Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

Abstract

Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.

Keywords: DNA repair; collision; genetic instability; non-B DNA; replication; transcription.

Figure 1

Schematic of several commonly studied non-B DNA structures. (A) Cruciform; (B) Left-handed Z-DNA; (C) Intramolecular triplex H-DNA; (D) G-quadruplex/tetraplex; (E) Stem-loop (left) or bubble (right) formed at slipped DNA, (from [24], with permission).

Figure 2

Effects of H-DNA orientation on DNA replication and genetic instability in mammalian cells. Reporter shutter vectors, pCEX and pMEXY and pMEXU, were transfected into mammalian COS-7 cells. The SV40 replication origin on the plasmids supports bi-directional replication in COS-7 cells. (A) Effects of orientation on H-DNA-induced replication stalling in mammalian COS-7 cells. Replication intermediates of plasmids were recovered 24 h post-transfection and were separated via 2-D gel electrophoresis. The fragments containing the H-DNA-forming or control sequences were probed by Southern blotting. The arrow designates the bulge on the Y-shaped replication arc, indicative of the accumulation of stalled replication intermediates. A representative image of three independent repeats is shown; (B) Effects of orientation on H-DNA-induced mutation frequencies in mammalian COS-7 cells. Mutation-reporter plasmids were recovered 48 h post-transfection, followed by DpnI digestion to remove the un-replicated plasmid DNA. Mutants generated were screened in indicator bacterial MBM7070 cells. Error bars show the standard errors of the mean value of three independent experiments.

Figure 3

Models of non-B DNA-induced replication and transcription collision at repetitive regions. (A) Schematic diagram of non-B DNA-induced “head-on” replication-transcription collision. (1) DNA replication progresses from chromosome location “X” to “Y”; (2) Transcription progresses within the same region, but from the opposite direction (from “Y” to “X”) after (or before) DNA replication is complete in that area; (3) A non-B DNA structure formed between chromosome loci “X” and “Y” interrupts the initiation and/or progression of replication and transcription, resulting in “head-on” replication-transcription collision (shown as a lightning bolt). (B) Schematic diagram of non-B DNA-induced “co-directional” replication-transcription collision. (1) DNA replication and transcription occur simultaneously and “co-directionally” on the chromosome without collision; (2) A non-B DNA structure formed in front of the transcription machinery stalls transcription progression; (3) A DNA replication fork runs into the transcription machinery, resulting in a “co-directional” replication-transcription collision (shown as a lightning bolt).