A Multigraph model of the 3D genome

Abstract

Spatial organisation of the genome has a fundamental effect on its biological functions. Chromatin-chromatin interactions and 3D spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts as a whole to environmental stimuli, the linear sequence information needs to be interpreted in 3-dimensional space. While recent advances in chromatin conformation capture technologies including Hi-C, considerably advanced our understanding of the genomes, defining the DNA, as it is organized in the cell nucleus is still a challenging task. 3D genome modelling needs to reflect the DNA as a flexible polymer, which can wind up to the fraction of its total length and greatly unwind and stretch to implement a multitude of functions. Here we propose a novel approach to model genomes as a multigraph based on Hi-C contact data. Multigraph-based 3D genome modelling of barley and rice revealed the well-known Rabl and Rosetta chromatin organizations, respectively, as well as other higher order structures. Our results shows that the well-established toolset of Graph theory is highly valuable in modelling large genomes in 3D.

Between submission and pain. Shades of BDSM practices

“…The concepts BDSM and S/M in literature are often treated as synonyms. In our paper we make a certain differentiation, which is partly in accordance with the suggestion made by Michael Makai [51]. The concept of S/M is used with reference to the relationship in which the basic element is dependence and experiencing pain, in other words the relationship conditioned by sadist or masochist preferences (but not in psychopathological meaning).…”

“…Therefore, one may conclude that some essential aspects of BDSM relationships are communication, openness to preferences, and trust, determining whether a given practice is safe. It is crucial to strictly follow these rules so that practitioners can enjoy the experiences [50][51][52]. Among BDSM practitioners, there is a motto which in short describes their practices, whose author is probably David Stein -"Safe, Sane and Consensual" [53].…”