Project participants
Julia Madsen Østerbye, Aurélie Bellanger, Natalia Galigniana, Mohamed Abdelhalim, Kristin Vekterud; collaborations with Jonas Paulsen (Institute of Biosciences, University of Oslo); David Tremethick, Australian National University, Canberra; Lee H. Wong (Monash University, Melbourne); Erwan Delbarre (Oslo Metropolitan University); Jacques Grill (Institut Gustave Roussy, Paris)
Image: 3D structural model of the genome in a human fibroblast nucleus. Model generated using our Chrom3D software, from Hi-C and lamin ChIP-seq input data to infer chromosomal interactions and positioning of chromatin domains towards the nuclear periphery. Each chromosome is labeled in a different color.
Ongoing research
- Interplay between genomic organizers such as the nuclear envelope, LADs and TADs on nuclear architecture in stem cells and cancer cells
- Mechanism of formation and disassembly of TAD cliques
- Role of histone variant H3.3 on radial chromatin organization
- Computational methods for 3D genome modeling
Recent findings
- Cliques of topologically-associating domains shape the 3D genome during adipogenic differentiation (Paulsen 2019 Nat Genet 51, 835-843)
- Chrom3D: a computational platform for 3D genome modeling from Hi-C and lamin-genome contacts (Paulsen 2017 Genome Biol 18:21; Paulsen 2018 Nat Protoc 13, 1137-1152)
- 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 11, e1004396)
- Mechanisms of H3.3 deposition into chromatin via PML nuclear bodies (Delbarre 2013 Genome Res 23, 440-451; Ivanauskiene 2014 Genome Res 24, 1584-1594)
- Identification of PML-associated domains (PADs); PML modulates H3.3 deposition for heterochromatin maintenance (Delbarre 2017 Genome Res 27, 9913-21)
- Enriched Domain Detector (EDD): a domain calling algorithm to map LADs and other broad genomic domains (Lund 2014 Nucl Acids Res 42, e92)
- EDD on github: https://github.com/CollasLab/edd