Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

DNA inverted repeats (IRs) are hotspots of genomic instability in both prokaryotes and eukaryotes. This feature is commonly attributed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA replication and other genetic processes. However, direct evidence that I...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2008-07, Vol.105 (29), p.9936-9941
Main Authors: Voineagu, Irina, Narayanan, Vidhya, Lobachev, Kirill S, Mirkin, Sergei M
Format: Article
Language:English
Subjects:
Alu Elements
Animals
Biochemistry
Biological Sciences
Cell Cycle Proteins - metabolism
Cercopithecus aethiops
COS Cells
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA Replication
DNA, Bacterial - chemistry
DNA, Bacterial - genetics
DNA, Bacterial - metabolism
DNA, Fungal - chemistry
DNA, Fungal - genetics
DNA, Fungal - metabolism
DNA-Binding Proteins
Electrophoresis, Gel, Two-Dimensional
Escherichia coli - genetics
Escherichia coli - metabolism
Eukaryotes
Eukaryotic cells
Gels
Genomic Instability
Genomics
Humans
Models, Biological
Nucleic Acid Conformation
Plasmids
Prokaryotes
Proteins
Repetitive Sequences, Nucleic Acid
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - metabolism
Saccharomyces cerevisiae Proteins - metabolism
Sequence homology
Stall
Yeasts
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Summary:DNA inverted repeats (IRs) are hotspots of genomic instability in both prokaryotes and eukaryotes. This feature is commonly attributed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA replication and other genetic processes. However, direct evidence that IRs are replication stall sites in vivo is currently lacking. Here, we show by 2D electrophoretic analysis of replication intermediates that replication forks stall at IRs in bacteria, yeast, and mammalian cells. We found that DNA hairpins, rather than DNA cruciforms, are responsible for the replication stalling by comparing the effects of specifically designed imperfect IRs with varying lengths of their central spacer. Finally, we report that yeast fork-stabilizing proteins, Tof1 and Mrc1, are required to counteract repeat-mediated replication stalling. We show that the function of the Tof1 protein at DNA structure-mediated stall sites is different from its previously described effect on protein-mediated replication fork barriers.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0804510105