We studied the functional role of three dimensional conformation of the genome in the cell nucleus on gene expression regulation. Long-range chromatin interactions arise as a result of the three-dimensional (3D) conformation of chromosomes in the cell nucleus and can result in the co-localization of co-regulated genes. To assess the influence of 3D conformation on gene co-expression, we used chromatin conformation capture (Hi-C) data from the mouse cortex to build a chromatin interaction network (CIN) of genes. We show that by characterizing the topology of the CIN at different scales it is possible to accurately predict spatial co-expression between genes in the mouse cortex.
- Sepideh Babaei (TU Delft)
- Ahmed Mahfouz
- Marc Hulsman (TU Delft)
- Boudewijn P.F. Lelieveldt
- Jeroen de Ridder (TU Delft)
- Marcel Reinders (TU Delft)
- Babaei S, Mahfouz A, Hulsman M, Lelieveldt BPF, de Ridder J, Reinders MJT (2015) Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex. PLOS Comput Biol 11(5):e1004221.
- Mahfouz A. Chromatin interactions predict co-expression in the mouse cortex [v1; not peer reviewed]. F1000Research 2015, 4(ISCB Comm J):584 (poster) (doi: 10.7490/f1000research.1110227.1)