Project participants
Julia Madsen Østerbye, Aurélie Bellanger, Natalia Galigniana, Mohamed Abdelhalim, Anita Sørensen; collaborations with Jonas Paulsen, Institute of Biosciences, University of Oslo; Owen Marshall, University of Tasmania, Hobart; David Tremethick, Australian National University, Canberra; Lee H. Wong, Monash University, Melbourne
Ongoing research
- Interplay between the nuclear lamina, LADs and TADs in the differentiation of adipose tissue and muscle stem cells
- Control of gene expression at the nuclear lamina
- Role of lamins on lineage-specific differentiation of adipose stem cells
- Nuclear lamins and the epithelial-to-mesenchymal transition
- Computational methods for 3D genome modeling
Recent findings
- Enhancer-gene connectivity at the nuclear lamina (Madsen-Østerbye 2023 Genes)
- 'Pockets' of euchromatin and active genes in LADs (Madsen-Østerbye 2022 Genome Biol)
- Variable LADs during early adipocyte differentiation are linked to adipose cell identity
- 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 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
- ChIP protocol for nuclear lamins (Oldenburg 2016 Method Mol Biol)
- 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 (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