Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

Kind, Jop; Pagie, Ludo; Vries, Sandra S. de; Nahidiazar, Leila; Dey, Siddharth S.; Bienko, Magda; Ye, Zhan; Lajoie, Bryan R.; Graaf, Carolyn A. de; Amendola, Mario; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A.; Jalink, Kees; Dekker, Job; Oudenaarden, Alexander van; Steensel, Bas van

doi:10.1016/j.cell.2015.08.040

Cited by 406 publications

(567 citation statements)

References 43 publications

(81 reference statements)

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“…First, the investigators found the locus Pard3 among the contacted hubs in human embryonic stem (ES) cells. Then in human HCT116 cells, in which Pard3 was expressed in a circadian manner, the locus was rhythmically recruited to the nuclear lamina, a well-known repressive compartment of the nucleus (Kind et al 2015). Interestingly, this recruitment was dependent on CTCF and PARP1 protein functions, the latter having been previously linked to the clockwork machinery in the mouse liver (Asher et al 2010).…”

Section: Rhythmic Transcription In a Three-dimensional Nucleusmentioning

confidence: 84%

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Yeung

Naef

2016

Cold Spring Harb Perspect Biol

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Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating light input from the retina and synchronizes other tissues to the same internal rhythm. The molecular clocks that drive these circadian rhythms are ticking in nearly all cells in the body. Efforts in systems chronobiology are now being directed at understanding, on a comprehensive scale, how the circadian clock controls different layers of gene regulation to provide robust timing cues at the cellular and tissue level. In this review, we introduce some basic concepts underlying periodicity of gene regulation, and then highlight recent genome-wide investigations on the propagation of rhythms across multiple regulatory layers in mammals, all the way from chromatin conformation to protein accumulation.

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Section: Rhythmic Transcription In a Three-dimensional Nucleusmentioning

confidence: 84%

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Yeung

Naef

2016

Cold Spring Harb Perspect Biol

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“…We thank Ophelie Cosnefroy for helpful discussions; Bas van Steensel for sharing definitions of human lamina-associated regions (49); the ENCODE consortium for providing HepG2 gene-expression data (GEO accession code GSE87958); the staff at I03, Diamond Light Source for assistance with X-ray data collection; and Phil Walker and Andrew Purkiss for X-ray crystallography software support. This work was supported by NIH Grants GM082251 (to A.N.E.…”

Section: Methodsmentioning

confidence: 99%

Structural basis for spumavirus GAG tethering to chromatin

Lesbats

Serrao

Maskell

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region. Here, we show that the PFV CBS is essential and sufficient for a direct interaction with nucleosomes and present a crystal structure of the CBS bound to a mononucleosome. The CBS interacts with the histone octamer, engaging the H2A-H2B acidic patch in a manner similar to other acidic patch-binding proteins such as herpesvirus latency-associated nuclear antigen (LANA). Substitutions of the invariant arginine anchor residue in GAG result in global redistribution of PFV and macaque simian foamy virus (SFV mac ) integration sites toward centromeres, dampening the resulting proviral expression without affecting the overall efficiency of integration. Our findings underscore the importance of retroviral structural proteins for integration site selection and the avoidance of genomic junkyards.retrovirus | integration | nucleosome | chromatin-binding

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“…LADs are reported to significantly overlap with TADs, chromosome regions displaying preferential local interactions Fraser et al 2015;Kind et al 2015;Jabbari and Bernardi 2017). As TADs are largely invariant between cell types (Rao et al 2014;Dixon et al 2015;Fraser et al 2015), we hypothesized that regions with altered peripheral localization would be delimited to single TADs rather than spanning multiple TADs.…”

Section: Tads Form the Unit Of Gene Repositioningmentioning

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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Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

Cited by 406 publications

References 43 publications

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Structural basis for spumavirus GAG tethering to chromatin

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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