Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination

Neumann, Frank; Dion, Vincent; Gehlen, Lutz R.; Tsai-Pflugfelder, Monika; Schmid, Roger; Taddei, Angela; Gasser, Susan M.

doi:10.1101/gad.176156.111

Cited by 161 publications

(243 citation statements)

References 71 publications

(121 reference statements)

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“…Recent work shows that the targeting of ATP-dependent nucleosome remodelers leads to increased mobility, suggesting that the shifting or removal of nucleosomes changes the flexibility of the chromatin fiber and, in turn, its mobility (Gehlen et al 2006;Neumann et al 2012). This is consistent with the notion that a chromosome can be modeled as a flexible polymer chain subject to random forces and tethering effects (Klenin et al 1998;Gehlen et al 2006;Rosa and Everaers 2008;Neumann et al 2012).…”

Section: Chromatin Dynamicssupporting

confidence: 73%

“…Indeed, telomeres, centromeres, and silent chromatin, which are tethered through protein-protein interactions at the NE, move within smaller radii of constraint than coding and noncoding regions along the longer chromosome arms (telomeric Rc , 0.4 vs. 0.6 mm for active loci) (Hediger et al 2002;Gartenberg et al 2004;Cabal et al 2006;Dion et al 2012;Neumann et al 2012). Recent work shows that the targeting of ATP-dependent nucleosome remodelers leads to increased mobility, suggesting that the shifting or removal of nucleosomes changes the flexibility of the chromatin fiber and, in turn, its mobility (Gehlen et al 2006;Neumann et al 2012). This is consistent with the notion that a chromosome can be modeled as a flexible polymer chain subject to random forces and tethering effects (Klenin et al 1998;Gehlen et al 2006;Rosa and Everaers 2008;Neumann et al 2012).…”

Section: Chromatin Dynamicsmentioning

confidence: 99%

“…The movement of chromatin is ATPdependent and varies between G1-and S-phase cells, yet can be quite accurately quantified by a mean squared displacement analysis as a constrained random walk (Figure 3). Not unexpectedly, different loci move within domains of different size within the nucleus, which are defined as radii of constraint (Rc) (Marshall et al 1997;Heun et al 2001b;Gasser 2002;Neumann et al 2012). Indeed, telomeres, centromeres, and silent chromatin, which are tethered through protein-protein interactions at the NE, move within smaller radii of constraint than coding and noncoding regions along the longer chromosome arms (telomeric Rc , 0.4 vs. 0.6 mm for active loci) (Hediger et al 2002;Gartenberg et al 2004;Cabal et al 2006;Dion et al 2012;Neumann et al 2012).…”

Section: Chromatin Dynamicsmentioning

confidence: 99%

“…Not unexpectedly, different loci move within domains of different size within the nucleus, which are defined as radii of constraint (Rc) (Marshall et al 1997;Heun et al 2001b;Gasser 2002;Neumann et al 2012). Indeed, telomeres, centromeres, and silent chromatin, which are tethered through protein-protein interactions at the NE, move within smaller radii of constraint than coding and noncoding regions along the longer chromosome arms (telomeric Rc , 0.4 vs. 0.6 mm for active loci) (Hediger et al 2002;Gartenberg et al 2004;Cabal et al 2006;Dion et al 2012;Neumann et al 2012). Recent work shows that the targeting of ATP-dependent nucleosome remodelers leads to increased mobility, suggesting that the shifting or removal of nucleosomes changes the flexibility of the chromatin fiber and, in turn, its mobility (Gehlen et al 2006;Neumann et al 2012).…”

Section: Chromatin Dynamicsmentioning

confidence: 99%

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Structure and Function in the Budding Yeast Nucleus

2012

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Budding yeast, like other eukaryotes, carries its genetic information on chromosomes that are sequestered from other cellular constituents by a double membrane, which forms the nucleus. An elaborate molecular machinery forms large pores that span the double membrane and regulate the traffic of macromolecules into and out of the nucleus. In multicellular eukaryotes, an intermediate filament meshwork formed of lamin proteins bridges from pore to pore and helps the nucleus reform after mitosis. Yeast, however, lacks lamins, and the nuclear envelope is not disrupted during yeast mitosis. The mitotic spindle nucleates from the nucleoplasmic face of the spindle pole body, which is embedded in the nuclear envelope. Surprisingly, the kinetochores remain attached to short microtubules throughout interphase, influencing the position of centromeres in the interphase nucleus, and telomeres are found clustered in foci at the nuclear periphery. In addition to this chromosomal organization, the yeast nucleus is functionally compartmentalized to allow efficient gene expression, repression, RNA processing, genomic replication, and repair. The formation of functional subcompartments is achieved in the nucleus without intranuclear membranes and depends instead on sequence elements, protein-protein interactions, specific anchorage sites at the nuclear envelope or at pores, and long-range contacts between specific chromosomal loci, such as telomeres. Here we review the spatial organization of the budding yeast nucleus, the proteins involved in forming nuclear subcompartments, and evidence suggesting that the spatial organization of the nucleus is important for nuclear function. TABLE OF CONTENTS Abstract 107Introduction 108

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Section: Chromatin Dynamicssupporting

confidence: 73%

Section: Chromatin Dynamicsmentioning

confidence: 99%

Section: Chromatin Dynamicsmentioning

confidence: 99%

Section: Chromatin Dynamicsmentioning

confidence: 99%

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Structure and Function in the Budding Yeast Nucleus

2012

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“…The fourth SUMO residue in the chain retained the full SUMO sequence, including the diglycine motif. Targeted binding is described in Neumann et al (2012) and Horigome et al (2014).…”

Section: Plasmids Yeast Strains and Techniquesmentioning

confidence: 99%

PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL

et al. 2016

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High-resolution imaging shows that persistent DNA damage in budding yeast localizes in distinct perinuclear foci for repair. The signals that trigger DNA double-strand break (DSB) relocation or determine their destination are unknown. We show here that DSB relocation to the nuclear envelope depends on SUMOylation mediated by the E3 ligases Siz2 and Mms21. In G1, a polySUMOylation signal deposited coordinately by Mms21 and Siz2 recruits the SUMO targeted ubiquitin ligase Slx5/Slx8 to persistent breaks. Both Slx5 and Slx8 are necessary for damage relocation to nuclear pores. When targeted to an undamaged locus, however, Slx5 alone can mediate relocation in G1-phase cells, bypassing the requirement for polySUMOylation. In contrast, in S-phase cells, monoSUMOylation mediated by the Rtt107-stabilized SMC5/6-Mms21 E3 complex drives DSBs to the SUN domain protein Mps3 in a manner independent of Slx5. Slx5/Slx8 and binding to pores favor repair by ectopic break-induced replication and imprecise end-joining.

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Scoring and Manipulating Gene Position and Dynamics Using FROS in Budding Yeast

2014

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The spatial organization of the genome within the nucleus is now seen as a key contributor to genome function. Studying chromatin dynamics in living cells has been rendered possible by the development of fast microscopy coupled with fluorescent repressor operator systems (FROS). In these systems, arrays of protein‐binding sites integrated at specific loci by homologous recombination are monitored through the fluorescence of tagged DNA‐binding proteins. In the budding yeast, where homologous recombination is efficient, this technique, combined with targeting assay and genetic analysis, has been extremely powerful for studying the determinants and function of chromatin dynamics in living cells. However, issues have been recurrently raised in different species regarding the use of these systems. Here we discuss the different uses of gene tagging with FROS and their limitations, focusing in budding yeast as a model organism. Curr. Protoc. Cell Biol. 62:22.17.1‐22.17.14. © 2014 by John Wiley & Sons, Inc.

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Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination

Cited by 161 publications

References 71 publications

Structure and Function in the Budding Yeast Nucleus

Structure and Function in the Budding Yeast Nucleus

PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL

Scoring and Manipulating Gene Position and Dynamics Using FROS in Budding Yeast

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