scholarly journals Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations

2018 ◽  
Author(s):  
Henrike Johanna Gothe ◽  
Britta Annika Maria Bouwman ◽  
Eduardo Gade Gusmao ◽  
Rossana Piccinno ◽  
Sergi Sayols ◽  
...  
Keyword(s):  
Hot Spots ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Transcriptional Elongation ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Physiological Relevance ◽  
Topoisomerase 2 ◽  
Active Transcription ◽  
Transcriptional Output

How spatial chromosome organization influences genome integrity is still poorly understood. Here we show that DNA double-strand breaks (DSBs) mediated by topoisomerase 2 (TOP2) activities, are enriched at chromatin loop anchors with high transcriptional activity. Recurrent DSBs occur at CTCF/cohesin bound sites at the bases of chromatin loops and their frequency positively correlates with transcriptional output and directionality. The physiological relevance of this preferential positioning is indicated by the finding that genes recurrently translocating to drive leukemias, are highly transcribed and are enriched at loop anchors. These genes accumulate DSBs at recurrent hot spots that give rise to chromosomal fusions relying on the activity of both TOP2 isoforms and on transcriptional elongation. We propose that transcription and 3D chromosome folding jointly pose a threat to genomic stability, and are key contributors to the occurrence of genome rearrangements that drive cancer.

scholarly journals Transcription-associated topoisomerase 2α activity is a major effector of cytotoxicity induced by G-quadruplex ligands

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Madeleine Bossaert ◽  
Angélique Pipier ◽  
Jean-Francois Riou ◽  
Céline Noirot ◽  
Linh-Trang Nguyễn ◽  
...  
Keyword(s):  
Small Molecules ◽  
Double Strand Breaks ◽  
Transcriptional Elongation ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Dna Structures ◽  
Topoisomerase 1 ◽  
G Quadruplex ◽  
Topoisomerase 2 ◽  
Topoisomerase 2 Alpha

G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2-alpha (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology. We show that both TOP2 activity and transcription account for DNA break production following G4 ligand treatments. In contrast, clastogenic activity of these G4 ligands is countered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promoting transcriptional elongation. Altogether our results support that clastogenic G4 ligands act as DNA structure-driven TOP2-poisons at transcribed regions bearing G4 structures.

scholarly journals Hot spots of DNA double-strand breaks in human rDNA units are produced in vivo

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Nickolai A. Tchurikov ◽  
Dmitry V. Yudkin ◽  
Maria A. Gorbacheva ◽  
Anastasia I. Kulemzina ◽  
Irina V. Grischenko ◽  
...  
Keyword(s):  
Hot Spots ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Strand Breaks

scholarly journals Endogenous Hot Spots ofDe NovoTelomere Addition in the Yeast Genome Contain Proximal Enhancers That Bind Cdc13

2016 ◽  
Vol 36 (12) ◽  
pp. 1750-1763 ◽  
Author(s):  
Udochukwu C. Obodo ◽  
Esther A. Epum ◽  
Margaret H. Platts ◽  
Jacob Seloff ◽  
Nicole A. Dahlson ◽  
...  
Keyword(s):  
Hot Spots ◽  
High Frequency ◽  
Genome Stability ◽  
De Novo ◽  
Dna Binding Protein ◽  
Double Strand Breaks ◽  
Yeast Genome ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Mutagenic Process

DNA double-strand breaks (DSBs) pose a threat to genome stability and are repaired through multiple mechanisms. Rarely, telomerase, the enzyme that maintains telomeres, acts upon a DSB in a mutagenic process termed telomere healing. The probability of telomere addition is increased at specific genomic sequences termed sites of repair-associated telomere addition (SiRTAs). By monitoring repair of an induced DSB, we show that SiRTAs on chromosomes V and IX share a bipartite structure in which a core sequence (Core) is directly targeted by telomerase, while a proximal sequence (Stim) enhances the probability ofde novotelomere formation. The Stim and Core sequences are sufficient to confer a high frequency of telomere addition to an ectopic site. Cdc13, a single-stranded DNA binding protein that recruits telomerase to endogenous telomeres, is known to stimulatede novotelomere addition when artificially recruited to an induced DSB. Here we show that the ability of the Stim sequence to enhancede novotelomere addition correlates with its ability to bind Cdc13, indicating that natural sites at which telomere addition occurs at high frequency require binding by Cdc13 to a sequence 20 to 100 bp internal from the site at which telomerase acts to initiatede novotelomere addition.

scholarly journals Distinctive nuclear zone for RAD51-mediated homologous recombinational DNA repair

2021 ◽  
Author(s):  
Yasunori Horikoshi ◽  
Hiroki Shima ◽  
Wataru Kobayashi ◽  
Jiying Sun ◽  
Volker J Schmid ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Nuclear Architecture ◽  
Super Resolution ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Sister Chromatids ◽  
Super Resolution Microscopy ◽  
Damaged Dna

Genome-based functions are inseparable from the dynamic higher-order architecture of the cell nucleus. In this context, the repair of DNA damage is coordinated by precise spatiotemporal controls that target and regulate the repair machinery required to maintain genome integrity. However, the mechanisms that pair damaged DNA with intact template for repair by homologous recombination (HR) without illegitimate recombination remain unclear. This report highlights the intimate relationship between nuclear architecture and HR in mammalian cells. RAD51, the key recombinase of HR, forms spherical foci in S/G2 phases spontaneously. Using super-resolution microscopy, we show that following induction of DNA double-strand breaks RAD51 foci at damaged sites elongate to bridge between intact and damaged sister chromatids; this assembly occurs within bundle-shaped distinctive nuclear zones, requires interactions of RAD51 with various factors, and precedes ATP-dependent events involved the recombination of intact and damaged DNA. We observed a time-dependent transfer of single-stranded DNA overhangs, generated during HR, into such zones. Our observations suggest that RAD51-mediated homologous pairing during HR takes place within the distinctive nuclear zones to execute appropriate recombination.

scholarly journals Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

2020 ◽  
Author(s):  
Coline Arnould ◽  
Vincent Rocher ◽  
Thomas Clouaire ◽  
Pierre Caron ◽  
Philippe. E. Mangeot ◽  
...  
Keyword(s):  
Chromatin Modification ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Dna Double Strand Breaks ◽  
Chromatin Domains ◽  
Chromosome Conformation ◽  
Strand Breaks ◽  
3D Genome ◽  
Damage Response ◽  
Transcription And Replication

DNA Double-Strand Breaks (DSBs) repair is essential to safeguard genome integrity. Upon DSBs, the ATM PI3K kinase rapidly triggers the establishment of megabase-sized, γH2AX-decorated chromatin domains which further act as seeds for the formation of DNA Damage Response (DDR) foci1. How these foci are rapidly assembled in order to establish a “repair-prone” environment within the nucleus is yet unclear. Topologically Associating Domains (TADs) are a key feature of 3D genome organization that regulate transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we found that TADs are functional units of the DDR, instrumental for the correct establishment of γH2AX/53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model whereby H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the critical impact of chromosome conformation in the maintenance of genome integrity and provides the first example of a chromatin modification established by loop extrusion.

scholarly journals Control of meiotic double-strand-break formation by ATM: local and global views

2017 ◽  
Author(s):  
Agnieszka Lukaszewicz ◽  
Julian Lange ◽  
Scott Keeney ◽  
Maria Jasin
Keyword(s):  
Strand Break ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Future Research ◽  
Dna Double Strand Breaks ◽  
Time Loss ◽  
Strand Breaks ◽  
Research Perspectives ◽  
The Right ◽  
Break Formation

ABSTRACTDNA double-strand breaks (DSBs) generated by the SPO11 protein initiate meiotic recombination, an essential process for successful chromosome segregation during gametogenesis. The activity of SPO11 is controlled by multiple factors and regulatory mechanisms, such that the number of DSBs is limited and DSBs form at distinct positions in the genome and at the right time. Loss of this control can affect genome integrity or cause meiotic arrest by mechanisms that are not fully understood. Here we focus on the DSB-responsive kinase ATM and its functions in regulating meiotic DSB numbers and distribution. We review the recently discovered roles of ATM in this context, discuss their evolutionary conservation, and examine future research perspectives.

scholarly journals RSC Mobilizes Nucleosomes To Improve Accessibility of Repair Machinery to the Damaged Chromatin

2006 ◽  
Vol 27 (5) ◽  
pp. 1602-1613 ◽  
Author(s):  
Eun Yong Shim ◽  
Soo Jin Hong ◽  
Ji-Hyun Oum ◽  
Yvonne Yanez ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Dna Double Strand Breaks ◽  
Base Pairs ◽  
Dsb Repair ◽  
Strand Breaks ◽  
Free Dna ◽  
Key Questions

ABSTRACT Repair of DNA double-strand breaks (DSBs) protects cells and organisms, as well as their genome integrity. Since DSB repair occurs in the context of chromatin, chromatin must be modified to prevent it from inhibiting DSB repair. Evidence supports the role of histone modifications and ATP-dependent chromatin remodeling in repair and signaling of chromosome DSBs. The key questions are, then, what the nature of chromatin altered by DSBs is and how remodeling of chromatin facilitates DSB repair. Here we report a chromatin alteration caused by a single HO endonuclease-generated DSB at the Saccharomyces cerevisiae MAT locus. The break induces rapid nucleosome migration to form histone-free DNA of a few hundred base pairs immediately adjacent to the break. The DSB-induced nucleosome repositioning appears independent of end processing, since it still occurs when the 5′-to-3′ degradation of the DNA end is markedly reduced. The tetracycline-controlled depletion of Sth1, the ATPase of RSC, or deletion of RSC2 severely reduces chromatin remodeling and loading of Mre11 and Yku proteins at the DSB. Depletion of Sth1 also reduces phosphorylation of H2A, processing, and joining of DSBs. We propose that RSC-mediated chromatin remodeling at the DSB prepares chromatin to allow repair machinery to access the break and is vital for efficient DSB repair.

scholarly journals Genome integrity and neurogenesis of postnatal hippocampal neural stem/progenitor cells require a unique regulator Filia

2020 ◽  
Vol 6 (44) ◽  
pp. eaba0682 ◽  
Author(s):  
Jingzheng Li ◽  
Yafang Shang ◽  
Lin Wang ◽  
Bo Zhao ◽  
Chunli Sun ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Neurodevelopmental Disorders ◽  
Double Strand Breaks ◽  
Genome Integrity ◽  
Replication Forks ◽  
Proof Of Concept ◽  
Dna Double Strand Breaks ◽  
Dsb Repair ◽  
Strand Breaks ◽  
Neural Stem Progenitor Cells

Endogenous DNA double-strand breaks (DSBs) formation and repair in neural stem/progenitor cells (NSPCs) play fundamental roles in neurogenesis and neurodevelopmental disorders. NSPCs exhibit heterogeneity in terms of lineage fates and neurogenesis activity. Whether NSPCs also have heterogeneous regulations on DSB formation and repair to accommodate region-specific neurogenesis has not been explored. Here, we identified a regional regulator Filia, which is predominantly expressed in mouse hippocampal NSPCs after birth and regulates DNA DSB formation and repair. On one hand, Filia protects stalling replication forks and prevents the replication stress-associated DNA DSB formation. On the other hand, Filia facilitates the homologous recombination–mediated DNA DSB repair. Consequently, Filia−/− mice had impaired hippocampal NSPC proliferation and neurogenesis and were deficient in learning, memory, and mood regulations. Thus, our study provided the first proof of concept demonstrating the region-specific regulations of DSB formation and repair in subtypes of NSPCs.

scholarly journals Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks

2012 ◽  
Vol 197 (2) ◽  
pp. 189-199 ◽  
Author(s):  
Maria Poulsen ◽  
Claudia Lukas ◽  
Jiri Lukas ◽  
Simon Bekker-Jensen ◽  
Niels Mailand
Keyword(s):  
Deoxyribonucleic Acid ◽  
Double Strand Breaks ◽  
Negative Regulator ◽  
Nonhomologous End Joining ◽  
Genome Integrity ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Dsb Repair ◽  
Strand Breaks ◽  
Protein Recruitment

Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid double-strand breaks (DSBs), mediated by the RNF8/RNF168 ubiquitin ligases, plays a key role in recruiting repair factors, including 53BP1 and BRCA1, to reestablish genome integrity. In this paper, we show that human RNF169, an uncharacterized E3 ubiquitin ligase paralogous to RNF168, accumulated in DSB repair foci through recognition of RNF168-catalyzed ubiquitylation products by its motif interacting with ubiquitin domain. Unexpectedly, RNF169 was dispensable for chromatin ubiquitylation and ubiquitin-dependent accumulation of repair factors at DSB sites. Instead, RNF169 functionally competed with 53BP1 and RAP80–BRCA1 for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of their recruitment to DSB sites. By delaying accumulation of 53BP1 and RAP80 at damaged chromatin, RNF169 stimulated homologous recombination and restrained nonhomologous end joining, affecting cell survival after DSB infliction. Our results show that RNF169 functions in a noncanonical fashion to harness RNF168-mediated protein recruitment to DSB-containing chromatin, thereby contributing to regulation of DSB repair pathway utilization.

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