Project participants
Julia Madsen Østerbye, Aurélie Bellanger, Natalia Galigniana, Mohamed Abdelhalim, Kristin Vekterud, Anita Sørensen; collaborations with Jonas Paulsen (Institute of Biosciences, University of Oslo); Erwan Delbarre, Oslo Metropolitan University; David Tremethick, Australian National University, Canberra; Lee H. Wong, Monash University, Melbourne
Image: 3D model of chromatin in a human fibroblast nucleus. Model generated using Chrom3D , from Hi-C and lamin ChIP-seq data to infer chromosomal interactions and positioning of chromatin towards the nuclear periphery.
Ongoing research
- Interplay between the nuclear lamina, LADs and TADs as genomic organizers in stem cells and cancer cells
- Formation and disassembly of TAD cliques during differentiation
- Nuclear lamins and EMT
- Histone variant H3.3 and chromatin organization in pediatric glioblastomas
- Computational methods for 3D genome modeling
Recent findings
- A polymer model of chromatin to infer chromatin behavior at the nuclear lamina (Brunet 2021 Nucleus)
- TAD cliques shape the 4D genome during adipose differentiation (Paulsen 2019 Nature Genet)
- Chrom3D: a computational platform for 3D genome modeling from Hi-C and LAD data (Paulsen 2017 Genome Biol; Paulsen 2018 Nature Protoc)
- Chrom3D on github: https://github.com/Chrom3D/Chrom3D
- Manifold-based optimization for 3D modeling of chromatin from sparse Hi-C data (Paulsen 2015 PLoS Comput Biol)
- Mechanisms of H3.3 deposition into chromatin via PML nuclear bodies (Delbarre 2013 Genome Res; Ivanauskiene 2014 Genome Res); (Delbarre 2017 Genome Res)
- Enriched Domain Detector (EDD) to identify LADs and other broad genomic domains (Lund 2014 Nucl Acids Res)
- EDD on github: https://github.com/CollasLab/edd