In vitro chromatin templates to study nucleotide excision repair.


:In eukaryotic cells, DNA associates with histones and exists in the form of a chromatin hierarchy. Thus, it is generally believed that many eukaryotic cellular DNA processing events such as replication, transcription, recombination and DNA repair are influenced by the packaging of DNA into chromatin. This mini-review covers the current knowledge of DNA damage and repair in chromatin based on in vitro studies. Specifically, nucleosome assembly affects DNA damage formation in both random sequences and sequences with strong nucleosome-positioning signals such as 5S rDNA. At least three systems have been used to analyze the effect of nucleosome folding on nucleotide excision repair (NER) in vitro: (a) human cell extracts that have to rely on labeling of repair synthesis to monitor DNA repair, due to very low repair efficacy; (b) Xenopus oocyte nuclear extracts, that have very robust DNA repair efficacy, have been utilized to follow direct removal of DNA damage; (c) six purified human DNA repair factors (RPA, XPA, XPC, TFIIH, XPG, and XPF-ERCC1) that have been used to reconstitute excision repair in vitro. In general, the results have shown that nucleosome folding inhibits NER and, therefore, its activity must be enhanced by chromatin remodeling factors like SWI/SNF. In addition, binding of transcription factors such as TFIIIA to the 5S rDNA promoter also modulates NER efficacy.


DNA Repair (Amst)


DNA repair


Liu X




Has Abstract


2015-12-01 00:00:00












  • Poetry in motion: Increased chromosomal mobility after DNA damage.

    abstract::Double-strand breaks (DSBs) are among the most lethal DNA lesions, and a variety of pathways have evolved to manage their repair in a timely fashion. One such pathway is homologous recombination (HR), in which information from an undamaged donor site is used as a template for repair. Although many of the biochemical s...

    journal_title:DNA repair

    pub_type: 杂志文章,评审


    authors: Smith MJ,Rothstein R

    更新日期:2017-08-01 00:00:00

  • The splicing component ISY1 regulates APE1 in base excision repair.

    abstract::The integrity of cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. If DNA damage is not removed in a timely fashion the replisome may stall at DNA lesions, causing fork collapse and genetic instability. Base excision DNA repair (BER) is the most important pathway for the remov...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Jaiswal AS,Williamson EA,Srinivasan G,Kong K,Lomelino CL,McKenna R,Walter C,Sung P,Narayan S,Hromas R

    更新日期:2020-02-01 00:00:00

  • Stimulation of direct-repeat recombination by RNA polymerase III transcription.

    abstract::Eukaryotic cells have to regulate the progression and integrity of DNA replication forks through concomitantly transcribed genes. A transcription-dependent increase of recombination within protein-coding and ribosomal genes of eukaryotic cells is well documented. Here we addressed whether tRNA transcription and tRNA-d...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: de la Loza MC,Wellinger RE,Aguilera A

    更新日期:2009-05-01 00:00:00

  • The endonuclease domain of Bacillus subtilis MutL is functionally asymmetric.

    abstract::DNA mismatch repair is an evolutionarily conserved repair pathway that corrects replication errors. In most prokaryotes and all eukaryotes, the mismatch repair protein MutL is a sequence-unspecific endonuclease that nicks the newly synthesized strand and marks it for repair. Although the sequence of the endonuclease d...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Liu L,Ortiz Castro MC,Rodríguez González J,Pillon MC,Guarné A

    更新日期:2019-01-01 00:00:00

  • RAD51D protects against MLH1-dependent cytotoxic responses to O(6)-methylguanine.

    abstract::S(N)1-type methylating agents generate O(6)-methyl guanine (O(6)-meG), which is a potently mutagenic, toxic, and recombinogenic DNA adduct. Recognition of O(6)-meG:T mismatches by mismatch repair (MMR) causes sister chromatid exchanges, which are representative of homologous recombination (HR) events. Although the MMR...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Rajesh P,Rajesh C,Wyatt MD,Pittman DL

    更新日期:2010-04-04 00:00:00

  • O6-methylguanine-DNA-methyltransferase (MGMT) gene therapy targeting haematopoietic stem cells: studies addressing safety issues.

    abstract::As haematopoietic stem cell gene therapy utilizing O(6)-methylguanine-DNA-methyltransferase has reached the clinical stage, safety-related questions become increasingly important. These issues concern insertional mutagenesis of viral vectors, the acute toxicity of pre-transplant conditioning protocols and in vivo sele...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Sorg UR,Kleff V,Fanaei S,Schumann A,Moellmann M,Opalka B,Thomale J,Moritz T

    更新日期:2007-08-01 00:00:00

  • Detection of the small oligonucleotide products of nucleotide excision repair in UVB-irradiated human skin.

    abstract::UVB radiation results in the formation of potentially mutagenic photoproducts in the DNA of epidermal skin cells. In vitro approaches have demonstrated that the nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small (∼30-nt-long), excised, damage-containing DNA oligonucleotid...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Choi JH,Han S,Kemp MG

    更新日期:2020-02-01 00:00:00

  • Influence of XPB helicase on recruitment and redistribution of nucleotide excision repair proteins at sites of UV-induced DNA damage.

    abstract::The XPB DNA helicase, a subunit of the basal transcription factor TFIIH, is also involved in nucleotide excision repair (NER). We examined recruitment of NER proteins in XP-B cells from patients with mild or severe xeroderma pigmentosum (XP) having different XPB mutations using local UV-irradiation through filters wit...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Oh KS,Imoto K,Boyle J,Khan SG,Kraemer KH

    更新日期:2007-09-01 00:00:00

  • High levels of oxidatively generated DNA damage 8,5'-cyclo-2'-deoxyadenosine accumulate in the brain tissues of xeroderma pigmentosum group A gene-knockout mice.

    abstract::Xeroderma pigmentosum (XP) is a genetic disorder associated with defects in nucleotide excision repair, a pathway that eliminates a wide variety of helix-distorting DNA lesions, including ultraviolet-induced pyrimidine dimers. In addition to skin diseases in sun-exposed areas, approximately 25% of XP patients develop ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Mori T,Nakane H,Iwamoto T,Krokidis MG,Chatgilialoglu C,Tanaka K,Kaidoh T,Hasegawa M,Sugiura S

    更新日期:2019-08-01 00:00:00

  • The 8-oxoguanine DNA glycosylase 1 (ogg1) decreases the vulnerability of the developing brain to DNA damage.

    abstract::The developing brain is particularly vulnerable to oxidative DNA damage, which may be the cause of most major congenital mental anomalies. The repair enzyme ogg1 initiates the highly conserved base-excision repair pathway. However, its function in the embryonic brain is largely unknown. This study is the first to vali...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Gu A,Ji G,Yan L,Zhou Y

    更新日期:2013-12-01 00:00:00

  • A shared DNA-damage-response pathway for induction of stem-cell death by UVB and by gamma irradiation.

    abstract::Both UVB radiation and DNA-breaking agents were previously reported to kill Arabidopsis stem cells. We demonstrate that death induced by UVB or by ionizing radiation (IR) requires Suppressor of Gamma Response 1 (SOG1), a transcription factor already found to govern many responses to these agents in Arabidopsis. DNA-da...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Furukawa T,Curtis MJ,Tominey CM,Duong YH,Wilcox BW,Aggoune D,Hays JB,Britt AB

    更新日期:2010-09-04 00:00:00

  • Oxidative DNA damage repair in mammalian cells: a new perspective.

    abstract::Oxidatively induced DNA lesions have been implicated in the etiology of many diseases (including cancer) and in aging. Repair of oxidatively damaged bases in all organisms occurs primarily via the DNA base excision repair (BER) pathway, initiated with their excision by DNA glycosylases. Only two mammalian DNA glycosyl...

    journal_title:DNA repair

    pub_type: 杂志文章,评审


    authors: Hazra TK,Das A,Das S,Choudhury S,Kow YW,Roy R

    更新日期:2007-04-01 00:00:00

  • DNA damage response and breast cancer development: Possible therapeutic applications of ATR, ATM, PARP, BRCA1 inhibition.

    abstract::Breast cancer is the most common and significant cancers in females regarding the loss of life quality. Similar to other cancers, one of the etiologic factors in breast cancer is DNA damage. A plethora of molecules are responsible for sensing DNA damage and mediating actions which lead to DNA repair, senescence, cell ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Mirza-Aghazadeh-Attari M,Recio MJ,Darband SG,Kaviani M,Safa A,Mihanfar A,Sadighparvar S,Karimian A,Alemi F,Majidinia M,Yousefi B

    更新日期:2020-12-17 00:00:00

  • Contribution of DNA unwrapping from histone octamers to the repair of oxidatively damaged DNA in nucleosomes.

    abstract::Reactive oxygen species generate ~20,000 oxidative lesions in the DNA of every cell, every day. Most of these lesions are located within nucleosomes, which package DNA in chromatin and impede base excision repair (BER). We demonstrated previously that periodic, spontaneous partial unwrapping of DNA from the underlying...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Maher RL,Prasad A,Rizvanova O,Wallace SS,Pederson DS

    更新日期:2013-11-01 00:00:00

  • DNA mismatch repair preferentially safeguards actively transcribed genes.

    abstract::DNA mismatch repair (MMR) is an evolutionally conserved genome maintenance pathway and is well known for its role in maintaining replication fidelity by correcting biosynthetic errors generated during DNA replication. However, recent studies have shown that MMR preferentially protects actively transcribed genes from m...

    journal_title:DNA repair

    pub_type: 杂志文章,评审


    authors: Huang Y,Li GM

    更新日期:2018-11-01 00:00:00

  • Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis.

    abstract::Eukaryotic genomes are duplicated by a complex machinery, utilizing high fidelity replicative B-family DNA polymerases (pols) α, δ and ε. Specialized error-prone pol ζ, the fourth B-family member, is recruited when DNA synthesis by the accurate trio is impeded by replication stress or DNA damage. The damage tolerance ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Stepchenkova EI,Tarakhovskaya ER,Siebler HM,Pavlov YI

    更新日期:2017-01-01 00:00:00

  • Guanine repeat-containing sequences confer transcription-dependent instability in an orientation-specific manner in yeast.

    abstract::Non-B DNA structures are a major contributor to the genomic instability associated with repetitive sequences. Immunoglobulin switch Mu (Sμ) region sequence is comprised of guanine-rich repeats and has high potential for forming G4 DNA, in which one strand of DNA folds into an array of guanine quartets. Taking advantag...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Kim N,Jinks-Robertson S

    更新日期:2011-09-05 00:00:00

  • Characterization in vitro and in vivo of the DNA helicase encoded by Deinococcus radiodurans locus DR1572.

    abstract::Deinococcus radiodurans survives extremely high doses of ionizing and ultraviolet radiation and treatment with various DNA-damaging chemicals. As an effort to identify and characterize proteins that function in DNA repair in this organism, we have studied the protein encoded by locus DR1572. This gene is predicted to ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Cao Z,Julin DA

    更新日期:2009-05-01 00:00:00

  • Minding the gap: the underground functions of BRCA1 and BRCA2 at stalled replication forks.

    abstract::The hereditary breast and ovarian cancer predisposition genes, BRCA1 and BRCA2, participate in the repair of DNA double strand breaks by homologous recombination. Circumstantial evidence implicates these genes in recombinational responses to DNA polymerase stalling during the S phase of the cell cycle. These responses...

    journal_title:DNA repair

    pub_type: 杂志文章,评审


    authors: Nagaraju G,Scully R

    更新日期:2007-07-01 00:00:00

  • Tousled homolog, TLK1, binds and phosphorylates Rad9; TLK1 acts as a molecular chaperone in DNA repair.

    abstract::The Tousled-like kinases are involved in chromatin assembly, DNA repair, transcription, and chromosome segregation. In this work, we show that overexpression of TLK1B hastens repair of double strand breaks (DSBs) in mouse cells. We have identified Rad9 as a protein interacting tightly with TLK1B. TLK1B phosphorylates ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Sunavala-Dossabhoy G,De Benedetti A

    更新日期:2009-01-01 00:00:00

  • Deficient global genome repair of UV-induced cyclobutane pyrimidine dimers in terminally differentiated myocytes and proliferating fibroblasts from the rat heart.

    abstract::Nucleotide excision repair (NER) is the principal pathway for the removal of a wide range of DNA helix-distorting lesions. Two NER subpathways have been identified, i.e. global genome repair (GGR) and transcription-coupled repair (TCR). Little is known about the expression of NER pathways in differentiated cells. We a...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: van der Wees CG,Vreeswijk MP,Persoon M,van der Laarse A,van Zeeland AA,Mullenders LH

    更新日期:2003-12-09 00:00:00

  • Mice defective in the mismatch repair gene Msh2 show increased predisposition to UVB radiation-induced skin cancer.

    abstract::Mice defective in the mismatch repair (MMR) gene Msh2 manifest an enhanced predisposition to skin cancer associated with exposure to UVB radiation. This predisposition is further heightened if the mice are additionally defective for the nucleotide excision repair gene Xpc. To test the hypothesis that the predispositio...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Meira LB,Cheo DL,Reis AM,Claij N,Burns DK,te Riele H,Friedberg EC

    更新日期:2002-11-03 00:00:00

  • Novel role of tyrosine in catalysis by human AP endonuclease 1.

    abstract::Apurinic/apyrimidinic endonuclease (AP endo, HAP1) recognizes abasic sites in ds DNA and makes a single nick in the backbone 5' to the abasic site. In this report we examine the roles of three conserved tyrosine residues in close proximity to the active site. We show that Tyr(128) and Tyr(269), which interact upstream...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Mundle ST,Fattal MH,Melo LF,Coriolan JD,O'Regan NE,Strauss PR

    更新日期:2004-11-02 00:00:00

  • Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition.

    abstract::Short-wave ultra-violet light promotes the formation of DNA dimers between adjacent thymine bases, and if unrepaired these dimers may induce skin cancer. Living cells have a very robust repair system capable of repairing hundreds of lesions every day. Although many of the details of the dimer repair mechanism are know...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Blagoev KB,Alexandrov BS,Goodwin EH,Bishop AR

    更新日期:2006-07-13 00:00:00

  • Examining the potential role of DNA polymerases eta and zeta in triplet repeat instability in yeast.

    abstract::Triplet repeats undergo frequent mutations in human families afflicted with certain neurodegenerative diseases and also in model organisms. Although the molecular mechanisms of triplet repeat instability are still being identified, it is likely that aberrant DNA synthesis plays an important role. Many DNA polymerases ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Dixon MJ,Lahue RS

    更新日期:2002-09-04 00:00:00

  • Sensitivity of human cells expressing low-fidelity or weak-catalytic-activity variants of DNA polymerase ζ to genotoxic stresses.

    abstract::Translesion DNA polymerases (TLS pols) play critical roles in defense mechanisms against genotoxic agents. The defects or mutations of TLS pols are predicted to result in hypersensitivity of cells to environmental mutagens. In this study, human cells expressing DNA polymerase ζ (Pol ζ) variants with low fidelity or we...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Suzuki T,Grúz P,Honma M,Adachi N,Nohmi T

    更新日期:2016-09-01 00:00:00

  • DNA decay and limited Rad53 activation after liquid holding of UV-treated nucleotide excision repair deficient S. cerevisiae cells.

    abstract::The DNA damage checkpoint is a surveillance mechanism activated by DNA lesions and devoted to the maintenance of genome stability. It is considered as a signal transduction cascade, involving a sensing step, the activation of a set of protein kinases and the transmission and amplification of the damage signal through ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Giannattasio M,Lazzaro F,Siede W,Nunes E,Plevani P,Muzi-Falconi M

    更新日期:2004-12-02 00:00:00

  • Reversibility of replicative senescence in Saccharomyces cerevisiae: effect of homologous recombination and cell cycle checkpoints.

    abstract::Primary human somatic cells grown in culture divide a finite number of times, exhibiting progressive changes in metabolism and morphology before cessation of cycling. This telomere-initiated cellular senescence occurs because cells have halted production of telomerase, a DNA polymerase required for stabilization of ch...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Becerra SC,Thambugala HT,Erickson AR,Lee CK,Lewis LK

    更新日期:2012-01-02 00:00:00

  • Transcription coupled nucleotide excision repair in Escherichia coli can be affected by changing the arginine at position 529 of the beta subunit of RNA polymerase.

    abstract::The proposed mechanism for transcription coupled nucleotide excision repair (TCR) invokes RNA polymerase (RNAP) blocked at a DNA lesion as a signal to initiate repair. In Escherichia coli, TCR requires the interaction of RNAP with a transcription-repair coupling factor encoded by the mfd gene. The interaction between ...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: Ganesan AK,Smith AJ,Savery NJ,Zamos P,Hanawalt PC

    更新日期:2007-10-01 00:00:00

  • Novel DNA mismatch-repair activity involving YB-1 in human mitochondria.

    abstract::Maintenance of the mitochondrial genome (mtDNA) is essential for proper cellular function. The accumulation of damage and mutations in the mtDNA leads to diseases, cancer, and aging. Mammalian mitochondria have proficient base excision repair, but the existence of other DNA repair pathways is still unclear. Deficienci...

    journal_title:DNA repair

    pub_type: 杂志文章


    authors: de Souza-Pinto NC,Mason PA,Hashiguchi K,Weissman L,Tian J,Guay D,Lebel M,Stevnsner TV,Rasmussen LJ,Bohr VA

    更新日期:2009-06-04 00:00:00