Fig. 1

Lamin B1 associates with euchromatin regions. a UCSC Genome Browser overview of one region across chromosome 11 (mm9) of the lamin B1 ChIP-seq profiles in NMuMG cells that were untreated (blue) or treated with TGF-β for 8 h (orange) or 24 h (red). Lamin B1 + sites identified at each condition (black), previously published lamina-associated domains (LADs) (green), and the RefSeq gene track (dark blue) are shown. b Genome distribution of lamin B1 ChIP-seq peaks. The distal region is that within 2.5 and 0.5 Kb upstream of a gene’s TSS, and the proximal region, within 0.5 Kb of a gene’s TSS (top). The average distribution of lamin B1 ChIP-seq reads is shown, as well as the corresponding IgG control experiments, at 2 Kb around the TSS of lamin B1 + genes (bottom). c ChIP-qPCR of a canonical LAD (cLAD)-selected region. Data are expressed as the fold-change relative to data obtained from the IgG experiments. Data are shown as mean ± SD, n = 4. d Western blotting of chromatin immunoprecipitated with lamin B1 or IgG antibodies from normal or KD cells. e AT/CG content of the sequences of lamin B1 + sites. f Expression of lamin B1 + genes computed in FPKM (fragment per kilobase of transcript per million mapped reads) in untreated cells (blue) or those treated with TGF-β for 8 h (orange) or 24 h (red), as compared with the rest of genes in the genome (white) (top). Promoter ATAC-seq enrichment of lamin B1 + genes measured in number of normalized reads in untreated cells (blue) or those treated with TGF-β for 8 h (orange) or 24 h (red), as compared with the rest of genes in the genome (white) (bottom). The bottom and top fractions in the boxes represent the first and third quartiles, and the line, the median. Whiskers denote the interval between 1.5 times the interquartile range (IQR) and the median. g Average distribution of lamin B1 ChIP-seq reads at 2 Kb around the TSS of mouse genes that were classified into four categories (silent, low, medium, and high) according to their expression levels