Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of...
The spatial conformation of chromatin within the nucleus is of the uttermost importance for transcriptional regulation and therefore for phenomena such as cell differentiation. In particular, epigenetic modifications play a crucial role as they are believed to affect the spatial folding and the accessibility of the genome to transcription factors and proteins.
Understanding and quantifying...
The mechanism responsible for the organization of bacterial DNA inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about thousand times larger outside from the cell....
Folding of nucleosome chains influences DNA availability for functional interactions necessary for the regulation of transcription, DNA replication and repair. Despite the existing models based on studies in vitro, the nucleosome chain geometry within the crowded cell nucleus has remained elusive. Cryo-electron tomography (Cryo-ET) is the only method that provides a sufficient resolution to...
Single-molecule localization microscopy (SMLM) is a powerful super-resolution imaging technique that can image biological structures at near-molecular scales (resolutions down to ~20 nm or better), enabling broad applications in the life sciences. With standard reconstruction methods, SMLM typically requires ~10⁴-10⁵ low-resolution frames to generate a single super-resolution image, hence the...
It is well known that the enhancer-promoter interactions are essential for gene expression, but the role of RNA Polymerase II (Pol II)-mediated activity on genome folding is remain controversial. Here by investigating Micro-C data for mESCs and Drosophila embryo, we show a significant correlation between gene compaction and Pol II occupancy inside the gene, independent of cohesin-dependent...