Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
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13059_2024_Article_3212.pdf
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Author(s)
Pujadas Liwag, Emily M.
Wei, Xiaolong
Acosta, Nicolas
Carter, Lucas M.
Yang, Jiekun
Almassalha, Luay M.
Jain, Surbhi
Daneshkhah, Ali
Rao, Suhas S. P.
Seker-Polat, Fidan
Date Issued
March 22, 2024
Journal
Genome Biology
Publisher
Springer Science and Business Media LLC
Citation
Genome Biology. 2024 Mar 22;25(1):77
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
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DOI of Published Version
https://doi.org/10.1186/s13059-024-03212-y
