Review
DNA replication timing, genome stability and cancer: Late and/or delayed DNA replication timing is associated with increased genomic instability

https://doi.org/10.1016/j.semcancer.2013.01.001Get rights and content

Abstract

Normal cellular division requires that the genome be faithfully replicated to ensure that unaltered genomic information is passed from one generation to the next. DNA replication initiates from thousands of origins scattered throughout the genome every cell cycle; however, not all origins initiate replication at the same time. A vast amount of work over the years indicates that different origins along each eukaryotic chromosome are activated in early, middle or late S phase. This temporal control of DNA replication is referred to as the replication-timing program. The replication-timing program represents a very stable epigenetic feature of chromosomes. Recent evidence has indicated that the replication-timing program can influence the spatial distribution of mutagenic events such that certain regions of the genome experience increased spontaneous mutagenesis compared to surrounding regions. This influence has helped shape the genomes of humans and other multicellular organisms and can affect the distribution of mutations in somatic cells. It is also becoming clear that the replication-timing program is deregulated in many disease states, including cancer. Aberrant DNA replication timing is associated with changes in gene expression, changes in epigenetic modifications and an increased frequency of structural rearrangements. Furthermore, certain replication timing changes can directly lead to overt genomic instability and may explain unique mutational signatures that are present in cells that have undergone the recently described processes of “chromothripsis” and “kataegis”. In this review, we will discuss how the normal replication timing program, as well as how alterations to this program, can contribute to the evolution of the genomic landscape in normal and cancerous cells.

Introduction

In order to divide a eukaryotic cell must undergo precise DNA replication to ensure that an exact copy of its genetic content is passed on to its daughter cells. This process occurs during S phase and proceeds via the coordinated initiation of DNA replication at hundreds of replication origins scattered throughout the length of each chromosome [1]. Interestingly, the cell begins preparation for DNA synthesis in telophase of the prior cell cycle [2]. This is when the pre-replicative complex (pre-RC) begins to form on each potential origin of replication. However, not all pre-RCs will go on to become active replication origins. In mid-G1, at the origin decision point (ODP), some pre-RCs are chosen to become initiators of DNA replication while others remain inactive throughout S-phase [3], [4]. The addition of other replication factors to a subset of the pre-RCs transforms them into pre-initiation complexes (pre-ICs) [5]. Shortly after the pre-IC is formed, DNA polymerase and primase are recruited to each origin and DNA synthesis begins in a bidirectional manner. DNA replication proceeds from each origin until the replication forks from two neighboring origins meet and the nascent DNA strands are ligated [6].

While DNA replication can initiate from any active origin within a given S-phase, the timing at which initiation takes place can vary widely between origins. Adjacent origins tend to initiate DNA replication at the same time resulting in large, synchronously replicating chromosomal domains called “replicon clusters” [7], [8]. Some replicon clusters begin replication at the onset of S-phase while others begin later during the middle or near the end of S-phase. This coordination of the temporal control of DNA replication is referred to as the replication-timing program. The replication-timing program is established shortly after mitosis at a point in the G1 phase, preceding the ODP, called the timing decision point (TDP) [9], [10]. The TDP is established coincidently with a global reorganization of chromatin into specified regions within the nucleus [10].

The replication-timing program is mitotically stable, heritable and subject to differential regulation during differentiation and development, making it a robust epigenetic feature of all eukaryotic chromosomes [11]. The biological significance of this replication-timing program is currently unknown; however, the existence of aberrant replication timing in many different genetic diseases suggests that it is a vital cellular process [12], [13], [14], [15], [16]. Not surprisingly, the 3-dimensional chromosome architecture in the nucleus is highly coordinated with DNA replication timing. In most, if not all, eukaryotic organisms, early-replicating DNA resides in the interior of the nucleus while the later-replicating regions remain at the nuclear periphery or near the nucleolus [10], [17], [18]. Molecular analysis has also revealed that late-replicating regions tend to cluster with other late-replicating regions in the nucleus and vice versa [19]. Additional complex associations have been observed with genome sequence, structure and replication timing. For example, early-replicating regions tend to positively correlate with gene expression, G + C rich sequences, light-staining Giemsa bands, and active chromatin marks, while late-replicating regions tend to be gene-poor, A + T rich, and have repressive chromatin marks [17], [20], [21]. It should be pointed out that while these correlations are significant they are not absolute, as some expressed genes with transcriptional active chromatin marks reside in late-replicating regions [8].

DNA synthesis occurs in replication factories within the 3-dimensional space of the nucleus. In these factories, regions of similar replication timing cluster together in the nucleus, with early-replicating regions residing in the nuclear interior and late-replicating regions remaining at the nuclear periphery or near the nucleolus [9], [17], [19], [22]. Additionally, replication-timing changes that occur during development are accompanied by changes in nuclear architecture, indicating that these two features are very closely linked [23]. Therefore, regions that replicate at comparable times in S phase tend to have a closer spatial association than regions that replicate at different times. This association has been highlighted using the HiC method, which probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing [19], [24].

One prominent disease that is characterized by replication-timing aberrations is cancer. Cancer develops when normal cells acquire genetic and epigenetic alterations that lead to uncontrolled growth and the ability to evade cell death. These genetic and epigenetic alterations are generally thought to drive carcinogenesis by deregulating key pathways that control cell growth and proliferation [25]. Genetic alterations can arise during cancer progression through normal cellular processes, induced or spontaneous mutagenesis, or as a result of genomic instability. Mutagenesis refers to the process by which genetic changes occur, either spontaneously or as a consequence of exposure to mutagens, resulting in a change in the DNA sequence. Genomic instability, on the other hand, refers to an increase in the rate of mutagenesis per unit time. While normal cells have a very low intrinsic mutation rate, any mechanism that increases the mutation rate can be said to cause genomic instability. Current models suggest that an underlying genomic instability is responsible for the rapid accumulation of the genetic and epigenetic changes that affect gene function in cancer [25]. Therefore, it is very difficult to understand cancer development without understanding the mechanisms that cause genomic instability.

In this review, we highlight research suggesting that the normal DNA replication-timing program has a profound impact on the distribution of mutations that arise during the evolution of species as well as during the evolution of cancer. Aberrant DNA replication timing is associated with altered gene expression, mutagenesis and genomic instability. Furthermore, we propose that certain DNA replication-timing aberrations can explain the newly described processes of “chromothripsis” and “kataegis”, which have been found to generate unique genomic signatures in the genomes of some tumor cells [26], [27].

Section snippets

DNA replication timing and the evolution of the genomic landscape

The conventional view of evolution assumes that DNA mutations occur randomly throughout the genome and the eventual presence or absence of those DNA changes in the population is determined through the process of natural selection. While natural selection remains the most potent force shaping the evolution of the genomic landscape, the notion that DNA mutations occur randomly in the genome has become outdated. We now know that mutation rate varies widely throughout the genome and is influenced

DNA replication timing and the evolution of the cancer genome

The observations described above indicate that replication timing influences the mutation rate of different genomic regions in the germline, and over long periods of time differences in replication timing can contribute to the genetic variation within and between species. However, there is also increasing evidence that replication timing influences the mutation rate in somatic cells and may be a contributing factor to the distribution of genomic changes that arise during cancer development.

Concluding remarks

Changes in the replication timing of individual loci throughout the genome in cancer cells can occur in two ways: either the advanced replication of individual loci or the delayed replication of individual loci. It currently appears that the advanced replication of individual loci is more common than delayed replication and it is unclear why this is. Furthermore, the change in replication timing of individual loci generally appears to result in aberrant asynchronous replication, but it is not

Funding

The study was supported by National Cancer Institute (CA104693 and CA131967).

Conflict of interest

None.

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