Location of Repository

Nonspaced inverted DNA repeats are preferential targets for homology-directed gene repair in mammalian cells

By Maarten Holkers, Antoine A. F. de Vries and Manuel A. F. V. Gonçalves

Abstract

DNA repeats constitute potential sites for the nucleation of secondary structures such as hairpins and cruciforms. Studies performed mostly in bacteria and yeast showed that these noncanonical DNA structures are breakage-prone, making them candidate targets for cellular DNA repair pathways. Possible culprits for fragility at repetitive DNA sequences include replication and transcription as well as the action of structure–specific nucleases. Despite their patent biological relevance, the parameters governing DNA repeat-associated chromosomal transactions remain ill-defined. Here, we established an episomal recombination system based on donor and acceptor complementary DNA templates to investigate the role of direct and inverted DNA repeats in homologous recombination (HR) in mammalian cells. This system allowed us also to ascertain in a stringent manner the impact of repetitive sequence replication on homology-directed gene repair. We found that nonspaced DNA repeats can, per se, engage the HR pathway of the cell and that this process is primarily dependent on their spacing and relative arrangement (i.e. parallel or antiparallel) rather than on their sequence. Indeed, our data demonstrate that contrary to direct and spaced inverted repeats, nonspaced inverted repeats are intrinsically recombinogenic motifs in mammalian cells lending experimental support to their role in genome dynamics in higher eukaryotes

Topics: Genome Integrity, Repair and Replication
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3300023
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Preview

    Citations

    1. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
    2. (2005). Adeno-associated virus: from defective virus to effective vector.
    3. (2006). Assaying double-strand break repair pathway choice in mammalian cells using a targeted endonuclease or the RAG recombinase.
    4. (1996). Characterization of 911: a new helper cell line for the titration and propagation of early region 1-deleted adenoviral vectors.
    5. (2009). Chromosomal instability mediated by non-B DNA: cruciform conformation and not DNA sequence is responsible for recurrent translocations in humans.
    6. (2007). Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.
    7. (1998). Cruciform-extruding regulatory element controls cell-specific activity of the tyrosine hydroxylase gene promoter.
    8. (2002). Development of multiple cloning site cis-vectors for recombinant adeno-associated virus production.
    9. (1998). Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations.
    10. (2002). Efficient generation and amplification of high-capacity adeno-associated virus/adenovirus hybrid vectors.
    11. (2010). Folded DNA in action: hairpin formation and biological functions in prokaryotes.
    12. (2010). GEN1/Yen1 and the SLX4 complex: solutions to the problem of Holliday junction resolution.
    13. (2006). Gene amplification: yeast takes a turn.
    14. (2001). Generation of a high-capacity hybrid vector: packaging of recombinant adenoassociated virus replicative intermediates in adenovirus capsids overcomes the limited cloning capacity of adenoassociated virus vectors.
    15. (2007). Hairpin- and cruciform-mediated chromosome breakage: causes and consequences in eukaryotic cells.
    16. (2008). Identification of Holliday junction resolvases from humans and yeast.
    17. (2000). Inverted Alu repeats unstable in yeast are excluded from the human genome.
    18. (2003). Mfold web server for nucleic acid folding and hybridization prediction.
    19. (2009). Models for chromosomal replication-independent non-B DNA structure-induced genetic instability.
    20. (2008). New insight into the recognition of branched DNA structure by junction-resolving enzymes.
    21. (2010). Non-B DNA structure-induced genetic instability and evolution.
    22. (1991). On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo.
    23. (2006). Palindromes and genomic stress fractures: bracing and repairing the damage.
    24. (2009). Progressive GAA TTC repeat expansion in human cell lines.
    25. (2003). Rapid, stabilizing palindrome rearrangements in somatic cells by the center-break mechanism.
    26. (2009). Recovering genome rearrangements in the mammalian phylogeny.
    27. (2005). Repeat instability: mechanisms of dynamic mutations.
    28. (2008). Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins.
    29. (2008). SbcCD causes a double-strand break at a DNA palindrome in the Escherichia coli chromosome.
    30. (1999). Spectral and physical characterization of the inverted terminal repeat DNA structure from adenoassociated virus 2.
    31. (2009). Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease.
    32. (2009). SV40 DNA replication: from the A gene to a nanomachine.
    33. (2002). The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements.
    34. (1983). The relaxation time for a cruciform structure in superhelical DNA.
    35. (2008). Two different forms of palindrome resolution in the human genome: deletion or translocation.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.