Project participants
Thomas Germier, Julia Madsen Østerbye, Aurélie Bellanger, Mohamed Abdelhalim, Kristin Vekterud; collaborations with Jonas Paulsen (now at the Institute of Biosciences, University of Oslo), Erwan Delbarre (now at Oslo Metropolitan University OsloMet), Lee H. Wong (Monash University, Melbourne) and 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 distinctly labeled.
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 the radial organization of chromatin
- 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