Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor

Abstract

Lamina-associated domains (LADs) are megabase-sized genomic regions anchored to the nuclear lamina (NL). Factors controlling the interactions of the genome with the NL have largely remained elusive. Here, we identified DNA topoisomerase 2 beta (TOP2B) as a regulator of these interactions. TOP2B binds predominantly to inter-LAD (iLAD) chromatin and its depletion results in a partial loss of genomic partitioning between LADs and iLADs, suggesting that its activity might protect specific iLADs from interacting with the NL. TOP2B depletion affects LAD interactions with lamin B receptor (LBR) more than with lamins. LBR depletion phenocopies the effects of TOP2B depletion, despite the different positioning of the two proteins in the genome. This suggests a complementary mechanism for organising the genome at the NL. Indeed, co-depletion of TOP2B and LBR causes partial LAD/iLAD inversion, reflecting changes typical of oncogene-induced senescence. We propose that a coordinated axis controlled by TOP2B in iLADs and LBR in LADs maintains the partitioning of the genome between the NL and the nuclear interior. HighlightsO_LILADs and iLADs differ in supercoiling state C_LIO_LITOP2B controls genome partitioning between nuclear lamina and nuclear interior C_LIO_LITOP2B depletion preferentially affects genome interactions with LBR C_LIO_LISimilar impact of TOP2B depletion and LBR depletion on genome-NL interactions C_LIO_LICo-depletion of TOP2B and LBR recapitulates LAD reshaping typical of oncogene-induced senescence. C_LI