Biology subjects

Gonzalez-Aleman, R.

Publications and source records attributed to Gonzalez-Aleman, R..

3 recordsLinked to original sources

bioRxiv2026

Deinococcus radiodurans HU: a versatile architect of nucleoid structure and plasticity

Nucleoid-associated proteins are known to compact and organise bacterial genomes, but how their local DNA binding shapes higher-order chromatin architecture remains unclear. Using in vitro and in situ approaches, we investigated how Deinococcus radiodurans HU (DrHU) orchestrates nucleoid organisation. DrHU engages DNA through two synergistic binding modes: high-affinity {beta}-hairpin-mediated stabilisation of DNA loops and low-affinity, multivalent interaction via its N-terminal tail, driving parallel, uniformly spaced DNA alignment. In vitro, DrHU organises supercoiled plasmid DNA into regular 2D lattices of double-spirals, while in situ, UV-C light induces a nucleoid transition from a loose DNA mesh to a blue liquid crystalline phase characterised by DNA swirls. The striking structural similarity and shared inter-filament spacing of these two arrangements suggests that DrHU plays a pivotal role in genome organisation through its versatile binding properties that enable DNA loop stabilisation, protection and DNA bridging, linking molecular interactions to 3D genome ordering and stress-induced remodelling.

microbiology↗

bioRxiv2025

InterMap: Accelerated Detection of Interaction Fingerprints on Large-Scale Molecular Ensembles

MotivationMolecular dynamics is a key technique for exploring biomolecular systems at the atomic level. The rapid growth in accessible system sizes and timescales has intensified the need for efficient post-processing methods that extract meaningful insights from the resulting data. Interaction fingerprint (IFP) analyses are a valuable tool for elucidating key atomic interactions within molecular ensembles, yet current specialized software often struggle with extensive trajectories or complex systems. Here, we introduce InterMap, a Python package designed to accelerate IFP detection on large-scale molecular ensembles. ResultsBy actively exploiting k-d trees, InterMap efficiently handles the massive amount of distance calculations necessary to detect IFPs, particularly when dealing with intra-molecular interactions. The seamless integration with MDAnalysis ensures broad format compatibility and allows using SMARTS patterns for flexible interaction definitions. InterMap adopts a deeply compressed binary encoding to manage IFPs, which makes it very memory-friendly. Furthermore, convenient interactive visualizations are provided to enhance data interpretation through a locally hosted web-browser application. Benchmark results indicate that InterMap significantly outperforms existing tools for processing complex biomolecular systems, achieving up to a 99% reduction in both runtime and peak memory usage. AvailabilityInterMaps code and issue tracker are available at https://github.com/Delta-Research-Team/intermap.git, while documentation and tutorials can be found at https://delta-research-team.github.io/intermap/. Contactroy.gonzalez-aleman@inria.fr, yasaman.karami@inria.fr Supplementary informationSupplementary data are available at Nucleic Acid Research online.

bioinformatics↗

bioRxiv2025

Structure, dynamics, and processing of 8oxoG:A in the nucleosome

Eukaryotic genomic DNA is packaged into chromatin through a repeating unit known as the nucleosome. In this chromatin environment, DNA is constantly exposed to several sources of DNA damage, such as reactive oxygen species (ROS), which can lead to the formation of 8-oxo-7,8-dihydroguanine (8oxoG). 8oxoG can base pair with cytosine (8oxoG:C) or form a mutagenic base pair with adenine (8oxoG:A), which can lead to single base transversions if left unrepaired. To date, the structure and dynamics of these two possible 8oxoG base pairs in the nucleosome remain unclear. Furthermore, whether MutY homologue (MUTYH) excises 8oxoG:A base pairs in the nucleosome remains elusive. Here using a combination of cryogenic-electron microscopy, molecular dynamics simulations, and biochemistry we determined the structure and dynamics of 8oxoG:C and 8oxoG:A base pairs in the nucleosome and characterize MUTYH activity in nucleosomal DNA. We found that nucleosomal 8oxoG:C forms a stable base pair using its anti conformation, while nucleosomal 8oxoG:A forms a more dynamic base pair using its syn conformation that is unable to be processed by MUTYH. This work provides fundamental insight into the accommodation of oxidative damage in the nucleosome and how this damage contributes to increased mutagenic transversions in nucleosomal compared to linker DNA.

biochemistry↗