The nuclear pore primes recombination-dependent DNA synthesis at arrested forks by promoting SUMO removal

Kramarz, Karol; Schirmeisen, Kamila; Boucherit, Virginie; Saada, Anissia Ait; Lovo, Claire; Palancade, Benoı̂t; Freudenreich, Catherine H.; Lambert, Sarah

doi:10.1038/s41467-020-19516-z

Cited by 49 publications

(82 citation statements)

References 67 publications

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“…We note that this mechanism contrasts with recent studies showing that nuclear pore localisation enhances DNA repair (100) and suppresses R-loops (101). Indeed, it is clear that more than one mutational pathway acts even at CUP1; we focus here on adaptive CUP1 amplification and find this to be Rad51- and Sic1-dependent, but maladaptive CUP1 contractions assayed in our screen and another recent study (102) are Rad51-independent, Rad59-dependent and suppressed by Sic1.…”

Section: Discussioncontrasting

confidence: 99%

Stimulation of adaptive gene amplification by origin firing under replication fork constraint

Aj¹,

King²,

Rm³

et al. 2021

Preprint

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Adaptive mutations can cause drug resistance in cancers and pathogens, and increase the tolerance of agricultural pests and diseases to chemical treatment. When and how adaptive mutations form is often hard to discern, but we have shown that adaptive copy number amplification of the copper resistance gene CUP1 occurs in response to environmental copper due to CUP1 transcriptional activation. Here we dissect the mechanism by which CUP1 transcription in budding yeast stimulates copy number variation (CNV). We show that transcriptionally stimulated CNV requires TREX-2 and Mediator, such that cells lacking TREX-2 or Mediator respond normally to copper but cannot acquire increased resistance. Mediator and TREX-2 cause replication stress by tethering transcribed loci to nuclear pores, a process known as gene gating, and transcription at the CUP1 locus causes a TREX-2-dependent accumulation of replication forks indicative of replication fork stalling. TREX-2-dependent CUP1 gene amplification occurs by a Rad52 and Rad51-mediated homologous recombination mechanism that is enhanced by histone H3K56 acetylation and repressed by Pol32, factors known to alter the frequency of template switching during break induced replication (BIR). CUP1 amplification is also critically dependent on late firing replication origins present in the CUP1 repeats, and mutations that remove or inactivate these origins strongly suppress the acquisition of copper resistance. We propose that replicative stress imposed by nuclear pore association causes replication bubbles from these origins to collapse soon after firing, leaving an epigenetic scar of H3K56 acetylation that promotes template switching during later break induced replication events. The capacity for inefficient replication origins to promote copy number variation renders certain genomic regions more fragile than others, and therefore more likely to undergo adaptive evolution through de novo gene amplification.

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Section: Discussioncontrasting

confidence: 99%

Stimulation of adaptive gene amplification by origin firing under replication fork constraint

Aj¹,

King²,

Rm³

et al. 2021

Preprint

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“…As discussed previously, live imaging demonstrated movement of stressed replication loci towards the nuclear periphery, consistent with putative interaction of replication stressed chromatin and NPCs [20]. Genomic replication stress originating from aphidicolin or hydroxyurea [20,45], structure-forming DNA sequences [51], or site-specific, protein-mediated replication fork collapse [52]; all localized to the inner nuclear edge. In agreement, yeast Nup1 is essential for relocation of multiple types of stalled forks to the nuclear periphery [53].…”

Section: Npcs and Dna Repairsupporting

confidence: 75%

Chromatin mobility and relocation in DNA repair

Lamm

Rogers

Cesare

2021

Trends in Cell Biology

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The nucleus is a dynamic environment containing chromatin, membraneless organelles, and specialized molecular structures at the nuclear membrane. Within the spectrum of DNA repair activities are observations of increased mobility of damaged chromatin and the displacement of DNA lesions to specific nuclear environments. Here, we focus on the role that nuclear-specific filamentous actin plays in mobilizing damaged chromatin in response to DNA double-strand breaks and replication stress. We also examine nuclear pore complexes and promyelocytic leukemia-nuclear bodies as specialized platforms for homology-directed repair. The literature suggests an emerging model where specific types of DNA lesions are subjected to nuclear-derived forces that mobilize damaged chromatin and promote interaction with repair hubs to facilitate specialized repair reactions. Nuclear dynamics in genome stabilityThe nucleus is now appreciated as a dynamic entity subjected to regulated physical alteration in response to cellular stress. A core nuclear function is to maintain genome integrity by facilitating repair of the genetic material when the need arises. Recent advances have illuminated added levels of regulation in DNA repair processes. Namely, the discovery of nuclear-specific cytoskeleton forces that potentiate movement of damaged chromatin and the directed displacement of DNA lesions to nuclear structures that function as hubs of specialized repair reactions. While there is a growing appreciation for chromatin mobility in DNA repair, the cellular mechanisms that dictate when, how, and which types of genomic lesions are mobilized, and which repair processes ensue thereafter, are continuing to be elucidated.

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“…Distinct functions for monomeric and polymeric SUMO modification are particularly important in regulating the association of proteins with chromatin. SUMO proteases in yeast and human cells, for example, have a specialized role in facilitating DNA replication initiation, replication stress responses and other chromatin-associated functions by limiting untimely production of polymeric SUMO chains (Psakhye et al, 2019;Wagner et al, 2019;Kramarz et al, 2020).…”

Section: Molecular Features Defining Sumo1 and Sumo2 Non-redundant Functionsmentioning

confidence: 99%

SUMO paralogue–specific functions revealed through systematic analysis of human knockout cell lines and gene expression data

Bouchard

Wang

Yang

et al. 2021

MBoC

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The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogs with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogs, and also the best studied. To what extent SUMO1, SUMO2 and the other paralogs impart unique and non-redundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogs during development and studies in cell culture have relied largely on transient paralog overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralog gene expression levels in normal human tissues and found unique patterns of SUMO1-3 expression across 30 tissue types, suggesting paralog-specific functions in adult human tissues. To systematically identify and characterize unique and non-redundant functions of the SUMO paralogs in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, PML nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal non-redundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.

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The nuclear pore primes recombination-dependent DNA synthesis at arrested forks by promoting SUMO removal

Cited by 49 publications

References 67 publications

Stimulation of adaptive gene amplification by origin firing under replication fork constraint

Stimulation of adaptive gene amplification by origin firing under replication fork constraint

Chromatin mobility and relocation in DNA repair

SUMO paralogue–specific functions revealed through systematic analysis of human knockout cell lines and gene expression data

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