Local rewiring of genome - nuclear lamina interactions by transcription

Abstract

Transcriptionally inactive genes are often positioned at the nuclear lamina (NL), as part of large lamina-associated domains (LADs). Activation of such genes is often accompanied by repositioning towards the nuclear interior. How this process works and how it impacts flanking chromosomal regions is poorly understood. We addressed these questions by systematic manipulation of gene activity and detailed analysis of NL interactions. Activation of genes inside LADs typically causes detachment of the entire transcription unit but rarely more than 50-100 kb of flanking DNA, even when multiple neighboring genes are activated. The degree of detachment depends on the expression level and the length of the activated gene. Loss of NL interactions coincides with a switch from late to early replication timing, but the latter can involve longer stretches of DNA. These findings show how NL interactions can be shaped locally by transcription and point to a remarkable flexibility of interphase chromosomes.

Perturbations in 3D genome organization can promote acquired drug resistance

“…In addition to this, we could also observe a possibly 'compensatory' movement of the regions further from the ABCB1 locus, which increased NL contacts in the taxol-resistant cell lines (Fig 2C, red line). Interestingly, this phenomena has been previously reported in other loci 44 . Overall, these results indicate that a local rewiring of NL interactions occur in the ABCB1 genomic region in the RPE-1 taxol resistant cells.…”

“…To further explore the role of NL in ABCB1 regulation, we examined whether NL detachment would lead to ABCB1 gene activation. It has been previously described that the CRISPRa induces detachment of genes from the NL, and in some instances this also causes detachment of flanking genes 44 . We therefore attempted to detach ABCB1 from the NL by activation of its neighboring genes.…”

Engineering 3D genome organization

“…The degree of detachment correlates well with the level of gene transcription. This work demonstrates a role of gene transcription machinery in regulating genome-nuclear lamina interactions 151 .…”

“…Alterations of DNA replication timing can be profiled by Repli-Seq 7,24 . Changes in chromatin-lamina interactions can be studied by the DamID method 39,151 . Moreover, imaging-based methods such as FISH and CRISPR live-cell imaging are being used to investigate the temporal and spatial organization of specific genomic regions and the relationship with different protein/RNA components and nuclear compartments 35,43,44,46,47,49,50 .…”

“…Recently, Brueckner et al applied the CRISPR-SunTag activation (CRISPRa) system in human RPE-1 cells to recruit multiple copies of VP64 to the individual promoters of 12 genes within lamina-associated domains for gene activation 151 . SunTag is a system that can recruit multiple single-chain variable fragment (scFv)-fusion protein copies to a repetitive peptide array 152 .…”