Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search.

DNA loop formation by structural maintenance of chromosome (SMC) proteins, including cohesin, condensin, and the SMC5/6 complex, plays a pivotal role in genome organization. Despite its importance, the molecular mechanism underlying SMC-mediated loop formation, particularly how these complexes achieve persistent directionality (rectification) while minimizing backward steps during the formation of large loops, remains poorly understood. Here, we use atomic force microscopy (AFM) and computational simulation to uncover a key geometric feature of the yeast condensin SMC complex enabling rectified loop growth.

Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers.

We study a spherically confined mixture of polymers and colloidal rings. Unlike in standard colloid-polymer mixtures, the polymers interact topologically with the rings by threading them. We find that, above a critical value of the ring radius, threading yields a topological transition from a fluid to a gel-like phase characterized by a space-spanning network of interlocked polymers and rings, which we refer to as a bicomponent gel, or bigel.

Combinatorics and topological weights of chromatin loop networks.

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network.

Topological Spectra and Entropy of Chromatin Loop Networks.

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin.

Topological gelation of reconnecting polymers.

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement.

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events.

The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins.

Three-dimensional loop extrusion.

Loop extrusion convincingly describes how certain structural maintenance of chromosome (SMC) proteins mediate the formation of large DNA loops. Yet most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks, and perform steps longer than their own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion, which not only reproduces the experimental features of loop extrusion by one SMC complex but also predicts the formation of so-called Z-loops via the interaction of two or more SMCs extruding along the same DNA substrate.

Bridging-induced phase separation induced by cohesin SMC protein complexes.

Structural maintenance of chromosome (SMC) protein complexes are able to extrude DNA loops. While loop extrusion constitutes a fundamental building block of chromosomes, other factors may be equally important. Here, we show that yeast cohesin exhibits pronounced clustering on DNA, with all the hallmarks of biomolecular condensation.

Combining dendritic cells and B cells for presentation of oxidised tumour antigens to CD8 T cells.

The dendritic cell (DC) is the foremost antigen-presenting cell (APC) for expansion of tumour-specific patient T cells. Despite marked responses in some patients following reinfusion of DC-activated autologous or HLA-matched donor T cells, overall response rates remain modest in solid tumours. Furthermore, most studies aim to generate immune responses against defined tumour-associated antigens (TAA), however, meta-analysis reveals that those approaches have less clinical success than those using whole tumour cells or their components.

The role of the peroxisome proliferator-activated receptor-alpha (PPAR-alpha) in the regulation of acute inflammation.

The peroxisome proliferator-activated receptor-alpha (PPAR-alpha) is a member of the nuclear receptor superfamily of ligand-dependent transcription factors related to retinoid, steroid, and thyroid hormone receptors. The aim of the present study was to evaluate the role of the PPAR-alpha receptor on the development of acute inflammation. To address this question, we used two animal models of acute inflammation (carrageenan-induced paw edema and carrageenan-induced pleurisy).