scholarly journals Transcription-associated events affecting genomic integrity

2017 ◽  
Vol 372 (1731) ◽  
pp. 20160288 ◽  
Author(s):  
Robin Sebastian ◽  
Philipp Oberdoerffer

Accurate maintenance of genomic as well as epigenomic integrity is critical for proper cell and organ function. Continuous exposure to DNA damage is, thus, often associated with malignant transformation and degenerative diseases. A significant, chronic threat to genome integrity lies in the process of transcription, which can result in the formation of potentially harmful RNA : DNA hybrid structures (R-loops) and has been linked to DNA damage accumulation as well as dynamic chromatin reorganization. In sharp contrast, recent evidence suggests that active transcription, the resulting transcripts as well as R-loop formation can play multi-faceted roles in maintaining and restoring genome integrity. Here, we will discuss the emerging contributions of transcription as both a source of DNA damage and a mediator of DNA repair. We propose that both aspects have significant implications for genome maintenance, and will speculate on possible long-term consequences for the epigenetic integrity of transcribing cells. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.

2021 ◽  
Vol 22 (19) ◽  
pp. 10384
Author(s):  
Hirotomo Takatsuka ◽  
Atsushi Shibata ◽  
Masaaki Umeda

Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 606-606
Author(s):  
Ji Hye Park ◽  
Robert S Welner ◽  
Daniel G. Tenen ◽  
Catherine T. Yan

Abstract Blood cells of all lineages are generated from small pools of long-term hematopoietic stem cells (LT-HSCs) that continually replenish throughout life. LT-HSCs regulate the balanced turnover of all mature blood lineages by switching between self-renewal, differentiation and quiescence, thereby maintaining hematopoietic homeostasis in steady state and in response to injury. In any given cell, some DNA damage may remain despite the action of DNA repair processes, including in LT-HSCs. Over time, HSCs lose their long-term capability to self-renew due to misrepair of DNA breaks and increased accumulation of DNA damage, resulting in loss of regenerative plasticity and immune fitness. The accrual of DNA damage is the principal factor that contributes to functional decline in HSC renewal and in the immune system during ageing. In recent studies, the capacity of aging HSCs to self-renew is shown to be dependent on DNA repair pathways, with non-homologous end-joining (NHEJ) as the principle pathway implicated in DNA repair in quiescent HSCs from ex-vivo cell-based assays. Although NHEJ in particular has been implicated in this process in LT-HSCs, there has so far been very little evidence of this activity in vivo. DNA Ligase IV (Lig4), which catalyzes the end-ligation of broken DNA ends mediated by NHEJ, has no known functions outside of NHEJ. Because a deficiency in Lig4 in mice is embryonic lethal, here we assessed the role of Lig4 in HSC homeostasis by assaying HSC functions in a knockin mouse model of a hypomorphic homozygous R278H mutation in Lig4 that had been identified in the first DNA Lig4 Syndrome patient. The R278H mutation significantly impairs the end-ligation function of the Lig4 protein, and mice homozygous for the R278H mutation (Lig4R/R) showed diminished DSB repair capacity and age-dependent lymphopenia that implicated potential HSC defects. Consistent with a defect in NHEJ, we show the Lig4 R278H mutation severely limited HSC self-renewal. Lig4R/R HSC reconstitutions were skewed towards the myeloid lineage and resulted in severely reduced chimerism, confirming the capacity of HSCs to self-renew requires functional DNA repair. Next, we examined if there is increased DNA damage with/without ionizing irradiation (IR). Lig4R/R LT-HSCs showed an increase in reactive oxygen species (ROS), abnormal cycling and increased apoptosis from accumulated DNA damage in steady state and slow DNA double strand breaks (DSBs) repair kinetics in response to low dose IR because of improper Lig4 function. This led us to check the LT-HSC pool more carefully. It has been shown that the HSC pool is intact and phenotypically increased with age. Strikingly, we found that the HSCs in both young and old Lig4R/R mice are markedly reduced to 20% of wild-type levels. The severe LT-HSC reduction and lethality of disease in Lig4R/Rmice was completely rescued by transplantation with wild type bone marrow. These evidences support the notion of a critical role for Lig4 in maintenance of the LT-HSC pool. In a recent study, it was reported that the steady state pool of murine adult LT-HSCs can be further distinguished into quiescent (~20%) and variably cycling (~80%) populations. Since LT-HSCs in young Lig4R/R mice are maintained in steady state at 20% of WT HSCs, we hypothesized that the reduced pool of LT-HSCs in the Lig4R/R mice is caused by the loss of cycling LT-HSCs that continually replenish blood lineages during aging. To compare these populations, microarray analysis was done on the pool of WT and Lig4R/R LT-HSCs, versus sorted populations of quiescent and variably cycling LT-HSCs. Microarray analysis clearly showed that the Lig4R/RLT-HSCs correlated with the quiescent LT-HSCs, indicating NHEJ regulates the homeostasis of the faster cycling LT-HSC pool. Our study suggest that the slowest cycling LT-HSCs serve to replenish the overall LT-HSC pool and HSC homeostasis is maintained by capacity of faster cycling LT-HSC pool to revert to quiescence in response to stress/injury. Additionally, defective NHEJ depletes the faster cycling LT-HSC pool and underlies early HSC exhaustion in Lig4R/R mice. Our findings demonstrate for the first time a physiological role for Lig4 in the maintenance of HSC homeostasis. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Author(s):  
Matías Capella ◽  
Imke K. Mandemaker ◽  
Lucía Martín Caballero ◽  
Boris Pfander ◽  
Andreas G. Ladurner ◽  
...  

AbstractRibosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to active transcription and their repetitive nature. Compartmentalization of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be released to the nucleoplasm to allow repair by homologous recombination. The process of rDNA relocation is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP component Nur1, releasing nuclear membrane-tethered rDNA repeats from the nucleolus in Saccharomyces cerevisiae. Cooperating with Nur1 phosphorylation, SUMOylation targets the rDNA tethering complex for disassembly mediated by the segregase Cdc48/p97, which recognizes SUMOylated CLIP-cohibin through its cofactor, Ufd1. Consistent with the conservation of this mechanism, UFD1L depletion impairs rDNA release in human cells. The dynamic and regulated assembly and disassembly of the CLIP-cohibin complex is therefore a key, conserved determinant of nucleolar rDNA release and genome integrity.


Cancers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1793 ◽  
Author(s):  
Susanna Ambrosio ◽  
Barbara Majello

In recent years, a considerable correlation has emerged between autophagy and genome integrity. A range of mechanisms appear to be involved where autophagy participates in preventing genomic instability, as well as in DNA damage response and cell fate decision. These initial findings have attracted particular attention in the context of malignancy; however, the crosstalk between autophagy and DNA damage response is just beginning to be explored and key questions remain that need to be addressed, to move this area of research forward and illuminate the overall consequence of targeting this process in human therapies. Here we present current knowledge on the complex crosstalk between autophagy and genome integrity and discuss its implications for cancer cell survival and response to therapy.


2021 ◽  
Vol 23 (1) ◽  
pp. 96
Author(s):  
Ahmed Sidali ◽  
Varsha Teotia ◽  
Nadeen Shaikh Solaiman ◽  
Nahida Bashir ◽  
Radhakrishnan Kanagaraj ◽  
...  

Genome integrity must be tightly preserved to ensure cellular survival and to deter the genesis of disease. Endogenous and exogenous stressors that impose threats to genomic stability through DNA damage are counteracted by a tightly regulated DNA damage response (DDR). RNA binding proteins (RBPs) are emerging as regulators and mediators of diverse biological processes. Specifically, RBPs that bind to adenine uridine (AU)-rich elements (AREs) in the 3′ untranslated region (UTR) of mRNAs (AU-RBPs) have emerged as key players in regulating the DDR and preserving genome integrity. Here we review eight established AU-RBPs (AUF1, HuR, KHSRP, TIA-1, TIAR, ZFP36, ZFP36L1, ZFP36L2) and their ability to maintain genome integrity through various interactions. We have reviewed canonical roles of AU-RBPs in regulating the fate of mRNA transcripts encoding DDR genes at multiple post-transcriptional levels. We have also attempted to shed light on non-canonical roles of AU-RBPs exploring their post-translational modifications (PTMs) and sub-cellular localization in response to genotoxic stresses by various factors involved in DDR and genome maintenance. Dysfunctional AU-RBPs have been increasingly found to be associated with many human cancers. Further understanding of the roles of AU-RBPS in maintaining genomic integrity may uncover novel therapeutic strategies for cancer.


2019 ◽  
Vol 476 (24) ◽  
pp. 3791-3804 ◽  
Author(s):  
Steven Cupello ◽  
Yunfeng Lin ◽  
Shan Yan

Oxidative DNA damage represents one of the most abundant DNA lesions. It remains unclear how DNA repair and DNA damage response (DDR) pathways are co-ordinated and regulated following oxidative stress. While XRCC1 has been implicated in DNA repair, it remains unknown how exactly oxidative DNA damage is repaired and sensed by XRCC1. In this communication, we have demonstrated evidence that XRCC1 is dispensable for ATR-Chk1 DDR pathway following oxidative stress in Xenopus egg extracts. Whereas APE2 is essential for SSB repair, XRCC1 is not required for the repair of defined SSB and gapped plasmids with a 5′-OH or 5′-P terminus, suggesting that XRCC1 and APE2 may contribute to SSB repair via different mechanisms. Neither Polymerase beta nor Polymerase alpha is important for the repair of defined SSB structure. Nonetheless, XRCC1 is important for the repair of DNA damage following oxidative stress. Our observations suggest distinct roles of XRCC1 for genome integrity in oxidative stress in Xenopus egg extracts.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1041-1041
Author(s):  
Fengshan Liang ◽  
Simonne Longerich ◽  
Caroline Tang ◽  
Olga Buzovestsky ◽  
Yong Xiong ◽  
...  

Abstract Background: Fanconi anemia (FA), a cancer-prone genetic disease, is caused by defects in the FA-DNA repair pathway. In response to DNA interstrand crosslink (ICL)-induced DNA damage, FANCI-FANCD2 mono-ubiquitination licenses the execution of downstream DNA damage signaling and repair steps, including repair by homologous recombination (HR) that utilizes the recombinase RAD51 and its cohort of accessory factors. Timely deubiquitination of FANCD2 by the UAF1-USP1 deubiquitinating enzyme complex is also critically important for the FA pathway. As such, UAF1 depletion results in persistent FANCD2 ubiquitination and DNA damage hypersensitivity. UAF1 deficient cells are also impaired for DNA repair by homologous recombination. UAF1 physically associates with RAD51AP1, a protein that enhances the activity of the RAD51 recombinase. It remains to be defined how UAF1 regulates homologous recombination and genome stability. Methods: Highly purified proteins were used to define the DNA binding activity and protein interaction of UAF1. In vitroD-loop formation reaction and synaptic complex assembly assay were used to discover the function of UAF1 in RAD51 recombinase enhancement. HeLa and U2OS-DR-GFP cell lines with impaired UAF1-RAD51AP1 interaction or UAF1 DNA binding were generated to examine DNA-damage agent sensitivity and HR efficiency. Results: (1) UAF1 possesses a DNA binding activity capable of engaging ssDNA, dsDNA and has a preference for the D-loop DNA substrate. We further identified that the N-terminus but not C-terminal SLD domain of UAF1 binds DNA. (2) UAF1 forms a dimeric complex with RAD51AP1. Our results also revealed a trimeric complex of RAD51-RAD51AP1-UAF1, with RAD51AP1 providing a tethering function between the other two proteins. (3) The RAD51AP1-UAF1 interaction interface was defined showing a novel SIM motif in the middle portion of RAD51AP1and the SLD1-SLD2 domain of UAF1 mediate protein complex formation. Based on the domain mapping results, point mutants of RAD51AP1 and UAF1 that are specifically compromised for the formation of the RAD51AP1-UAF1 complex were generated. (4) UAF1 synergizes with RAD51AP1 in the RAD51-mediated D-loop reaction and that this functional synergy requires the RAD51AP1-UAF1 complex and also the DNA and RAD51 binding attributes of RAD51AP1. (5) RAD51AP1-UAF1 works in conjunction with the RAD51 presynaptic filament in the capture of the duplex DNA partner and in the assembly of the synaptic complex. (6) Human cell lines impaired for RAD51AP1-UAF1 complex formation are compromised for the ability to repair DNA damage and to execute HR. (7) DNA repair function of the RAD51AP1-UAF1 complex is likely USP1-independent. Conclusions: The physical interaction between UAF1 and RAD51AP1 is indispensable for functional synergy in vitro and, accordingly, for the biological function of UAF1 in HR and DNA damage repair. Our findings provide insights into a novel USP1-independent regulatory mechanism of UAF1 on homologous recombination-mediated genome maintenance. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 21 (21) ◽  
pp. 8273
Author(s):  
Antje M. Wengner ◽  
Arne Scholz ◽  
Bernard Haendler

Steroid hormone signaling induces vast gene expression programs which necessitate the local formation of transcription factories at regulatory regions and large-scale alterations of the genome architecture to allow communication among distantly related cis-acting regions. This involves major stress at the genomic DNA level. Transcriptionally active regions are generally instable and prone to breakage due to the torsional stress and local depletion of nucleosomes that make DNA more accessible to damaging agents. A dedicated DNA damage response (DDR) is therefore essential to maintain genome integrity at these exposed regions. The DDR is a complex network involving DNA damage sensor proteins, such as the poly(ADP-ribose) polymerase 1 (PARP-1), the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the ataxia–telangiectasia-mutated (ATM) kinase and the ATM and Rad3-related (ATR) kinase, as central regulators. The tight interplay between the DDR and steroid hormone receptors has been unraveled recently. Several DNA repair factors interact with the androgen and estrogen receptors and support their transcriptional functions. Conversely, both receptors directly control the expression of agents involved in the DDR. Impaired DDR is also exploited by tumors to acquire advantageous mutations. Cancer cells often harbor germline or somatic alterations in DDR genes, and their association with disease outcome and treatment response led to intensive efforts towards identifying selective inhibitors targeting the major players in this process. The PARP-1 inhibitors are now approved for ovarian, breast, and prostate cancer with specific genomic alterations. Additional DDR-targeting agents are being evaluated in clinical studies either as single agents or in combination with treatments eliciting DNA damage (e.g., radiation therapy, including targeted radiotherapy, and chemotherapy) or addressing targets involved in maintenance of genome integrity. Recent preclinical and clinical findings made in addressing DNA repair dysfunction in hormone-dependent and -independent prostate and breast tumors are presented. Importantly, the combination of anti-hormonal therapy with DDR inhibition or with radiation has the potential to enhance efficacy but still needs further investigation.


2017 ◽  
Vol 372 (1731) ◽  
pp. 20160289 ◽  
Author(s):  
Ashby J. Morrison

Chromatin modification is conserved in all eukaryotes and is required to facilitate and regulate DNA-templated processes. For example, chromatin manipulation, such as histone post-translational modification and nucleosome positioning, play critical roles in genome stability pathways. The INO80 chromatin-remodelling complex, which regulates the abundance and positioning of nucleosomes, is particularly important for proper execution of inducible responses to DNA damage. This review discusses the participation and activity of the INO80 complex in DNA repair and cell cycle checkpoint pathways, with emphasis on the Saccharomyces cerevisiae model system. Furthermore, the role of ATM/ATR kinases, central regulators of DNA damage signalling, in the regulation of INO80 function will be reviewed. In addition, emerging themes of chromatin remodelling in mitotic stability pathways and chromosome segregation will be introduced. These studies are critical to understanding the dynamic chromatin landscape that is rapidly and reversibly modified to maintain the integrity of the genome. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.


Reproduction ◽  
2015 ◽  
Vol 149 (1) ◽  
pp. 101-111 ◽  
Author(s):  
C Fernández-Díez ◽  
S González-Rojo ◽  
J Montfort ◽  
A Le Cam ◽  
J Bobe ◽  
...  

Zygotic repair of the paternal genome is a key event after fertilization. Spermatozoa accumulate DNA strand breaks during spermatogenesis and can suffer additional damage by different factors, including cryopreservation. Fertilization with DNA-damaged spermatozoa (DDS) is considered to promote implantation failures and abortions, but also long-term effects on the progeny that could be related with a defective repair. Base excision repair (BER) pathway is considered the most active in zygotic DNA repair, but healthy oocytes contain enzymes for all repairing pathways. In this study, the effects of the inhibition of the BER pathway in the zygote were analyzed on the progeny obtained after fertilization with differentially DDS. Massive gene expression (GE; 61 657 unique probes) was analyzed after hatching using microarrays. Trout oocytes are easily fertilized with DDS and the high prolificacy allows live progeny to be obtained even with a high rate of abortions. Nevertheless, the zygotic inhibition of Poly (ADP-ribose) polymerase, upstream of BER pathway, resulted in 810 differentially expressed genes (DEGs) after hatching. DEGs are related with DNA repair, apoptosis, telomere maintenance, or growth and development, revealing a scenario of impaired DNA damage signalization and repair. Downregulation of the apoptotic cascade was noticed, suggesting a selection of embryos tolerant to residual DNA damage during embryo development. Our results reveal changes in the progeny from defective repairing zygotes including higher malformations rate, weight gain, longer telomeres, and lower caspase 3/7 activity, whose long-term consequences should be analyzed in depth.


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