Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes

Abstract

The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains. These localized interactions are associated with distinct transcriptional outcomes in a manner dependent on local chromatin modifications. Down-regulation of lamin A/C leads to dissociation of lamin A/C from promoters and remodels repressive and permissive histone modifications by enhancing transcriptional permissiveness, but is not sufficient to elicit gene activation. Adipogenic differentiation resets a large number of lamin-genome associations globally and at subpromoter levels and redefines associated transcription outputs. We propose that lamin A/C acts as a modulator of local gene expression outcome through interaction with adjustable sites on promoters, and that these position-dependent transcriptional readouts may be reset upon differentiation.

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

“…Figure 3A shows, for MNase-digested and sonicated chromatin, ChIP/Input log ratios for LMNA in consecutive 10 kb bins for indicated genes (top panels), and whether these genes are localized in a LiD or not (bottom panels; bar [LiD] or no bar [no LiD]). Consistent with our earlier findings, 12 a gene may be partially associated with LMNA and yet be localized outside a LiD (e.g. SCN10A, Sonic) or within a LiD (e.g., LDHB, Sonic), or a gene may be entirely bound by LMNA and found in a LiD (e.g.…”

“…4C), again consistent with an association of LMNA with both repressed and active genes. 12 Collectively, our results reveal a specific chromatin composition of a subset of LMNA LiDs that are only detected in MNasedigested chromatin. They also indicate that MNase-digested chromatin contains a significant set of lamin-interacting domains identifiable by ChIP and under-represented in sonicated chromatin.…”

“…We name these domains LiDs, indistinctively for Aand B-type lamin-interacting domains, to distinguish them from the previously designated lamina-associated domains (LADs), which stricto sensu refer to domains interacting with lamins at the nuclear lamina (as opposed to all nuclear lamins), and hence at the nuclear periphery. Given evidence put forward here and earlier 12 that A-type lamins can interact with chromatin not only at the nuclear periphery but also in the nuclear interior, LiDs are by definition less spatially restricted in the nucleus than LADs. We identify here LMNA LiDs specific to MNase-digested or sonicated chromatin, which are differentially enriched in gene density, histone modifications and H2A.Z.…”

“…We examined 5 promoter regions for which we previously reported interaction patterns with LMNA, 12 3 gene bodies and 3 intergenic regions. We determined whether these regions mapped to LiDs in our HeLa ChIP-seq datasets (Supplementary Table S1, LiD information).…”

“…2 Features of LADs include residence in overall transcriptionally silent heterochromatin 2,9 consistent with enrichment of this compartment at the nuclear periphery, 5,10,11 and a gene-poor content. 2 Large chromatin domains with similar properties have also been identified by chromatin immunoprecipitation (ChIP) of lamin A/C (referred to here as LMNA) or lamin B1 (LMNB1) coupled to array hybridization 12 or highthroughput sequencing (ChIP-seq). [13][14][15] The published datasets reveal significant overlap in genomic coverage of lamin-interacting domains discovered by DamID and ChIP 15 despite differences between the 2 methods.…”