Identification of lamin B–regulated chromatin regions based on chromatin landscapes

Zheng, Xiaobin; Kim, Young-Jo; Zheng, Yixian

doi:10.1091/mbc.e15-04-0210

Cited by 52 publications

(75 citation statements)

References 44 publications

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“…The nuclear lamina constitutes the molecular interface between the inner nuclear envelope membrane and the peripheral chromatin domains. Lamin B1 is expressed in nearly every cell type and has been shown to play important roles for transcriptional regulation and chromatin organization [37]. We confirmed that GM1 is co-localized with the nuclear lamin of neurons (Fig.1a).…”

Section: Resultssupporting

confidence: 79%

GM1 Ganglioside is Involved in Epigenetic Activation Loci of Neuronal Cells

Tsai

Itokazu

2015

Neurochem Res

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Gangliosides are sialic acid-containing glycosphingolipids that are most abundant in the nerve tissues. The quantity and expression pattern of gangliosides in brain change drastically throughout development and are mainly regulated through stage-specific expression of glycosyltransferase (ganglioside synthase) genes. We previously demonstrated that acetylation of histones H3 and H4 on the N-acetylgalactosaminyltransferase I (GalNAcT, GA2/GM2/GD2/GT2-synthase) gene promoter resulted in recruitment of trans-activation factors. In addition, we reported that epigenetic activation of the GalNAcT gene was also detected as accompanied by an apparent induction of neuronal differentiation in neural stem cells responding to an exogenous supplement of ganglioside GM1. Here, we present evidence supporting the concept that nuclear GM1 is associated with gene regulation in neuronal cells. We found that nuclear GM1 binds acetylated histones on the promoters of the GalNAcT and NeuroD1 genes in differentiated neurons. Our study demonstrates for the first time that GM1 interacts with chromatin via acetylated histones at the nuclear periphery of neuronal cells.

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Section: Resultssupporting

confidence: 79%

GM1 Ganglioside is Involved in Epigenetic Activation Loci of Neuronal Cells

Tsai

Itokazu

2015

Neurochem Res

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“…Depletion of the single B-type lamin in Drosophila causes detachment of various genes from the NL (Kohwi et al, 2013; Shevelyov et al, 2009), while the only lamin gene in C. elegans, LMN-1, contributes to the sequestration of a heterochromatic transgene array at the nuclear periphery (Mattout et al, 2011). Surprisingly, deletion of all lamins in mouse embryonic stem cells has no or marginal effects on genome-wide contacts with the NL as determined by genomic interactions with emerin (Amendola and van Steensel, 2015; Zheng et al, 2015). Genetic studies in mouse suggest this result may be explained by redundant roles of Lamin A/C and the Lamin B receptor (LBR).…”

Section: Nl Proteins Involved In Nl – Lad Interactionsmentioning

confidence: 99%

Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression

Steensel

Belmont

2017

Cell

815

765

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In metazoan cell nuclei, hundreds of large chromatin domains are in close contact with the nuclear lamina. Such lamina-associated domains (LADs) are thought to help organize chromosomes inside the nucleus and have been associated with gene repression. Here, we discuss the properties of LADs, the molecular mechanisms that determine their association with the nuclear lamina, their dynamic links with other nuclear compartments, and their proposed roles in gene regulation.

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“…Genome regions proximal to the lamin intermediate filament polymer lining the inner nuclear membrane are called lamina-associated domains (LADs) (Guelen et al 2008). However, while they are implicated in genome organization (Mewborn et al 2010;Mattout et al 2011;Solovei et al 2013), it remains unclear if lamins themselves are absolutely required for tethering LADs to the periphery (Amendola and van Steensel 2015;Zheng et al 2015). The nuclear periphery is generally repressive, with genes in LADs tending to contain silencing marks (Guelen et al 2008).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

et al. 2017

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The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation.

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Identification of lamin B–regulated chromatin regions based on chromatin landscapes

Cited by 52 publications

References 44 publications

GM1 Ganglioside is Involved in Epigenetic Activation Loci of Neuronal Cells

GM1 Ganglioside is Involved in Epigenetic Activation Loci of Neuronal Cells

Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

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