Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism
Cite this dataset
Pujadas Liwag, Emily et al. (2024). Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism [Dataset]. Dryad. https://doi.org/10.5061/dryad.bvq83bkh3
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.
README: Lamin B1, B2, and B1/B2-AID Hi-C Files
https://doi.org/10.5061/dryad.bvq83bkh3
Description of the data and file structure
Hi-C files from Pujadas et al., 2024. (Under Review) All related files/ codes are available at https://github.com/BackmanLab/Lamin-Project/tree/main
In this dataset, there is an Excel file entitled, "LMNB_project_Hi-C_wasabi_links" that contains all of the links to FASTQs and processed files for each experiment on Wasabi. Column A shows the name of the Hi-C data set that is related to the specific auxin treatment condition (e.g., untreated, 24-hour auxin, and auxin withdraw) for LMNB1, LMNB2, and LMNB1/B2 degradation using the AID system. There are also two replicates of a 48-hour auxin treatment condition for LMNB1/B2 degradation. Column B shows the name of the condition for the uploaded .HiC files. While not all of the .HiC files have been uploaded to Dryad, all of the conditions and .Hi-C files (both raw and processed) can be obtained using using the links in this spreadsheet. As the Hi-C data was obtained using a paired-end run, one R1 and one Read 2 (R2) FASTQ file was created for each sample for each lane. This is presented in Column C and D, respectively. Process files are found in Column E.
****NOTE:* The links included in the Excel file will begin to download once they are clicked. These files are quite large (.HiC files are ~ 2-10 GB and FASTQ files are ~ 1-5 GB).
Sharing/Access information
Links to other publicly accessible locations of the data:
https://www.ncbi.nlm.nih.gov/sra/PRJNA1078503
- Note: Both Hi-C and RNA-seq data can be found with this link.
Codes used to analyze the dataset:
- https://github.com/BackmanLab/Lamin-Project/tree/main
- Zenodo: DOI: 10.5281/zenodo.10680913
Data was derived from the following sources:
- HCT116 cell lines modified with the Auxin-Inducible Degron System (https://www.sciencedirect.com/science/article/pii/S1046202318303311) to target LMNB1, LMNB2, and LMNB1&B2 for degradation. Doxycycline-inducible promoter.
- Conditions: Untreated, 24-hour Auxin treatment (1000 µm IAA), and 24-hour Auxin treatment (1000 µm IAA) with 6 days of Auxin Withdraw. There is also a 48-hour Auxin treatment (1000 µm IAA) for LMNB1&B2.
Code/Software
DOI: 10.5281/zenodo.10680913
Funding
National Science Foundation, Award: EFMA-1830961
National Science Foundation, Award: EFMA-1830969
National Cancer Institute, Award: R01CA228272
National Cancer Institute, Award: U54 CA268084
National Cancer Institute, Award: U54 CA261694
Japan Society for the Promotion of Science, Award: JP21H0419
National Institutes of Health, Award: 5 UM1 HG012649
National Institutes of Health, Award: UM1HG009375
United States-Israel Binational Science Foundation, Award: 2019276
National Institutes of Health, Award: RM1HG011016-01A1
National Science Foundation, Award: NSF PHY-2019745
Cancer Support Center, Award: NCI CA060553
National Institutes of Health, Award: 1S10OD011996-01
National Institutes of Health, Award: 1S10OD026814-01
National Cancer Institute, Award: P30-CA044579