The molecular basis of lamin- chromatin interactions [SAMMY-Seq]

Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlying the inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation. Overall design: To investigate the role of lamin proteins in chromatin organization, we carried out a comprehensive analysis including 4fSAMMY-seq, RNA-seq, and ChIP-seq for H3K9me3 across wildtype (WT), Lmna-/- (LmnaKO), and Lmnb1-/-+Lmnb2-/- (LBDKO) mouse embryonic fibroblasts (MEFs).Additionally we perfomed ChIP-seq for euchromatin-associated H3K27ac and H3K4me3 histone modifications on WT. To investigate the role of Lamin A in chromatin 3D organization, we compared SAMMY-seq data from the transfection of full-length Lamin A (LA 1-646) and truncated Lamin A lacking the C-tail (LA 1-429) in WT MEFs.