DOI: 10.5061/dryad.bvq83bkh3
title: Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism

description: BACKGROUNDB-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.RESULTSUsing 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.CONCLUSIONSOur
 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.
description: # Lamin B1, B2, and B1/B2-AID Hi-C Files
 ## Description of the data
 and file structure Hi-C files from Pujadas et al., 2024. (*Under Review*)
 All related files/ codes are available at
 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: *
 * **Note:** Both
 Hi-C and RNA-seq data can be found with this link. Codes used to analyze
 the dataset: *
 * 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)
 ](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