Genome models integrating chromatin contacts and nuclear lamin-genome interactions reveal implications of laminopathy-causing lamin mutations on genome architecture

Processes shaping the 3-dimensional (3D) human genome remain elusive. We present Chrom3D, a user-friendly 3D whole-genome modeling software that dynamically simulates the radial positioning of topological domains (TADs) in the nucleus. We integrate Hi-C and lamin-associated domain (LAD) information to generate high-resolution ensembles of models that recapitulate single-cell TAD distribution. Chrom3D reveals dynamic TADs and TADs constitutively placed at the nuclear periphery or nuclear interior. TAD stability in these compartments is consistent with differences in TAD gene density and expression level. A- and B-type lamins as radial constraints differentially skew LAD distribution towards the nuclear interior or periphery. Predictions of radial LAD placement in model ensembles are validated by quantitative imaging. Chrom3D models reveal unexpected features of LAD regulation in the nuclear interior in cells from laminopathy patients with a LMNA mutation. Integration of radial positioning constraints in 3D genome models enables the study spatial gene regulation in disease contexts. Overall design: HeLa cells (American Type Culture Collection; CCL-2) were cultured in MEM containing Glutamax (Gibco), 1% non-essential amino acids and 10% fetal calf serum. Fibroblasts (abbreviated as "HSF" in the sample lists) were cultured in DMEM/F12/10% fetal calf serum, 10 ng/ml epidermal growth factor, 24 ng/ml basic fibroblast growth factor and 1% Penicillin-Streptomycin. Cultures were at passage 5-7 when used. The dataset contains LMNA ChIP-seq data for 3 control normal fibroblast samples (CTL-1, CTL-2, CTL-3) and 4 patient fibroblast samples all with the same LMNA p.R482W mutation (FPLD-p1, FPLD-p2, FPLD-p3, FPLD-p4). Chromatin from these samples was prepared by sonication (Bioruptor, Diagenode) after formaldehyde-crosslinking (15 min), and ChIPed using anti-lamin A/C antibodies (50 microgram antibody per 10e7 cells). ChIP DNA was eluted and isolated by phenol-chloroform isoamylalcohol extraction. The data also contains RNA -seq samples for the aforementioend 7 samples. The data also contain ChIP-sq samples from HeLa cells overexpressing Flag-tagged versions of LMNA wild-type (wt) and mutants (Flag-LMNA(R388P); Flag-LMNA(L647R)). For these samples, HeLa cells were transfected with the wt, R388P and L647R LMNA constructs; 24 h after transfection, cells were cross-linked with formaldehyde for 15 min, chromatin fragmented by sonicatioin (Bioruptor; Diagenode) and analysed by ChIP using anti-Flag antibodies (20 microgram antibody per 10e7 cells). ChIP DNA was eluted and isolated by phenol-chloroform isoamylalcohol extraction. For all ChIP samples, Illumina libraries were prepared from 12 ng DNA and sequenced on an Illumina HiSeq2500. The data also contains RNA -seq samples for the aforementioend 3 "CTL" and 4 "FLPD" samples. Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation. RNAseq libraries were prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.