Analikwu, B. T. | Search bioRxiv

bioRxiv2023

Telomere protein arrays stall DNA loop extrusion by condensin

DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It is unknown how loop extruders interact with telomeres where chromosome ends are covered with a dense array of tens of neighboring DNA-binding proteins. Using complementary in vivo and in vitro single-molecule approaches, we study the interaction between loop-extruding condensin and arrays of Rap1, the double-stranded-DNA-binding telomeric protein of Saccharomyces cerevisiae. We show that dense linear Rap1 arrays can completely halt DNA loop extrusion, where the blocking efficiency depends on the array length and the DNA gap size between neighboring proteins. In cells, Rap1 arrays in the chromosome are found to act as contact insulators and to accumulate condensin at their borders, with direct implications for the resolution of dicentric chromosomes produced by telomere fusions. Our findings show that linear arrays of DNA-bound proteins can efficiently halt DNA loop extrusion by SMC proteins, which may impact a wide range of cellular processes from telomere functions to transcription and DNA repair.

molecular biology↗

bioRxiv2023

Topology-dependent DNA binding

DNA stores our genetic information and is ubiquitous in biological and biotechnological applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and, in turn, can change the local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model of how the global constraints introduced by DNA topology modulate binding and create a complex interplay between topology and affinity. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Using bulk measurements, we show that DNA supercoiling can increase or decrease intercalation relative to an open topology depending on ligand concentration and the initial topology. Our model quantitatively accounts for observations obtained using psoralen for UV-induced DNA crosslinking, which is frequently used to quantify supercoiling in vivo. Finally, we observe topology-dependent binding in a single-molecule assay, which provides direct access to binding kinetics and DNA supercoil dynamics. Our results have broad implications for the detection and quantification of DNA and for the modulation of DNA binding in cellular contexts.

biophysics↗