SMC (structural maintenance of chromosomes) complexes condensin and cohesin are crucial for proper chromosome organization. Condensin has been reported to be a mechanochemical motor capable of forming chromatin loops, while cohesin passively diffuses along chromatin to tether sister chromatids. In budding yeast, the pericentric region is enriched in both condensin and cohesin. As in higher-eukaryotic chromosomes, condensin is localized to the axial chromatin of the pericentric region, while cohesin is enriched in the radial chromatin. Thus, the pericentric region serves as an ideal model for deducing the role of SMC complexes in chromosome organization. We find condensin-mediated chromatin loops establish a robust chromatin organization, while cohesin limits the area that chromatin loops can explore. Upon biorientation, extensional force from the mitotic spindle aggregates condensin-bound chromatin from its equilibrium position to the axial core of pericentric chromatin, resulting in amplified axial tension. The axial localization of condensin depends on condensin's ability to bind to chromatin to form loops, while the radial localization of cohesin depends on cohesin's ability to diffuse along chromatin. The different chromatin-tethering modalities of condensin and cohesin result in their geometric partitioning in the presence of an extensional force on chromatin.

ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNAbinding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates. These simulations provide testable hypotheses for condensin and other DNA-based motors functioning along interphase chromosomes. Our model reveals a novel mechanism for condensin enrichment in the pericentromeric region of mitotic chromosomes. Increased condensin dwell time at centromeres results in a high density of pericentric loops that in turn provide substrate for additional condensin.There has been a revolution in understanding the higher-order structure and organization of chromosome in the past decade. Several major approaches (3C, ChromEMT, and super-resolution microscopy) are indicative of a disordered array of loopy fibers that emanate from an axial core (Dostie and Bickmore 2012;Dekker et al. 2013;Ou et al. 2017). The hierarchical models of structural intermediates building from 11 to 30 nm and larger fibers are not borne out in these recent 3D and live-cell studies (Ou et al. 2017). DNA looping was first observed in squash preparations of salamander eggs under the light microscope by the embryologist Oskar Hertwig in the early 1900s (Hertwig 1906). Paulson and Laemmli (1977) observed DNA loops when examining chromosome spreads in isolated mammalian cells. In metaphase, the loops emanate from a protein-rich chromosome scaffold. The chromosome scaffold is enriched in topology-adjusting proteins, such as topoisomerase II and the SMC (structural maintenance of chromosomes) proteins, known as condensin (Earnshaw et al. 1985;Hirano 2006).Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al. 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another. Energy-requiring processes are also involved in loop formation. The earliest suggestion of loop extrusion came from the trombone model of DNA replication (Sinha et al. 1980;Alberts et al. 1983) and direct visualization of DNA looping at the replication fork (Park et al. 1998). More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al. 2017).Condensin is composed of five subunits, two coiledcoils SMC2 and 4, a kleisin ...

The rise of machine learning and deep learning technologies have allowed researchers to automate image classification. We describe a method that incorporates automated image classification and principal component analysis to evaluate computational models of biological structures. We use a computational model of the kinetochore to demonstrate our artificial-intelligence (AI)-assisted modeling method. The kinetochore is a large protein complex that connects chromosomes to the mitotic spindle to facilitate proper cell division. The kinetochore can be divided into two regions: the inner kinetochore, including proteins that interact with DNA; and the outer kinetochore, comprised of microtubule-binding proteins. These two kinetochore regions have been shown to have different distributions during metaphase in live budding yeast and therefore act as a test case for our forward modeling technique. We find that a simple convolutional neural net (CNN) can correctly classify fluorescent images of inner and outer kinetochore proteins and show a CNN trained on simulated, fluorescent images can detect difference in experimental images. A polymer model of the ribosomal DNA locus serves as a second test for the method. The nucleolus surrounds the ribosomal DNA locus and appears amorphous in live-cell, fluorescent microscopy experiments in budding yeast, making detection of morphological changes challenging. We show a simple CNN can detect subtle differences in simulated images of the ribosomal DNA locus, demonstrating our CNN-based classification technique can be used on a variety of biological structures.

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Molecular crowding of DNA loops exerts a radial force on the kinetochore. Previous observations of the kinetochore and pericentric cohesin revealed a paradox upon spindle perturbation. Using simulations of the thermodynamics of DNA, we resolve the experimental results and provide evidence for mechanical feedback between chromatin and the kinetochore.