Gene Regulatory Interactions at Lamina-Associated Domains

Genes (Basel). 2023 Jan 28;14(2):334. doi: 10.3390/genes14020334.

Abstract

The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.

Keywords: adipogenesis; adipose stem cell; chromatin loop; enhancer interaction; lamina-associated domain; nuclear lamina.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus* / genetics
  • Chromatin* / metabolism
  • Epistasis, Genetic
  • In Situ Hybridization, Fluorescence
  • Nuclear Lamina / genetics
  • Nuclear Lamina / metabolism

Substances

  • Chromatin

Grants and funding

This work was funded by the University of Oslo, South-East Heath Norway grant No. 2020052 and 2023080, and Research Council of Norway grant No. 313508.