Interactions between the genome and the nuclear lamina are multivalent and cooperative

Mammalian genomes contain hundreds of lamina-associated domains (LADs), which are large, often megabase-sized heterochromatin domains that interact with the nuclear lamina (NL). While LADs play a key role in the spatial organization of the genome and potently repress gene activity, it is not yet understood how their interactions with the NL are encoded in their DNA. Here, we investigated this by taking a LAD "scrambling" approach that employs transposon-mediated local hopping of loxP recombination sites to generate a large collection of clonal cell lines with systematic series of deletions and inversions up to ~2Mb in size, spanning LAD and their flanking inter-LAD sequences. Mapping of NL interactions in these rearrangements revealed that a single LAD contacts the NL through multiple regions. These regions act cooperatively or redundantly; some have more affinity for the NL than others and can pull neighbouring sequences to the NL. We also observed cooperativity between two neighbouring LADs, provided that they are close enough to each other. Changes in NL contacts were partially mirrored by the heterochromatin mark H3K9me3, with the latter being more predictive of changes in gene expression caused by the rearrangements. These results reveal how megabase-sized chromatin domains are positioned at the NL. In this repository, laboratory notebook prints and supplementary data such as gel images and Sanger sequencing data are deposited. Processed data and data analysis pipelines are deposited in the affiliated GitHub release on Zenodo.