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B-Type Lamins organize 3D chromatin architecture through associations with nuclear lamina and nuclear speckles [RNA-seq]

ABSTRACT: B-type lamins (Lamin B1 and B2) are key components of the nuclear lamina and play essential roles in three-dimensional (3D) chromatin organization by anchoring Lamina-Associated Domains (LADs). Recent studies have indicated that abnormal gene expression resulting from B-type lamin loss occurs in both LAD and non-LAD regions; however, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that the majority of differentially expressed genes (DEGs) in B-type lamin-depleted cells are predominantly located in non-LAD regions, which are characterized by a constitutive association with nuclear speckles. Through RNA-Seq combined with SC35 Tyramide Signal Amplification Sequencing (TSA-Seq) analysis, we find that aberrant gene regulation is closely associated with the repositioning of chromatin either toward or away from nuclear speckles. The absence of B-type lamins causes a global reorganization of chromatin rather than changes in its fine structure, leading to the disruption of constitutive Speckle-Associated Domains (cSPADs). Additionally, the loss of B-type lamins results in euchromatin deactivation and heterochromatin de-repression, which impairs cell viability by increasing apoptotic signaling and causes defective mRNA splicing. Our data reveal a novel role for B-type lamins in regulating transcriptional activity by conserving genome architecture between the nuclear lamina and nuclear speckles.

ORGANISM(S): Homo sapiens

PROVIDER: GSE275659 | GEO | 2026/04/08

REPOSITORIES: GEO

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Project description:Purpose: to qualify and quantify the rearrangement of interactions of nuclear lamins A/C and B with the genome, in relation to nuclearradial repositioning of loci and changes in gene expression, in HepG2 cells exposed to cyclosporin A. .To compare HepG2 cell line transcriptome profiling (RNA-seq) with radially positioning of the chromatin anchored at the nuclear periphery before and after CsA treatment. Methods: To this end, we mapped lamin A and lamin B lamina-associated domains (LADs) by chromatin immunoprecipitation-sequencing (ChIP-seq) of lamin A/C (antibody sc7292x, Santa Cruz Biotechnology) and lamin B1 (antibody ab16048, Abcam), respectively. HepG2 cells were either cultured under proliferative conditions (controls) or exposed for 3 days to 10 uM cyclosporin A. We also assesed the transcriptome by RNA-seq under each condition in duplicate cultures. Results: CsA elicits accumulation of pre-lamin A in HepG2 cells, raising the hypothesis of a global rearrangement of lamin-chromatin interactions. We show here the existence of overlapping and distinct lamin A and B lamina-associated domains (which we refer to as A- and B-LADs, respectively). Whereas B-LADs largely remain constitutive, CsA elicits the formation of facultative A-LADs. Re-localization of A-LADs occur mainly on preexisting B-LADs. However, LAD rearrangement does not correlate with systematic changes in gene expression within LADs. We find a reorganization of A- and B-LADs after CsA treatment, entailing distinct contributions of A- and B- type lamins. to genome organization. Indeed, classification of lamin A LADs and lamin B LADs into properties of ‘A-only’, ‘B-only’ and ‘A-B’ LADs show an overall loss of A-only LADs after CsA treatment. A- only and B-only LADs are highly dynamic with A-B LADs being more stable.The rearrangement of lamin association after CsA treatment correlates with repositioning of loci in the nuclear space with, notably, a loss of lamin B associated with a re-localization of loci towards the nuclear center and conversely, a gain of lamin B linked to a repositioning of loci towards the nuclear periphery. Predictions on radial repositioning of LADs, and of loci within, from 3D structural models of the genome were supported by fluorescence in situ hybridization (FISH) analyses. Conclusions: We show that, while they amply co-localize on well-conserved LADs, lamins A and B also interact with distinct genomic regions that can interchange (switch) between lamin A and B upon CsA treatment. We unveil distinct lamin A and B interactions with chromatin, suggesting complementary contributions to genome conformation. Our data suggest that and lamins A and B may differentially modulate genome organization.

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B-Type Lamins organize 3D chromatin architecture through associations with nuclear lamina and nuclear speckles [RNA-seq]

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