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

Abstract

Chromatin is hierarchically organized in a dynamic manner in the mammalian cell nucleus, but the causal relationship between physical 3D genome organization and transcriptional activity and genome activity remains to be fully understood. Genome-wide studies have suggested that the interplay of several principles leads to the emergence of the major organizational features of the genome, including polymer-polymer interactions, chromatin loop extrusion, phase separation, the physical interaction of chromatin with stable architectural elements of the nucleus (i.e., nuclear envelope), and chromatin dynamics. The nuclear lamina is the ultimate determinant of nuclear space that posits a structural limit on the 3D genome organization. Lamins are structural components of the nuclear lamina that provide mechanical support to the nucleus and regulate genome organization and transcription. However, identifying the direct roles of lamins on dynamic genome organization has been challenging as depletion of lamin proteins severely impacts cell viability. To overcome this challenge, we engineered colon carcinoma cells to rapidly and completely degrade endogenous B-type lamins using Auxin-induced degron (AID) technology. We utilized a suite of novel technologies such as live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, in situ Hi-C, and CRISPR-Sirius to demonstrate that acute lamin depletion increases chromatin dynamics at the nuclear periphery and weakens chromatin compartmentalization, as well as physically repositions gene-specific loci with respect to the nuclear periphery. Further, using the reversible AID system, we show that significantly altered genes after acute lamin depletion are enriched near LADs, and replenishment of lamins re-establishes their basal expression. Our findings provide a deeper understanding of the role B-type lamins in cell type-specific 3D genome organization and transcription.