Lamins organize the global three-dimensional genome from the nuclear periphery

AbstractLamins are structural components of the nuclear lamina (NL) that regulate genome organization and gene expression, but the mechanism remains unclear. Using Hi-C, we show that lamins maintain proper interactions among the topologically associated chromatin domains (TADs) but not their overall architecture. Combining Hi-C with fluorescence in situ hybridization (FISH) and analyses of lamina-associated domains (LADs), we reveal that lamin loss causes expansion or detachment of specific LADs in mouse ES cells. The detached LADs disrupt 3D interactions of both LADs and interior chromatin. 4C and epigenome analyses further demonstrate that lamins maintain the active and repressive chromatin domains among different TADs. By combining these studies with transcriptome analyses, we found a significant correlation between transcription changes and the changes of active and inactive chromatin domain interactions. These findings provide a foundation to further study how the nuclear periphery impacts genome organization and transcription in development and NL-associated diseases.HighlightsLamin loss does not affect the overall TAD structure but alters TAD-TAD interactionsLamin null ES cells exhibit decondensation or detachment of specific LAD regionsExpansion and detachment of LADs can alter genome-wide 3D chromatin interactionsAltered chromatin domain interactions are correlated with altered transcription

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In vitro morphological bud formation in organ-like three-dimensional structure from mouse ES cells induced by FGF10 signaling

Communicative & Integrative Biology ◽

10.4161/cib.20093 ◽

2012 ◽

Vol 5 (4) ◽

pp. 312-315 ◽

Cited By ~ 2

Author(s):

Toyoaki Ohbuchi ◽

Miyako Takaki ◽

Hiromi Misawa ◽

Hideaki Suzuki ◽

Yoichi Ueta

Keyword(s):

Es Cells ◽

Three Dimensional ◽

Dimensional Structure ◽

Bud Formation ◽

Three Dimensional Structure ◽

Mouse Es Cells

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A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

The Journal of Cell Biology ◽

10.1083/jcb.200706060 ◽

2008 ◽

Vol 180 (1) ◽

pp. 51-65 ◽

Cited By ~ 259

Author(s):

R. Ileng Kumaran ◽

David L. Spector

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Genetic Locus ◽

Nuclear Periphery ◽

Three Dimensional ◽

Nuclear Lamina ◽

Time Lapse ◽

Living Cells ◽

Cell System ◽

Transcriptional Induction

The peripheral nuclear lamina, which is largely but not entirely associated with inactive chromatin, is considered to be an important determinant of nuclear structure and gene expression. We present here an inducible system to target a genetic locus to the nuclear lamina in living mammalian cells. Using three-dimensional time-lapse microscopy, we determined that targeting of the locus requires passage through mitosis. Once targeted, the locus remains anchored to the nuclear periphery in interphase as well as in daughter cells after passage through a subsequent mitosis. Upon transcriptional induction, components of the gene expression machinery are recruited to the targeted locus, and we visualized nascent transcripts at the nuclear periphery. The kinetics of transcriptional induction at the nuclear lamina is similar to that observed at an internal nuclear region. This new cell system provides a powerful approach to study the dynamics of gene function at the nuclear periphery in living cells.

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Identification of decondensed large-scale chromatin regions by TSA-seq and their localization to a subset of chromatin domain boundaries

10.1101/2021.04.06.438686 ◽

2021 ◽

Author(s):

Omid Gholamalamdari ◽

Liguo Zhang ◽

Yu Chen ◽

Andrew Belmont

Keyword(s):

Genome Organization ◽

Large Scale ◽

Chromatin Domain ◽

Interphase Chromosome ◽

Chromatin Domains ◽

Nuclear Compartment ◽

Chromatin Compaction ◽

Domain Boundaries ◽

Chromatin Remodeling Complexes ◽

Local Enrichment

AbstractLarge-scale chromatin compaction is nonuniform across the human genome and correlates with gene expression and genome organization. Current methodologies for assessing large-scale chromatin compaction are indirect and largely based on assays that probe lower levels of chromatin organization, primarily at the level of the nucleosome and/or the local compaction of nearby nucleosomes. These assays assume a one-to-one correlation between local nucleosomal compaction and large-scale compaction of chromosomes that may not exist. Here we describe a method to identify interphase chromosome regions with relatively high levels of large-scale chromatin decondensation using TSA-seq, which produces a signal proportional to microscopic-scale distances relative to a defined nuclear compartment. TSA-seq scores that change rapidly as a function of genomic distance, detected by their higher slope values, identify decondensed large-scale chromatin domains (DLCDs), as then validated by 3D DNA-FISH. DLCDs map near a subset of chromatin domain boundaries, defined by Hi-C, which separate active and repressed chromatin domains and correspond to compartment, subcompartment, and some TAD boundaries. Most DLCDs can also be detected by high slopes of their Hi-C compartment score. In addition to local enrichment in cohesin (RAD21, SMC3) and CTCF, DLCDs show the highest local enrichment to super-enhancers, but are also locally enriched in transcription factors, histone-modifying complexes, chromatin mark readers, and chromatin remodeling complexes. The localization of these DLCDs to a subset of Hi-C chromatin domain boundaries that separate active versus inactive chromatin regions, as measured by two orthogonal genomic methods, suggests a distinct role for DLCDs in genome organization.

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Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons

10.1101/2020.01.08.898429 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sally Martin ◽

Daniel Poppe ◽

Nelly Olova ◽

Conor O’Leary ◽

Elena Ivanova ◽

...

Keyword(s):

Dna Methylation ◽

Es Cells ◽

Embryonic Stem ◽

Nuclear Lamina ◽

Neuronal Maturation ◽

Neuronal Marker ◽

Mouse Es Cells ◽

Primary Mouse

AbstractDNA methylation functions in genome regulation and is implicated in neuronal maturation. Early post-natal accumulation of atypical non-CG methylation (mCH) occurs in neurons of mice and humans, but its precise function remains unknown. Here we investigate mCH deposition in neurons derived from mouse ES-cells in vitro and in cultured primary mouse neurons. We find that both acquire comparable levels of mCH over a similar period as in vivo. In vitro mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic neuronal marker Rbfox3 (NeuN) and is enriched at the nuclear lamina. Despite these similarities, whole genome bisulfite sequencing reveals that mCH patterning in mESC-derived neurons partially differs from in vivo. mESC-derived neurons therefore represent a valuable model system for analyzing the mechanisms and functional consequences of correct and aberrantly deposited CG and non-CG methylation in neuronal maturation.

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Role of the Nuclear Lamina in Age-Associated Nuclear Reorganization and Inflammation

Cells ◽

10.3390/cells9030718 ◽

2020 ◽

Vol 9 (3) ◽

pp. 718

Author(s):

Lidya Kristiani ◽

Miri Kim ◽

Youngjo Kim

Keyword(s):

Inflammatory Responses ◽

Nuclear Periphery ◽

Three Dimensional ◽

Nuclear Lamina ◽

Global Gene Expression ◽

Nuclear Reorganization ◽

Gradual Loss

Aging is characterized by the gradual loss of tissue function and integrity. Activation of inflammatory responses accelerates the deterioration of cells and tissues. Many studies have shown that alteration of the components of the nuclear lamina is associated with inflammation, both in vivo and in vitro. However, the mechanism by which the nuclear lamina regulates inflammation is largely unknown. Recent studies have suggested that the nuclear lamina regulates both organization of the three-dimensional chromatin structure at the nuclear periphery and global gene expression, such as the expression of inflammatory response genes. Here, we discuss the current updates in the research on nuclear lamina alteration, activation of inflammation, and nuclear reorganization in models of cellular senescence and organismal aging.

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Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

10.1101/2021.11.12.468401 ◽

2021 ◽

Author(s):

Kartik Kamat ◽

Yifeng Qi ◽

Yuchuan Wang ◽

Jian Ma ◽

Bin Zhang

Keyword(s):

Phase Separation ◽

Genome Organization ◽

Large Scale ◽

Three Dimensional ◽

Nuclear Lamina ◽

Spatial Arrangement ◽

Nuclear Bodies ◽

Chromatin Interaction ◽

Nuclear Speckles ◽

Heterogeneous Distribution

The three-dimensional (3D) organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a co-phase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells, while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the non-specificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the co-phase separation provides a robust mechanism for encoding functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.

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TSA-Seq Mapping of Nuclear Genome Organization

10.1101/307892 ◽

2018 ◽

Cited By ~ 3

Author(s):

Yu Chen ◽

Yang Zhang ◽

Yuchuan Wang ◽

Liguo Zhang ◽

Eva K. Brinkman ◽

...

Keyword(s):

Genome Organization ◽

Spatial Organization ◽

Essential Feature ◽

Three Dimensional ◽

Nuclear Genome ◽

Nuclear Lamina ◽

Mapping Method ◽

Spatial Gradient ◽

Nuclear Speckles ◽

Genome Wide

SummaryWhile nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. Here we describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription “hot-zones”. Transcription hot-zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, house-keeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for nuclear spatial organization of transcription.

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Subnuclear localisation is associated with gene activation not repression or parental origin at the imprinted Dlk1-Dio3 locus

10.1101/2021.03.17.435843 ◽

2021 ◽

Author(s):

Rahia Mashoodh ◽

Lisa C Hulsmann ◽

Frances L Dearden ◽

Nozomi Takahashi ◽

Anne C Ferguson-Smith

Keyword(s):

Gene Expression ◽

Transcriptional Repression ◽

Es Cells ◽

In Situ Hybridisation ◽

Nuclear Periphery ◽

Gene Activation ◽

Three Dimensional ◽

Embryonic Stem ◽

Parental Origin ◽

Fluorescence In Situ Hybridisation

At interphase, de-condensed chromosomes have a non-random three-dimensional architecture within the nucleus, however, little is known about the extent to which nuclear organisation might influence expression or vice versa. Here, using imprinting as a model, we use 3D RNA- and DNA-fluorescence-in-situ-hybridisation in normal and mutant mouse embryonic stem cells to assess the relationship between imprinting control, gene expression and allelic distance from the nuclear periphery. We compared the two parentally inherited imprinted domains at the Dlk1-Dio3 domain and find a small but reproducible trend for the maternally inherited domain to be further away from the periphery if the maternally expressed gene Gtl2/Meg3 is active compared to when it is silenced. Using Zfp57KO ES cells, which harbour a paternal to maternal epigenotype switch, we observe active alleles significantly further away from the nuclear periphery with the distance from the periphery being proportional to the number of alleles active within the cell. This distribution of alleles suggests an activating effect of the nuclear interior rather than a repressive association with the nuclear periphery. Although we see a trend for the paternally inherited copy of the locus to be closer to the nuclear periphery, this appears to be linked to stochastic gene expression differences rather than parental origin. Our results suggest that transcriptional activity, rather than transcriptional repression or parental origin, defines sub-nuclear localisation at an endogenous imprinted domain.

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Lamin C is required to establish genome organization after mitosis

Genome Biology ◽

10.1186/s13059-021-02516-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xianrong Wong ◽

Victoria E. Hoskins ◽

Ashley J. Melendez-Perez ◽

Jennifer C. Harr ◽

Molly Gordon ◽

...

Keyword(s):

Genome Organization ◽

Mammalian Cells ◽

Nuclear Periphery ◽

Nuclear Lamina ◽

Lamin A ◽

Chromosome Architecture ◽

3D Genome ◽

Mouse Cells ◽

The Individual ◽

Differential Phosphorylation

Abstract Background The dynamic 3D organization of the genome is central to gene regulation and development. The nuclear lamina influences genome organization through the tethering of lamina-associated domains (LADs) to the nuclear periphery. Evidence suggests that lamins A and C are the predominant lamins involved in the peripheral association of LADs, potentially serving different roles. Results Here, we examine chromosome architecture in mouse cells in which lamin A or lamin C are downregulated. We find that lamin C, and not lamin A, is required for the 3D organization of LADs and overall chromosome organization. Striking differences in localization are present as cells exit mitosis and persist through early G1 and are linked to differential phosphorylation. Whereas lamin A associates with the nascent nuclear envelope (NE) during telophase, lamin C remains in the interior, surrounding globular LAD aggregates enriched on euchromatic regions. 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 global 3D genome organization, is perturbed only in cells depleted of lamin C, and not lamin A. Conclusions Lamin C regulates LAD dynamics during exit from mitosis and is a key regulator of genome organization in mammalian cells. This reveals an unexpectedly central role for lamin C in genome organization, including inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE, raising intriguing questions about the individual and overlapping roles of lamin A/C in cellular function and disease.

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Plant 3-D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years

Plant and Cell Physiology ◽

10.1093/pcp/pcab134 ◽

2021 ◽

Author(s):

Xinxin Zhang ◽

Tianzuo Wang

Keyword(s):

Genome Organization ◽

Gene Expression Regulation ◽

Epigenetic Modification ◽

Three Dimensional ◽

Chromatin Organization ◽

Chromatin Conformation ◽

D Genome ◽

Chromatin Domains ◽

Chromosome Conformation ◽

Chromatin Conformation Capture

Abstract Over the past few decades, eukaryotic linear genomes and epigenomes have been widely and extensively studied for understanding gene expression regulation. More recently, the three-dimensional (3-D) chromatin organization was found to be important for determining genome functionality, finely tuning physiological processes for appropriate cellular responses. With the development of visualization techniques and chromatin conformation capture (3C)-based techniques, increasing evidence indicates that chromosomal architecture characteristics and chromatin domains with different epigenetic modification in the nucleus are correlated to transcriptional activities. Subsequent studies have further explored the intricate interplay between 3-D genome organization and the function of interacting regions. In this review, we summarize spatial distribution patterns of chromatin, including chromatin positioning, configurations and domains, with a particular focus on the effect of a unique form of interaction between a variety of factors that shapes the 3-D genome conformation in plants. We further discuss the methods, advantages and limitations of various chromatin conformation capture (3C)-based techniques, highlighting the applications of these technologies in plants to identify chromatin domains, and address their dynamic changes and functional implications in evolution, and adaptation to development and changing environmental conditions. Moreover, the future implications and emerging research directions of 3-D genome organization are discussed.

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