Biology subjects

Wong, X.

Publications and source records attributed to Wong, X..

3 recordsLinked to original sources

bioRxiv2020

Lamin C regulates genome organization after mitosis

The dynamic 3D organization of the genome is central to the regulation of gene expression and developmental progression, with its disruption being implicated in various diseases. The nuclear lamina, a proteinaceous meshwork underlying the nuclear envelope (NE), provides both structural and regulatory influences on genome organization through the tethering of large inactive genomic regions, called Lamina Associated Domains (LADs), to the nuclear periphery. Evidence suggests that the A type lamins, lamins A and C, are the predominant lamins involved in the peripheral association of LADs, with these two isotypes forming distinct networks and potentially involved in different cellular processes. Here we tested whether lamins A and C have distinct roles in genome organization by examining chromosome architecture in cells in which lamin C or lamin A are specifically down-regulated. We find that lamin C (not lamin A) is required for the 3D organization of LADs and overall chromosome organization in the cell nucleus. Striking differences in the localization of lamin A and lamin C are present as cells exit mitosis that persist through early G1. Whereas lamin A associates with the nascent NE during telophase, lamin C remains in the interior surrounding nucleoplasmic LAD clusters. Lamin C association with the NE is delayed until several hours into G1 and correlates temporally and spatially with the post-mitotic NE association of LADs. Post-mitotic LAD association with the NE, and consequently global 3D genome organization, is perturbed only in cells depleted of lamin C, and not in cells depleted of lamin A. We conclude that lamin C regulates LAD dynamics after mitosis and is a key regulator of genome organization in mammalian cells. These findings reveal an unexpectedly central role for lamin C in genome organization, including both inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE.

cell biology↗

bioRxiv2019

Mapping the micro-proteome of the nuclear lamina and lamin associated domains

The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2{beta} to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.

genomics↗

bioRxiv2017

Chromosome Conformation Paints Reveal The Role Of Lamina Association In Genome Organization And Regulation

Non-random, dynamic three-dimensional organization of the nucleus is important for regulation of gene expression. Numerous studies using chromosome conformation capture strategies have uncovered ensemble organizational principles of individual chromosomes, including organization into active (A) and inactive (B) compartments. In addition, large inactive regions of the genome appear to be associated with the nuclear lamina, the so-called Lamina Associated Domains (LADs). However, the interrelationship between overall chromosome conformation and association of domains with the nuclear lamina remains unclear. In particular, the 3D organization of LADs within the context of the entire chromosome has not been investigated. In this study, we describe \"chromosome conformation paints\" to determine the relationship in situ between LAD and non-LAD regions of the genome in single cells. We find that LADs organize into constrained and compact regions at the nuclear lamina, and these findings are supported by an integrated analysis of both DamID and Hi-C data. Using a refined algorithm to identify active (A) and inactive (B) compartments from Hi-C data, we demonstrate that the LADs correspond to the B compartment. We demonstrate that in situ single cell chromosome organization is strikingly predicted by integrating both Hi-C and DamID data into a chromosome conformation model. In addition, using the chromosome conformation paints, we demonstrate that LAD (and B-compartment) organization is dependent upon both chromatin state and Lamin A/C. Finally, we demonstrate that small regions within LADs escape the repressive regime at the peripheral zone to interact with the A-compartment and are enriched for both transcription start sites (TSSs) and active enhancers.

cell biology↗