Fig. 1

Associations of chromatin with the nuclear envelope. a Association of chromatin with the nuclear envelope via inner nuclear membrane proteins, lamina interactions, and interactions with proteins of the NPC. A sample of INM proteins interacting with the nuclear lamina and chromatin is depicted. Chromatin interacting with the NPC is loose and euchromatic, in contrast to the compact and heterochromatic nature of domains interacting with the lamina and INM proteins (LADs). b A- and B-type lamins form distinct filaments in the nuclear lamina. c Browser view of LADs identified by lamin B DamID-seq and lamin B ChIP-seq in a region of human chromosome 2. DamID data (HT1080 cells) are from [13]; ChIP data (dermal fibroblasts) are from [14]. d Detection of LAD using the Enriched Domain Detector (EDD) algorithm is using a tunable gap penalty parameter (Gap). “Gap 1” (here, an arbitrary calling corresponding to EDD’s default gap penalty with this dataset) is more stringent than “Gap 2.” ChIP data are from [14]. e FISH visualization of 25 LADs in two nuclei: note the dispersion of LADs around the nuclear periphery and in the nucleoplasm. Reproduced from [15] with permission. f^m6A tracer visualization of LADs. The ^m6A tracer approach is a DamID variation enabling GFP labeling of Dam-methylated lamin-interacting sites in living cells [15]. Reproduced from [15] with permission. g Lamin A LAD (A-LAD) and lamin B LAD (B-LAD) detection by ChIP-seq analysis of lamin A/C and lamin B1 using the EDD algorithm [16], in a region of human chromosome 2. Boxed area, a variable A/B-LAD absent in adipose stem cells but detectable in adipocytes. LAD data are compiled from [8, 14, 16, 17]