MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions

"MoDLE is a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data, and does so orders of magnitude faster than existing approaches. MoDLE's speed opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings", says Jonas Paulsen, professor at the Department of Biosciences.

The preprint describing MoDLE's capabilities, design and implementation is available on bioRxiv at 10.1101/2022.04.13.488157

MoDLE is released under a permissive open-source license, and its source code is available on GitHub.

Paper abstract and fig. 1


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Schematic and simplified overview of MoDLE. Input files specify genome regions to be simulated (e.g. a chrom.sizes file) and their barrier positions (e.g. CTCF binding sites and orientation) in BED format. Optional parameters control the specifics of a simulation. Loop Extruding Factors (LEFs) bind to, extrude and release from the regions and interact with modeled barriers according to input parameters. Loop extrusion and intra-TAD contacts of a randomized subset of loops are recorded each epoch and aggregated into an output cooler file containing the final simulated contact frequencies. Simulation halts when a target number of epochs or a target number of loop extrusion contacts have been simulated.

Published Apr. 28, 2022 9:21 PM - Last modified Apr. 28, 2022 9:21 PM