• Colocalization single-molecule imaging
• DNA labeling
• DNA repair
• Fluorescence
• NHEJ
• Non-homologous end joining
• Protein labeling
• Single-molecule microscopy
• Stoichiometry

• Animals
• Single Molecule Imaging/methods
• Xenopus laevis/metabolism
• Ku Autoantigen/metabolism
• Ku Autoantigen/chemistry
• DNA End-Joining Repair
• Xenopus Proteins/metabolism
• Xenopus Proteins/chemistry
• Cell-Free System/metabolism
• Photobleaching
• DNA Breaks, Double-Stranded
• Ovum/chemistry
• Ovum/metabolism
• DNA/chemistry
• DNA/metabolism

• DNA‐PKcs
• NHEJ
• RET/PTC1 rearrangement
• low‐dose ionizing radiation
• thyroid cancer

• National Natural Science Foundation of China

• single-molecule biophysics
• non-homologous-end joining
• double-strand dna breaks

• DNA Ligase ATP/metabolism
• DNA Breaks, Double-Stranded
• DNA End-Joining Repair
• DNA Repair
• DNA Ligases/metabolism
• DNA/genetics
• DNA/metabolism

• R01 GM115487 NIGMS NIH HHS
• U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)

• Cancer therapy
• DNA repair
• Double-strand breaks
• MMEJ
• Microhomology mediated end joining
• NHEJ
• Nonhomologous DNA end joining

• Animals
• Female
• Humans
• Mice
• DNA Damage/genetics
• DNA End-Joining Repair
• DNA Ligase ATP/genetics
• DNA Ligase ATP/metabolism
• DNA Ligases/genetics
• DNA Ligases/metabolism
• DNA Repair/genetics
• Ligases/genetics
• Ligases/metabolism
• Uterine Cervical Neoplasms/genetics
• Uterine Cervical Neoplasms/metabolism

• DNA double strand break repair
• DNA end processing
• DNA end synapsis
• DNA repair
• Non-homologous end joining

• Animals
• DNA End-Joining Repair
• DNA
• DNA-Binding Proteins/metabolism
• DNA Breaks, Double-Stranded
• Chromosome Pairing
• DNA Repair

• R01 GM115487 NIGMS NIH HHS

Neoplasms contain tumor-initiating stem-like cells (TICs) that are characterized by increased drug resistance. The incidence of many cancer types have trended downward except for few cancer types, including hepatocellular carcinoma (HCC). Therefore mechanism of HCC development and therapy resistance needs to be understood. These multiple hits by hepatitis C virus (HCV) eventually promotes transformation and TIC genesis, leading to HCC development. This review article describes links between HCV-associated HCC and TICs. This review discusses 1) how HCV promotes genesis of TICs and HCC development; 2) how this process avails itself as a novel therapeutic target for HCC treatment; and 3) ten hall marks of TIC oncogenesis and HCC development as targets for novel therapeutic modalities.

• DNA curtain
• DNA repair
• FRET—fluorescence resonance energy transfer
• homologous recombination (HR)
• magnetic tweezers
• non homologous end joining (NHEJ)
• optical tweezers (OT)
• single-molecule

• R01 CA221858 NCI NIH HHS
• R01 CA236606 NCI NIH HHS
• R35 GM118026 NIGMS NIH HHS
• National Institutes of Health

• DNA repair
• Double-strand break
• Functional assays
• Repair capacity

• DNA binding domain and catalytic domain
• DNA ligase IV
• Lig4 syndrome
• biophysicochemical characterization
• hypomorphic mutants

• DNA double-strand break
• DNA end processing
• DNA end synapsis
• DNA repair
• nonhomologous end joining

• Aging
• DNA repair
• DNA repair reporter cassette
• Inflammation
• Rejuvenation
• Senescence

• Double-strand break DNA repair
• Homology-directed repair
• Non-homologous end joining
• PARP inhibitors
• Radiation therapy
• Synthetic lethality

• NHEJ
• end processing
• non-homologous end joining
• single-molecule
• smFRET

• DNA recombination and repair
• RNA processing
• mRNA splicing
• protein‐protein interaction
• proteomics

• AP endonuclease
• Arabidopsis
• DNA damage
• DNA glycosylase
• DNA repair

• DNA end processing
• Neocarzinostatin
• Nonhomologous end joining
• PNKP
• Radiosensitization

• Alternative NHEJ
• DNA damage
• Double-strand break repair
• Gene conversion
• Genomic instability
• MMEJ
• Mitochondrial genome stability
• NHEJ
• Reciprocal exchange

• Animals
• DNA Breaks, Double-Stranded
• DNA End-Joining Repair/genetics
• DNA Repair/genetics
• DNA, Mitochondrial/genetics
• DNA, Mitochondrial/metabolism
• HeLa Cells
• Homologous Recombination/physiology
• Humans
• Male
• Mammals
• Mitochondria/genetics
• Mitochondria/metabolism
• Rats
• Rats, Wistar

• 37(1579)/13/EMR-II CSIR, New Delhi
• DBT/BF/PR/INS/2011-12/IISc IISc-DBT partnership programme

• DNA damage
• DNA endonuclease
• DNA ligation
• DNA polymerase
• alternative end-joining pathway
• chromosomes
• deletions
• double-strand break
• genomic instability
• microhomology
• single-strand annealing
• translocation

Mutations in BLM in Bloom Syndrome patients predispose them to multiple types of cancers. Here we report that BLM is recruited in a biphasic manner to annotated DSBs. BLM recruitment is dependent on the presence of NBS1, MRE11 and ATM. While ATM activity is essential for BLM recruitment in early phase, it is dispensable in late phase when MRE11 exonuclease activity and RNF8-mediated ubiquitylation of BLM are the key determinants. Interaction between polyubiquitylated BLM and NBS1 is essential for the helicase to be retained at the DSBs. The helicase activity of BLM is required for the recruitment of HR and c-NHEJ factors onto the chromatin in S- and G1-phase, respectively. During the repair phase, BLM inhibits HR in S-phase and c-NHEJ in G1-phase. Consequently, inhibition of helicase activity of BLM enhances the rate of DNA alterations. Thus BLM utilizes its pro- and anti-repair functions to maintain genome stability.

Bloom helicase is recruited to double strand breaks in an ATM dependent manner. Here the authors show that Bloom helicase is recruited to double strand breaks in an ATM and MRN dependent manner with HR and NHEJ regulated by the helicase depending on the phase of the cell cycle.

• NHEJ
• Non-homologous end joining
• TDP1
• Tyrosyl-DNA phosphodiesterase 1
• XLF

DNA double-strand breaks (DSBs) are mostly repaired by nonhomologous end joining (NHEJ) and homologous recombination (HR) in higher eukaryotes. In contrast, HR-mediated DSB repair is the major double-strand break repair pathway in lower order organisms such as bacteria and yeast. Penaeus monodon, commonly known as black tiger shrimp, is one of the economically important crustaceans facing large-scale mortality due to exposure to infectious diseases. The animals can also get exposed to chemical mutagens under the culture conditions as well as in wild. Although DSB repair mechanisms have been described in mammals and some invertebrates, its mechanism is unknown in the shrimp species. In the present study, we show that HR-mediated DSB repair is the predominant mode of repair in P. monodon. Robust repair was observed at a temperature of 30 °C, when 2 µg of cell-free extract derived from hepatopancreas was used for the study. Although HR occurred through both reciprocal recombination and gene conversion, the latter was predominant when the bacterial colonies containing recombinants were evaluated. Unlike mammals, NHEJ-mediated DSB repair was undetectable in P. monodon. However, we could detect evidence for an alternative mode of NHEJ that uses microhomology, termed as microhomology-mediated end joining (MMEJ). Interestingly, unlike HR, MMEJ was predominant at lower temperatures. Therefore, the results suggest that, while HR is major DSB repair pathway in shrimp, MMEJ also plays a role in ensuring the continuity and stability of the genome.

• Double-strand break
• MMEJ
• Microhomology
• Nonhomologous DNA end joining
• homologous recombination

• DNA Repair
• DNA Repair Enzymes/genetics
• DNA Repair Enzymes/metabolism
• HeLa Cells
• Humans
• Neoplasms/genetics
• Telomere Homeostasis

• UL1 TR000090 NCATS NIH HHS
• R01 CA117898 NCI NIH HHS
• R21 CA198228 NCI NIH HHS
• T32 CA106196 NCI NIH HHS
• P30 CA016058 NCI NIH HHS
• KL2 TR000112 NCATS NIH HHS
• TL1 TR000091 NCATS NIH HHS

• DNA double-strand break repair
• Förster resonance energy transfer
• Nonhomologous end joining
• Single-molecule fluorescence
• Xenopus egg extract

• non-homologous end joining
• homologous recombination
• ovarian cancer
• parp inhibitors
• rucaparib
• cisplatin
• dna-pk
• xrcc6 (ku70)
• xrcc5 (ku80)

• Antineoplastic Agents
• Blotting, Western
• Cell Line, Tumor
• DNA End-Joining Repair/genetics
• Drug Resistance, Neoplasm/genetics
• Female
• Fluorescent Antibody Technique
• Humans
• Indoles
• Ovarian Neoplasms/genetics
• Real-Time Polymerase Chain Reaction
• Reverse Transcriptase Polymerase Chain Reaction

• C27826/A12498 Cancer Research UK

• Apoptosis/drug effects
• Cell Survival
• Cells, Cultured
• Chromones/pharmacology
• Composite Resins/toxicity
• Dental Pulp/cytology
• Dental Pulp/drug effects
• Enzyme Inhibitors/pharmacology
• Humans
• Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors
• Morpholines/pharmacology
• Necrosis
• Phosphoinositide-3 Kinase Inhibitors
• Phosphorylation
• Polyethylene Glycols/toxicity
• Polymethacrylic Acids/toxicity
• Protein Serine-Threonine Kinases/antagonists & inhibitors
• Protein-Tyrosine Kinases/antagonists & inhibitors
• Proto-Oncogene Proteins/antagonists & inhibitors
• Proto-Oncogene Proteins c-akt

• Individual radiodegeneration
• Individual radioresponse
• Individual radiosensitivity
• Individual radiosusceptibility

• DNA double strand break repair
• DNA ligase inhibitors
• Human DNA ligases
• Non-homologous end-joining

Genomic instability (IN) is a common feature of many human cancers. The TP53 tumour suppressor gene is mutated in approximately half of human cancers. Here, we show that BRCA1 and RAD17 genes, whose derived proteins play a pivotal role in DNA damage repair, are transcriptional targets of gain-of-function mutant p53 proteins. Indeed, high levels of mutp53 protein facilitate DNA damage accumulation and severely impair BRCA1 and RAD17 expression in proliferating cancer cells. The recruitment of mutp53/E2F4 complex onto specific regions of BRCA1 and RAD17 promoters leads to the inhibition of their expression. BRCA1 and RAD17 mRNA expression is reduced in HNSCC patients carrying TP53 mutations when compared to those bearing wt-p53 gene. Furthermore, the analysis of gene expression databases for breast cancer patients reveals that low expression of DNA repair genes correlates significantly with reduced relapse free survival of patients carrying TP53 gene mutations. Collectively, these findings highlight the direct involvement of transcriptionally active gain of function mutant p53 proteins in genomic instability through the impairment of DNA repair mechanisms.

• BRCA1
• DNA damage response
• RAD17
• gain-of-function
• genomic instability
• mutant p53

DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA—protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.

Poly(ADP-ribose) polymerase (PARP) is a critical nuclear enzyme which helps in DNA repair. In this study we report, synthesis and biological studies of novel pyridazine derivatives as PARP inhibitors.

Repair of double-strand breaks in mammalian mitochondria depends on microhomology-mediated end joining (MMEJ). Classical NHEJ is not detectable in mitochondria. DNA ligase III, but not ligase IV or ligase I, is involved in mitochondrial MMEJ. The protein machinery involved in miitochondrial MMEJ includes CtIP, FEN1, ligase III, MRE11, and PARP1.

Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.

Over the past few decades, major strides have advanced the techniques for early detection and treatment of cancer. However, metastatic tumor growth still accounts for the majority of cancer-related deaths worldwide. In fact, breast cancers are notorious for relapsing years or decades after the initial clinical treatment, and this relapse can vary according to the type of breast cancer. In estrogen receptor-positive breast cancers, late tumor relapses frequently occur whereas relapses in estrogen receptor-negative cancers or triple negative tumors arise early resulting in a higher mortality risk. One of the main causes of metastasis is tumor dormancy in which cancer cells remain concealed, asymptomatic, and untraceable over a prolonged period of time. Under certain conditions, dormant cells can re-enter into the cell cycle and resume proliferation leading to recurrence. However, the molecular and cellular regulators underlying this transition remain poorly understood. To date, three mechanisms have been identified to trigger tumor dormancy including cellular, angiogenic, and immunologic dormancies. In addition, recent studies have suggested that DNA repair mechanisms may contribute to the survival of dormant cancer cells. In this article, we summarize the recent experimental and clinical evidence governing cancer dormancy. In addition, we will discuss the role of DNA repair mechanisms in promoting the survival of dormant cells. This information provides mechanistic insight to explain why recurrence occurs, and strategies that may enhance therapeutic approaches to prevent disease recurrence.

• Quiescence
• Homologous recombination
• Non-homologous end joining
• Tumor dormancy
• DNA repair

• DNA Polθ
• MMEJ
• chromosomal translocations
• end joining
• homologous recombination
• microhomology

Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.

Apoptosis is the programmed cell death which maintains the healthy survival/death balance in metazoan cells. Defect in apoptosis can cause cancer or autoimmunity, while enhanced apoptosis may cause degenerative diseases. The apoptotic signals contribute into safeguarding the genomic integrity while defective apoptosis may promote carcinogenesis. The apoptotic signals are complicated and they are regulated at several levels. The signals of carcinogenesis modulate the central control points of the apoptotic pathways, including inhibitor of apoptosis (IAP) proteins and FLICE-inhibitory protein (c-FLIP). The tumor cells may use some of several molecular mechanisms to suppress apoptosis and acquire resistance to apoptotic agents, for example, by the expression of antiapoptotic proteins such as Bcl-2 or by the downregulation or mutation of proapoptotic proteins such as BAX. In this review, we provide the main regulatory molecules that govern the main basic mechanisms, extrinsic and intrinsic, of apoptosis in normal cells. We discuss how carcinogenesis could be developed via defective apoptotic pathways or their convergence. We listed some molecules which could be targeted to stimulate apoptosis in different cancers. Together, we briefly discuss the development of some promising cancer treatment strategies which target apoptotic inhibitors including Bcl-2 family proteins, IAPs, and c-FLIP for apoptosis induction.

• DNA Repair
• Peptide Interactions
• Peptides
• Protein-Protein Interactions
• Proteomics
• Short ORF

• Class-switch recombination
• DNA double-strand breaks (DSBs)
• DNA repair
• Non-homologous endjoining (NHEJ)
• Telomere
• V(D)J Recombination

• Antigens, Nuclear/chemistry
• Antigens, Nuclear/metabolism
• DNA/chemistry
• DNA Breaks, Double-Stranded
• DNA End-Joining Repair
• DNA-Binding Proteins/chemistry
• DNA-Binding Proteins/metabolism
• Electrophoretic Mobility Shift Assay
• HeLa Cells
• Humans
• Ku Autoantigen
• Nucleic Acid Conformation
• Oligonucleotides/chemistry
• Protein Binding
• Protein Interaction Maps
• RecQ Helicases/chemistry
• RecQ Helicases/metabolism

• G12 MD007597 NIMHD NIH HHS
• SC1 GM093999 NIGMS NIH HHS
• G12MD007597 NIMHD NIH HHS
• 5SC1GM093999-04 NIGMS NIH HHS

• N01AI40038 NIAID NIH HHS
• R24 AA012885 NIAAA NIH HHS
• RC2 AA019392 NIAAA NIH HHS
• R01 AA018857 NIAAA NIH HHS
• P30 DK048522 NIDDK NIH HHS
• R21 AA025470 NIAAA NIH HHS
• P30 CA014089 NCI NIH HHS
• R01 AA025204 NIAAA NIH HHS
• R01 CA108302 NCI NIH HHS
• P50 AA011999 NIAAA NIH HHS

• Animals
• DNA Breaks, Double-Stranded
• DNA Damage/genetics
• DNA End-Joining Repair/genetics
• DNA Repair/genetics
• DNA Topoisomerases, Type II/genetics
• DNA Topoisomerases, Type II/metabolism
• DNA Topoisomerases, Type II/therapeutic use
• DNA-Binding Proteins
• Genomic Instability
• Mice
• Phosphoric Diester Hydrolases/deficiency
• Phosphoric Diester Hydrolases/genetics
• Phosphoric Diester Hydrolases/metabolism
• Recombination, Genetic
• Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/deficiency
• Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/genetics
• Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/metabolism

• 13078 Cancer Research UK
• MR/J006750/1 Medical Research Council
• G0600776 Medical Research Council
• G0901606 Medical Research Council

• DNA damage
• DNA repair.
• heart failure
• left ventricular assist device
• oxidative stress

• dna damage
• dna repair
• drug action
• nucleic acid enzymology
• radiation biology
• cisplatin
• nhej

• Cell Line, Tumor
• Cisplatin/pharmacology
• DNA Breaks, Double-Stranded/drug effects
• Flow Cytometry
• Humans
• Microscopy, Fluorescence
• Signal Transduction/drug effects
• Signal Transduction/genetics

• R01 CA082741 NCI NIH HHS
• CA082741 NCI NIH HHS