of the architecture of the Tup1p N-terminal domain for self-association.

Ultra-high resolution imaging of DNA and nucleosomes using non-contact atomic force microscopy

Visualisation of nano-scale biomolecules aids understanding and development in molecular biology and nanotechnology. Detailed structure of nucleosomes adsorbed to mica has been captured in the absence of chemical-anchoring techniques, demonstrating the usefulness of non-contact atomic force microscopy (NC-AFM) for ultra-high resolution biomolecular imaging. NC-AFM offers significant advantages in terms of resolution, speed and ease of sample preparation when compared to techniques such as cryo-electron microscopy and X-ray crystallography. In the absence of chemical modification, detailed structure of DNA deposited on a gold substrate was observed for the first time using NC-AFM, opening up possibilities for investigating the electrical properties of unmodified DNA.

The In Vitro Reconstitution of Nucleosome and its Binding Patterns with HMG1/2 and HMG14/17 Proteins

Using atomic force microscopy (AFM), the dynamic process of the in vitro nucleosome reconstitution followed by slow dilution from high salt to low salt was visualized. Data showed that the histone octamers were dissociated from DNA at 1M NaCl. When the salt concentration was slowly reduced to 650 mM and 300 mM, the core histones bound to the naked DNA gradually. Once the salt concentration was reduced to 50 mM the classic "beads-on-a-string" structure was clearly visualized. Furthermore, using the technique of the in vitro reconstitution of nucleosome, the mono- and di- nucleosomes were assembled in vitro with both HS2core (-10681 to -10970 bp) and NCR2 (-372 to -194 bp) DNA sequences in the 5 flanking sequence of human b-globin gene. Data revealed that HMG 1/2 and HMG14/17 proteins binding to both DNA sequences are changeable following the assembly and disassembly of nucleosomes. We suggest that the changeable binding patterns of HMG 14/17 and HMG1/2 proteins with these regulatory elements may be critical in the process of nucleosome assembly, recruitment of chromatin-modifying activities, and the regulation of human b-globin gene expression.

Stretching and imaging single DNA molecules and chromatin

The advent of single-molecule biology has allowed unprecedented insight into the dynamic behavior of biological macromolecules and their complexes. Unexpected properties, masked by the asynchronous behavior of myriads of molecules in bulk experiments, can be revealed; equally importantly, individual members of a molecular population often exhibit distinct features in their properties. Finally, the single-molecule approaches allow us to study the behavior of biological macromolecules under applied tension or torsion: understanding the mechanical properties of these molecules helps us understand how they function in the cell. The aim of this chapter is to summarize and critically evaluate the properties of single DNA molecules and of single chromatin fibers. The use of the high-resolution imaging capabilities of the atomic force microscopy has been covered, together with manipulating techniques such as optical fibers, optical and magnetic tweezers, and flow fields. We have learned a lot about DNA and how it responds to applied forces. It is also clear that even though the study of the properties of individual chromatin fibers has just begun, the single-molecule approaches are expected to provide a wealth of information concerning the mechanical properties of chromatin and the way its structure changes during processes like transcription and replication.

Chromatin fibers, one-at-a-time

Eukaryotic DNA is presented to the enzymatic machineries that use DNA as a template in the form of chromatin fibers. At the first level of organization, DNA is wrapped around histone octamers to form nucleosomal particles that are connected with stretches of linker DNA; this beads-on-a-string structure folds further to reach a very compact state in the nucleus. Chromatin structure is in constant flux, changing dynamically to accommodate the needs of the cell to replicate, transcribe, and repair the DNA, and to regulate all these processes in time and space. The more conventional biochemical and biophysical techniques used to study chromatin structure and dynamics have been recently complemented by an array of single-molecule approaches, in which chromatin fibers are investigated one-at-a-time. Here we describe single-molecule efforts to see nucleosomes, touch them, put them together, and then take them apart, one-at-a-time. The beginning is exciting and promising, but much more effort will be needed to take advantage of the huge potential that the new physics-based techniques offer.

Atomic force microscopy study of chromosome surface structure changed by protein extraction

We applied atomic force microscopy (AFM) to investigate the surface structure of barley chromosome in combination with a chemical treatment method. As a result, we have obtained high-resolution topographic images of granular structures with a diameter of ca. 50 nm on the surface of critical-point dried metaphase chromosomes. Treatment with 2M NaCl significantly modified the chromosome surface structure: surface roughness was increased and chromosome thickness was decreased. The NaCl treatment extracted two major proteins with molecular weights of 4000 and 20,000 Da. These proteins might be belonging to non-histone protein families that do not contain any aromatic amino acid. The results demonstrate the advantage of the combined method of high-resolution AFM imaging and chemical treatments for understanding nano-scale surface structures of the chromosome.

Increased exchange rate of histone H1 on chromatin by exogenous myogenin expression

To explore the molecular mechanism of chromatin remodeling involved in the regulation of transcriptional activation of specific genes by a myogenic regulatory factor Myogenin, we used NIH3T3 fibroblasts with a stably integrated H1.1-GFP fusion protein to monitor histone H1 movement directly by fluorescence recovery after photobleaching (FRAP) in living cells. The observation from FRAP experiments with myogenin transfected fibroblasts showed that the exchange rate of histone H1 in chromatin was obviously increased, indicating that forced expression of exogenous Myogenin can induce chromatin remodeling. The hyperacetylation of histones H3 and H4 from myogenin transfected fibroblasts was detected by triton-acid-urea (TAU)/SDS (2-D) electrophoresis and Western blot with specific antibodies against acetylated N-termini of histones H3 and H4. RT-PCR analysis indicated that the nAChR alpha-subunit gene was expressed in the transfected fibroblasts. These results suggest that the expression of exogenous Myogenin can induce chromatin remodeling and activate the transcription of Myogenin-targeted gene in non-muscle cells.