STAT3-coordinated migration facilitates the dissemination of diffuse large B-cell lymphomas.

The motile characteristics and mechanisms that drive the dissemination of diffuse large B-cell lymphoma (DLBCL) are elusive. Here, we show that DLBCL initiates dissemination through activating STAT3-mediated amoeboid migration. Mechanistically, STAT3 activates RHOH transcription, which competes with the RhoGDP dissociation inhibitor RhoGDIγ to activate RhoA. In addition, activated STAT3 regulates microtubule dynamics and releases ARHGEF2 to activate RhoA. Both the JAK inhibitor ruxolitinib and the microtubule stabilizer Taxol suppress DLBCL cell dissemination in vivo. A clinical DLBCL sample analysis shows that STAT3-driven amoeboid movement is particularly important for the transition from stage I to stage II. This study elucidates the mechanism of DLBCL dissemination and progression and highlights the potential of combating advanced DLBCL with a JAK/STAT inhibitor or microtubule stabilizer to reduce DLBCL motility; these findings may have a great impact on the development of patient-tailored treatments for DLBCL.

Crowding-facilitated macromolecular transport in attractive micropost arrays.

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

Entropic attraction: Polymer compaction and expansion induced by nano-particles in confinement.

We investigated nanoparticle (NP)-induced coil-to-globule transition of a semi-flexible polymer in a confined suspension of ideal NP using Langevin dynamics. DNA molecules are often found to be highly compact, bound with oppositely charged proteins in a crowded environment within cells and viruses. Recent studies found that high concentration of electrostatically neutral NP also condenses DNA due to entropically induced depletion attraction between DNA segments. Langevin dynamics simulations with a semi-flexible chain under strong confinement were performed to investigate the competition between NP-induced monomer-monomer and monomer-wall attraction under different confinement heights and NP volume fractions. We found that whether NP induce polymer segments to adsorb to the walls and swell or to attract one another and compact strongly depends on the relative strength of the monomer-wall and the NP-wall interactions.

Characterization of nucleosome unwrapping within chromatin fibers using magnetic tweezers.

Nucleosomal arrays fold into chromatin fibers and the higher-order folding of chromatin plays a strong regulatory role in all processes involving DNA access, such as transcription and replication. A fundamental understanding of such regulation requires insight into the folding properties of the chromatin fiber in molecular detail. Despite this, the structure and the mechanics of chromatin fibers remain highly disputed. Single-molecule force spectroscopy experiments have the potential to provide such insight, but interpretation of the data has been hampered by the large variations in experimental force-extension traces. Here we explore the possibility that chromatin fibers are composed of both single-turn and fully wrapped histone octamers. By characterizing the force-dependent behavior of in vitro reconstituted chromatin fibers and reanalyzing existing data, we show the unwrapping of the outer turn of nucleosomal DNA at 3 pN. We present a model composed of two freely-jointed chains, which reveals that nucleosomes within the chromatin fiber show identical force-extension behavior to mononucleosomes, indicating that nucleosome-nucleosome interactions are orders-of-magnitude smaller than previously reported and therefore can be overcome by thermal fluctuations. We demonstrate that lowering the salt concentration externally increases the wrapping energy significantly, indicative of the electrostatic interaction between the wrapped DNA and the histone octamer surface. We propose that the weak interaction between nucleosomes could allow easy access to nucleosomal DNA, while DNA unwrapping from the histone core could provide a stable yet dynamic structure during DNA maintenance.

Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers.

The compaction of chromatin fibers regulates the accessibility of embedded DNA, highly associated with transcriptional activities [1]. Single molecule force spectroscopy has revealed the great details of the structural changes of chromatin fibers in the presence of external exerted force [2-7]. However, most of the studies focus on a specific force regime [2,3,8,9]. The data here show force-extension (FE) traces of chromatin fibers as measured with magnetic tweezers, covering the force regime from 0 pN to 27 pN. Those traces provide information for further studies at varied force regimes.

10 years of tension on chromatin: results from single molecule force spectroscopy.

The compact, yet dynamic organization of chromatin plays an essential role in regulating gene expression. Although the static structure of chromatin fibers has been studied extensively, the controversy about the higher order folding remains. In the past ten years a number of studies have addressed chromatin folding with single molecule force spectroscopy. By manipulating chromatin fibers individually, the mechanical properties of the fibers were quantified with piconewton and nanometer accuracy. Here, we review the results of force induced chromatin unfolding and compare the differences between experimental conditions and single molecule manipulation techniques like force and position clamps. From these studies, five major features appeared upon forced extension of chromatin fibers: the elastic stretching of chromatin's higher order structure, the breaking of internucleosomal contacts, unwrapping of the first turn of DNA, unwrapping of the second turn of DNA, and the dissociation of histone octamers. These events occur sequentially at the increasing force. Resolving force induced structural changes of chromatin fibers at the single molecule level will help to provide a physical understanding of processes involving chromatin that occur in vivo and will reveal the mechanical constraints that are relevant for processing and maintenance of DNA in eukaryotes.

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber.

The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all DNA processes. To unravel the higher-order folding of chromatin, we used magnetic tweezers and probed the mechanical properties of single 197-bp repeat length arrays of 25 nucleosomes. At forces up to 4 pN, the 30-nm fiber stretches like a Hookian spring, resulting in a three-fold extension. Together with a high nucleosome-nucleosome stacking energy, this points to a solenoid as the underlying topology of the 30-nm fiber. Unexpectedly, linker histones do not affect the length or stiffness of the fiber but stabilize its folding. Fibers with a nucleosome repeat length of 167 bp are stiffer, consistent with a two-start helical arrangement. The observed high compliance causes extensive thermal breathing, which forms a physical basis for the balance between DNA condensation and accessibility.