The role of B-type lamins in genome architecture, chromatin dynamics, and gene regulation

Pujadas, Emily M.; Acosta, Nicolas; Carter, Lucas; Daneshkahah, Ali; Agrawal, Vasundhara; Yang, Jiekun; Wei, Xiaolong; Rao, Suhas S.P.; Lieberman-Aiden, Erez; Kanemaki, Masato T.; Adli, Mazhar; Backman, Vadim

doi:10.1016/j.bpj.2022.11.2646

Cited by 2 publications

(3 citation statements)

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“…Raw and processed Hi-C data are also available as open data in the Dryad repository under a Creative Commons Public Domain License (CC0) and are available at the following URL: https:// datad ryad. org/ stash/ share/ XCJsT z8vWB TUrbx r5bbG x1eE8 wY-Q-2ezW6-mmUVA Kk [86]. The original source codes used to generate data in this study are available on GitHub…”

Section: Supplementary Informationmentioning

confidence: 99%

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

Pujadas Liwag,

Wei,

Acosta

et al. 2024

Genome Biol

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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.

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Section: Supplementary Informationmentioning

confidence: 99%

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

Pujadas Liwag,

Wei,

Acosta

et al. 2024

Genome Biol

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“…Chromatin packing scaling (D) can be calculated from these fluctuations in chromatin density. To obtain D measurements within nuclear blebs and nuclear bodies, we used HCT116 cells modified with the AID system to induce simultaneous rapid lamin B1 and lamin B2 degradation (Nishimura et al ., 2009; Yesbolatova et al ., 2019; Pujadas et al ., 2023), termed HCT116 LMN(B1&B2)-AID cells.…”

Section: Resultsmentioning

confidence: 99%

“…HCT116 LMN(B1&B2)-AID cells were grown in McCoy’s 5A Modified Medium (#16600-082, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FBS (#16000-044, Thermo Fisher Scientific, Waltham, MA) and penicillin-streptomycin (100 μg/ml; #15140-122, Thermo Fisher Scientific, Waltham, MA). To create these cells, HCT116 cells (ATCC, #CCL-247) were tagged with the AID system as previously described (Pujadas et al ., 2023). All cells were cultured under recommended conditions at 37°C and 5% CO2.…”

Section: Methodsmentioning

confidence: 99%

DNA density is a better indicator of a nuclear bleb than lamin B loss

Bunner,

Prince,

Srikrishna

et al. 2024

Preprint

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Nuclear blebs are herniations of the nucleus that occur in diseased nuclei that cause nuclear rupture leading to cellular dysfunction. Chromatin and lamins are two of the major structural components of the nucleus that maintain its shape and function, but their relative roles in nuclear blebbing remain elusive. Lamin B is reported to be lost in blebs by qualitative data while quantitative studies reveal a spectrum of lamin B levels in nuclear blebs dependent on perturbation and cell type. Chromatin has been reported to be decreased or de-compacted in nuclear blebs, but again the data are not conclusive. To determine the composition of nuclear blebs, we compared the immunofluorescence intensity of lamin B and DNA in the main nucleus body and nuclear bleb across cell types and perturbations. Lamin B nuclear bleb levels varied drastically across MEF wild type and chromatin or lamins perturbations, HCT116 lamin B1-GFP imaging, and human disease model cells of progeria and prostate cancer. However, DNA concentration was consistently decreased to about half that of the main nucleus body across all measured conditions. Using Partial Wave Spectroscopic (PWS) microscopy to measure chromatin density in the nuclear bleb vs body we find similar results that DNA is consistently less dense in nuclear blebs. Thus, our data spanning many different cell types and perturbations supports that decreased DNA is a better marker of a nuclear bleb than lamin B levels that vary widely.

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The role of B-type lamins in genome architecture, chromatin dynamics, and gene regulation

Cited by 2 publications

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

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

DNA density is a better indicator of a nuclear bleb than lamin B loss

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