A Role for the Nucleoporin Nup170p in Chromatin Structure and Gene Silencing

Vosse, David W. Van de; Wan, Yakun; Lapetina, Diego L.; Chen, Wei Ming; Chiang, Jung-Hsien; Aitchison, John D.; Wozniak, Richard W.

doi:10.1016/j.cell.2013.01.049

Cited by 134 publications

(185 citation statements)

References 86 publications

(84 reference statements)

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“…Several other studies have shown an association of NPCs with silenced genomic regions and chromatin boundary. Data from yeast and Drosophila revealed heterochromatin association with stable Nups, such as Nup100 or Nup84 (Galy et al, 2000;Ruben et al, 2011;Van de Vosse et al, 2013). In human HeLa cells, ChIP analysis of Nup93 also demonstrated that Nup93 interactions include silent gene regions marked by repressive histone modifications (Brown et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Fišerová

Efenberková

Sieger

et al. 2017

Journal of Cell Science

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The nuclear periphery (NP) plays a substantial role in chromatin organization. Heterochromatin at the NP is interspersed with active chromatin surrounding nuclear pore complexes (NPCs); however, details of the peripheral chromatin organization are missing. To discern the distribution of epigenetic marks at the NP of HeLa nuclei, we used structured illumination microscopy combined with a new MATLAB software tool for automatic NP and NPC detection, measurements of fluorescent intensity and statistical analysis of measured data. Our results show that marks for both active and nonactive chromatin associate differentially with NPCs. The incidence of heterochromatin marks, such as H3K27me2 and H3K9me2, was significantly lower around NPCs. In contrast, the presence of marks of active chromatin such as H3K4me2 was only decreased very slightly around the NPCs or not at all (H3K9Ac). Interestingly, the histone demethylases LSD1 (also known as KDM1A) and KDM2A were enriched within the NPCs, suggesting that there was a chromatinmodifying mechanism at the NPCs. Inhibition of transcription resulted in a larger drop in the distribution of H1, H3K9me2 and H3K23me2, which implies that transcription has a role in the organization of heterochromatin at the NP.

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Section: Introductionmentioning

confidence: 99%

Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Fišerová

Efenberková

Sieger

et al. 2017

Journal of Cell Science

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“…To test for an interaction between RSC and asymmetric nucleosomes, we analyzed the genome-wide nucleosome landscape upon partial RSC depletion ( Van de Vosse et al 2013). We observed that twofold RSC depletion resulted in an overall reduction in nucleosome occupancy at asymmetric positions ( Fig.…”

Section: Asymmetric Nucleosomes Are Sites Of Rsc Actionmentioning

confidence: 99%

“…For analysis of nucleosome positions following RSC depletion, we used published single-end nucleosome positioning data, in which the STH1 promoter was replaced by the MET3 promoter, allowing for twofold repression by a 2-h methionine treatment (Van de Vosse et al 2013; SRA accession number SRP011944). Reads from control and Sth1 depletion experiments were extended to 150 bp and smoothed with a kernel density function using a Gaussian kernel and a bandwidth of 20.…”

Section: Rsc Depletion Datamentioning

confidence: 99%

Asymmetric nucleosomes flank promoters in the budding yeast genome

2014

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Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequencebased profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.[Supplemental material is available for this article.]Nucleosomes, the fundamental units of chromatin, are dynamic structures characterized by spontaneous conformational fluctuations that lead to reversible loss of histone-DNA and histone-histone contacts. Every nucleosome in the genome has to disassemble at least once during the cell cycle to allow for passage of the DNA replication machinery (Annunziato 2005), and nucleosomes at active regions might turn over several times during each cell cycle (Dion et al. 2007;Deal et al. 2010). Intrinsic to nucleosome dynamics is the formation of nucleosomal intermediates with alternative structures. However, the nature of such intermediate nucleosome structures formed in vivo is not known.Intermediate nucleosome structures can potentially be identified in vivo using base-pair resolution methods that interrogate histone-DNA contacts genome-wide. The traditional method for high-resolution mapping of nucleosomes is to use micrococcal nuclease (MNase) digestion, which digests away linker regions between nucleosomes (Reeves and Jones 1976). Subjecting MNase-digested DNA fragments to paired-end sequencing (MNase-seq) results in a high-resolution map of nucleosome positions (Hughes and Rando 2014). An alternative method for mapping nucleosomes is H4S47C-anchored cleavage mapping (Brogaard et al. 2012b), which has been used to determine the precise position of nucleosomes in yeast genomes (Brogaard et al. 2012a;Moyle-Heyrman et al. 2013). In this method, histone H4 mutant S47C is derivatized ex vivo with a phenanthroline ligand, converting H4 into a site-specific DNA cleavage agent. Using a modified library preparation and a structural model for H4S47C-anchored cleavage, we extended this method to determine the precise position and orientation of half-nucleosomes (hemisomes) at centromeres (Henikoff et al. 2014), thus showing that alternative nucle...

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“…The dynamics of discrete chromosomal loci depend on their chromosomal and nuclear position, for which the nuclear envelope appears to play a crucial role. More specifically, the 32 chromosome ends of a haploid S. cerevisiae genome are tethered to the nuclear envelope through redundant pathways that involve Esc1, Mps3, Csm4, the silencing informatory regulator (Sir) proteins and the nuclear pore complex (NPC) (Bupp et al, 2007;Feuerbach et al, 2002;Galy et al, 2000;Hediger et al, 2002;Hiraga et al, 2008;Taddei et al, 2004;Therizols et al, 2006;Van de Vosse et al, 2013). As a result of their attachment to the nuclear envelope, subtelomere movements occur within a relatively confined environment (Heun et al, 2001;Therizols et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Evidence for actin dual role in regulating chromosome organization and dynamics in yeast

Spichal

Brion

Herbert

et al. 2016

Journal of Cell Science

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Eukaryotic chromosomes undergo movements that are involved in the regulation of functional processes such as DNA repair. To better understand the origin of these movements, we used fluorescence microscopy, image analysis and chromosome conformation capture to quantify the actin contribution to chromosome movements and interactions in budding yeast. We show that both the cytoskeletal and nuclear actin drive local chromosome movements, independently of Csm4, a putative LINC protein. Inhibition of actin polymerization reduces subtelomere dynamics, resulting in more confined territories and enrichment in subtelomeric contacts. Artificial tethering of actin to nuclear pores increased both nuclear pore complex (NPC) and subtelomere motion. Chromosome loci that were positioned away from telomeres exhibited reduced motion in the presence of an actin polymerization inhibitor but were unaffected by the lack of Csm4. We further show that actin was required for locus mobility that was induced by targeting the chromatin-remodeling protein Ino80. Correlated with this, DNA repair by homologous recombination was less efficient. Overall, interphase chromosome dynamics are modulated by the additive effects of cytoskeletal actin through forces mediated by the nuclear envelope and nuclear actin, probably through the function of actin in chromatin-remodeling complexes.

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A Role for the Nucleoporin Nup170p in Chromatin Structure and Gene Silencing

Cited by 134 publications

References 86 publications

Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Asymmetric nucleosomes flank promoters in the budding yeast genome

Evidence for actin dual role in regulating chromosome organization and dynamics in yeast

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