Fig. 8

Spatial positions of gene loci are altered upon Lamin A/C and Emerin depletion. a qRT-PCR showing expression changes in candidate genes from chromosome 18 and 19 upon treatment of DLD-1 cells with siLacZ (control), siLamin A/C, siEmerin and siLamin A/C + siEmerin. Expression levels were first normalized to internal control GAPDH and then to siLacZ. Pooled data from N = 3 independent biological replicates, *p < 0.05. b Schematic representation of the Lamina Associated Domain (LAD) status of KLK10, SMAD2/MADH2 and BCL2L12. Blue bars represent the Lamin B1 Dam-ID data from Netherlands Cancer Institute (NKI). Snapshots from the UCSC Genome Browser have been provided in Additional files 6 and 7. c Representative mid-optical sections from confocal z- stacks of Immuno-3D FISH for KLK10 (Chr. 19), MADH2 (Chr. 18) and BCL2L12 (Chr. 19) gene loci in DLD-1 cells treated with siLacZ (control), siLamin A/C, siEmerin and siLamin A/C+Emerin. Nuclear envelope was demarcated by immunostaining for Lamin B1. d Shortest distance of KLK10 (Chr. 19) gene loci from Lamin B1 immunostaining in DLD-1 cells treated with siLacZ (control, Median (M), M = 0.233 μm), siLamin A/C (M = 0.181 μm), siEmerin (M = 0.201 μm) and siLamin A/C + siEmerin (M = 0.223 μm). e Shortest distance of MADH2 (Chr. 18) gene loci from Lamin B1 immunostaining in DLD-1 cells treated with siLacZ (control, M = 0.169 μm), siLamin A/C (M = 0.266 μm), siEmerin (M = 0.235 μm) and siLamin A/C + siEmerin (M = 0.199 μm). f Shortest distance of BCL2L12 (Chr. 19) gene loci from Lamin B1 immunostaining in DLD-1 cells treated with siLacZ (control, M = 0.413 μm), siLamin A/C (M = 0.929 μm), siEmerin (M = 1.02 μm) and siLamin A/C + siEmerin (M = 1.05 μm). d-f, Horizontal bar - Median (M): Pooled data from N = 2 independent biological replicates, *** p < 0.001, ** p < 0.01, * p < 0.05. Scale bar ~ 10 μm