Rejoining of DNA Double-Strand Breaks as a Function of Overhang Length

Daley, James M.; Wilson, Thomas E.

doi:10.1128/mcb.25.3.896-906.2005

Cited by 96 publications

(103 citation statements)

References 42 publications

(50 reference statements)

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“…Oligonucleotide-modified Plasmids-OMPs were created as described previously (21). Briefly, two pairs of annealed oligonucleotides designed to restore the ADE2 coding sequence in plasmid pTW423 were ligated onto the ends of pTW423 digested with BglII and XhoI (supplemental Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Here, we sought to determine why only some joints that require gap filling are Pol4-dependent by using oligonucleotide-modified plasmids (OMPs) to perform a systematic analysis of DSB end configurations (21). We found that only NHEJ events that involve 3Ј-overhangs and require gap filling on both strands are strongly Pol4-dependent, with Pol4 promoting accurate repair.…”

mentioning

confidence: 99%

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DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining

Daley¹,

Laan

Suresh

et al. 2005

Journal of Biological Chemistry

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114

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DNA double strand breaks (DSBs) can be rejoined directly by the nonhomologous end-joining (NHEJ) pathway of repair. Nucleases and polymerases are required to promote accurate NHEJ when the terminal bases of the DSB are damaged. The same enzymes also participate in imprecise rejoining and joining of incompatible ends, important mutagenic events. Previous work has shown that the Pol X family polymerase Pol4 is required for some but not all NHEJ events that require gap filling in Saccharomyces cerevisiae. Here, we systematically analyzed DSB end configurations and found that gaps on both strands and overhang polarity are the principal factors that determine whether a joint requires Pol4. DSBs with 3-overhangs and a gap on each strand strongly depended on Pol4 for repair, DSBs with 5-overhangs of the same sequence did not. Pol4 was not required when 3-overhangs contained a gap on only one strand, however. Pol4 was equally required at 3-overhangs of all lengths within the NHEJ-dependent range but was dispensable outside of this range, indicating that Pol4 is specific to NHEJ. Loss of Pol4 did not affect the rejoining of DSBs that utilized a recessed microhomology or DSBs bearing 5-hydroxyls but no gap. Finally, mammalian Pol X polymerases were able to differentially complement a pol4 mutation depending on the joint structure, demonstrating that these polymerases can participate in yeast NHEJ but with distinct properties.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining

Daley¹,

Laan

Suresh

et al. 2005

Journal of Biological Chemistry

Self Cite

114

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“…TdT is only expressed in early B-and T-lymphocytes, making it most relevant to the NHEJ repair that occurs during V(D)J recombination, where it has a major role in promoting immunoglobulin diversity. DNA polymerases outside the Pol X family are able to incorporate nucleotides during NHEJ, but only in a template-dependent manner (16,17,(57)(58)(59).…”

Section: The Polymerases Of Nhejmentioning

confidence: 99%

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Pannunzio

Watanabe

Lieber

2018

Journal of Biological Chemistry

387

360

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Nonhomologous DNA end joining (NHEJ) is the predominant DSB repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol m and Pol l), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.

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“…We suspect that broken chromosome ends were incompatible to simply join in all cases except one (subject 70; Gajecka et al 2006b). NHEJ is synonymous with the Ku-and DNA ligase IV-dependent rejoining mechanisms (Daley and Wilson 2005). Broken DNA strands in derivative chromosome formation must be aligned and, after nucleolytic processing of broken DNA ends, small gaps need to be filled prior to DNA joining.…”

Section: Nonhomologous End-joining Involvement In Translocation Formamentioning

confidence: 99%

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

Gajęcka

Gentles²,

Tsai³

et al. 2008

Genome Res.

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Approximately one in 500 individuals carries a reciprocal translocation. Balanced translocations are usually associated with a normal phenotype unless the translocation breakpoints disrupt a gene(s) or cause a position effect. We investigated breakpoint junctions at the sequence level in phenotypically normal balanced translocation carriers. Eight breakpoint junctions derived from four nonrelated subjects with apparently balanced translocation t(1;22)(p36;q13) were examined. Additions of nucleotides, deletions, duplications, and a triplication identified at the breakpoints demonstrate high complexity at the breakpoint junctions and indicate involvement of multiple mechanisms in the DNA breakage and repair process during translocation formation. Possible detailed nonhomologous end-joining scenarios for t(1;22) cases are presented. We propose that cryptic imbalances in phenotypically normal, balanced translocation carriers may be more common than currently appreciated.[Supplemental material is available online at www.genome.org.]With the exception of benign copy number variation, it is generally assumed that a normal phenotype is associated only with a balanced genotype. However, a balanced translocation may produce an abnormal phenotype by disruption of a gene at the translocation breakpoint, through the formation of a novel fusion gene product, or by a position effect. Moreover, in apparently balanced translocations with abnormal phenotypes, duplications and deletions at the breakpoints have been identified that impact the phenotype. Baptista et al. (2005) hypothesized that breakpoints of normal individuals with apparently balanced chromosome rearrangements are relatively simple. However, their study was based on molecular cytogenetic methods (fluorescence in situ hybridization [FISH] and microarray-based comparative genomic hybridization [array CGH]) only. Breakpoints in only a few constitutional rearrangements in individuals with normal phenotypes have been examined at the DNA sequence level. These include translocations t(11;22) (Kurahashi et al. 2000(Kurahashi et al. , 2007, the most common constitutional translocation in humans, in which junction fragments were identified, and other translocation events including t(1;22)(p21.2;q11.2) (Gotter et al. 2004), t(4;22)(q35.1;q11.2) (Nimmakayalu et al. 2003), and t(8;22)(q24.13;q11.21) (Gotter et al. 2007). We have previously examined apparently balanced translocations in phenotypically normal individuals and found evidence that translocation junctions may show sequence inconsistency at the breakpoints created by addition of nucleotides and duplications (Gajecka et al. 2006b).The resolution of DNA double-strand breaks (DSBs) can result in translocation formation through a variety of different pathways. In homologous recombination repair, the DNA ends can be aligned and joined using sequence homology. Alternatively, the broken ends can be brought together and rejoined in the absence of long tracks of sequence homology through nonhomologous end-joining (NHEJ). Two ...

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Rejoining of DNA Double-Strand Breaks as a Function of Overhang Length

Cited by 96 publications

References 42 publications

DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining

DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

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