Hajj, B. | bioRxiv Science

bioRxiv2020

Genuage: a virtual reality platform for visualizing and analyzing multidimensional point cloud data

The quantity of experimentally recorded point cloud data, such generated in single-molecule experiments, is increasing continuously in both size and dimension. Gaining an intuitive understanding of the data and facilitating multi-dimensional data analysis remains a challenge. It is especially challenging when static distribution properties are not predictive of dynamical properties. Here, we report a new open-source software platform, Genuage, that enables the easy perception, interaction and analysis of complex multidimensional point cloud datasets by leveraging virtual reality. We illustrate the benefit of the Genuage with examples of three-dimensional static and dynamic localization microscopy datasets, as well as some synthetic datasets. Genuage has a large breadth of usage modes, due to its compatibility with arbitrary multidimensional data types extending beyond the single-molecule research community.

biophysics↗

bioRxiv2019

Molecular basis of CTCF binding polarity in genome folding

Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin proteins (Merkenschlager & Nora, 2016; Fudenberg, Abdennur, Imakaev, Goloborodko, & Mirny, 2017). While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize DNA loops (de Wit et al., 2015; Guo et al., 2015; Rao et al., 2014; Vietri Rudan et al., 2015), the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding or dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly, despite normal binding. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations provide a molecular explanation for how the polarity of CTCF binding sites determines the genomic distribution of chromatin loops.

molecular biology↗