Local rewiring of genome-nuclear lamina interactions by transcription

EMBO J. 2020 Mar 16;39(6):e103159. doi: 10.15252/embj.2019103159. Epub 2020 Feb 21.


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 toward the nuclear interior. How this process works and how it impacts flanking chromosomal regions are poorly understood. We addressed these questions by systematic activation or inactivation of individual genes, followed by detailed genome-wide analysis of NL interactions, replication timing, and transcription patterns. Gene activation inside LADs typically causes NL 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. Inactivation of active genes can lead to increased NL contacts. These extensive datasets are a resource for the analysis of LAD rewiring by transcription and reveal a remarkable flexibility of interphase chromosomes.

Keywords: genome organization; lamina-associated domains; nuclear lamina; replication timing; transcription.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Cell Nucleus / genetics
  • Chromatin / genetics
  • Chromosomes / genetics*
  • DNA Replication / genetics*
  • Embryonic Stem Cells
  • Female
  • Genome / genetics*
  • Humans
  • Interphase
  • Mice
  • Neuropilin-1 / genetics
  • Nuclear Lamina / genetics*
  • Promoter Regions, Genetic / genetics
  • SOXD Transcription Factors / genetics
  • Transcriptional Activation / genetics*
  • Transgenes


  • Chromatin
  • SOXD Transcription Factors
  • Sox6 protein, mouse
  • Neuropilin-1

Associated data

  • GEO/GSE133275
  • GEO/GSE71831