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Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism

Pujadas Liwag, Emily1; Wei, Xiaolong2; Acosta, Nicolas1; Carter, Lucas1; Yang, Jiekun3; Almassalha, Luay1; Jain, Surbhi1; Daneshkhah, Ali1; Rao, Suhas4; Seker-Polat, Fidan1; MacQuarrie, Kyle5; Ibarra, Joe5; Agrawal, Vasundhara1; Lieberman Aiden, Erez4; Kanemaki, Masato6; Backman, Vadim1; Adli, Mazhar1

Research facility: Northwestern University
Published Feb 02, 2024; Updated Feb 26, 2024 on Dryad. https://doi.org/10.5061/dryad.bvq83bkh3

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Feb 02, 2024 version files 64.61 GB
Feb 26, 2024 version files 64.61 GB

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Abstract

BACKGROUND
B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology.

RESULTS
Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and Fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci,
heterochromatin, and chromatin domains.

CONCLUSIONS
Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.