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Review
. 2017 Feb;18(2):101-116.
doi: 10.1038/nrg.2016.141. Epub 2016 Nov 21.

Order From Clutter: Selective Interactions at Mammalian Replication Origins

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Free PMC article
Review

Order From Clutter: Selective Interactions at Mammalian Replication Origins

Mirit I Aladjem et al. Nat Rev Genet. .
Free PMC article

Abstract

Mammalian chromosome duplication progresses in a precise order and is subject to constraints that are often relaxed in developmental disorders and malignancies. Molecular information about the regulation of DNA replication at the chromatin level is lacking because protein complexes that initiate replication seem to bind chromatin indiscriminately. High-throughput sequencing and mathematical modelling have yielded detailed genome-wide replication initiation maps. Combining these maps and models with functional genetic analyses suggests that distinct DNA-protein interactions at subgroups of replication initiation sites (replication origins) modulate the ubiquitous replication machinery and supports an emerging model that delineates how indiscriminate DNA-binding patterns translate into a consistent, organized replication programme.

Conflict of interest statement

Competing interests statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1. Organization of replication origins, replicons and replication-timing domains.
a | An illustration of a portion of a eukaryotic chromosome depicting five replicons, each defined by an origin of replication (A, B, C, D and E). Replication starts at different times during the S phase of the cell cycle. Origins A, B and C start replication first, concomitantly or in immediate succession, followed later by the initiation of DNA replication from origins D and E. The replicons containing origins A, B and C form an early replication-timing domain, and the replicons containing origins D and E form a late replication-timing domain. b | An example of possible replication-timing measurements revealing large megabase-sized replication-timing domains. Chromatin domains with similar replication timing (top panel) exhibit a similar copy number in an asynchronous cell population, with early-replicating domains (such as the domain including replicons A, B and C) containing more copies than late-replicating domains (such as the domain including replicons D and E). High-resolution mapping of replication timing (bottom panel) reveals subpeaks (indicated by white arrows) in large replication domains that correspond to individual replicons driven by distinct replication origins (for example, the subpeaks for origins A, B and C are visible within the large early-replicating domain). c | Nuclear distribution of replicons and replication domains. Replicating DNA (represented by ellipses) tends to cluster, with each replication cluster containing adjacent, concomitantly replicating regions with several active origins. Early-replicating clusters usually associate with open chromatin (euchromatin; typically in the centre of the nucleus). Late-replicating clusters (here shown containing origins that have not yet started replication, depicted as dark red circles) associate with silent, transcriptionally inactive chromatin (facultative and constitutive heterochromatin; typically near the nuclear envelope). Highly transcribed chromatin often replicates early during S phase, but replication rarely initiates within actively transcribed regions.
Figure 2
Figure 2. Genetic and epigenetic features of replication origins.
Although there are no strong consensus DNA sequences to anchor origins in metazoans, whole-genome sequence analyses have revealed several motifs that are present near or at origin sites. These include A:T- and G:C-rich motifs, CpG islands (CGIs), origin G-rich repeated elements (OGREs), DNase 1-hypersensitive sites (DNase-HS), quadruplex-like structures (G4) and ubiquitous chromatin-opening elements (UCOEs), which might increase the propensity of origins to unwind and adopt a non-B DNA structure. Groups of replication origins interact with proteins from the pre-replication complex and with proteins located at a subset of replication origins (such as replication-initiation determinant (RepID), DNA-unwinding element-binding protein B (DUEB) and RECQ-like DNA helicase type 4 (RECQL4)). Such interactions may also facilitate binding of transcription factors (TFs) such as forkhead box protein 1 (Fkh1), Fkh2, MYB, homeobox protein A (HOXA), HOXC, HOXD and E2F1) or other proteins that may regulate chromatin structure locally. Origins in early-replicating, open chromatin are preferentially enriched with euchromatin markers (such as H3K4 monomethylation (H3K4me), H3K4 dimethyation (H3K4me2), H3K4 trimethylation (H3K4me3), H3K9 acetylation (H3K9ac), H3K18ac, H3K36me3 and H3K29ac). Cell type-specific, late-replicating origins often associate with heterochromatin markers (such as H3K9me3, H3K27me3 and ORC-associated protein (ORCA), an ORC-binding protein that interacts with H3K9me3).
Figure 3
Figure 3. Long-range chromatin interactions can regulate origin activation and replication timing.
Cell type-specific transcription and/or chromatin-modifier complexes can bind both an origin of replication and a locus control region of a distant gene (dark red rectangle), modulating both the expression of a tissue-specific gene and replication initiation. Origin activation by distal interactions may enable local chromatin remodelling and the establishment of a more open chromatin configuration.
Figure 4
Figure 4. Replication origin choice and origin dormancy.
Constitutive origins (depicted as black oval-shaped outlines) initiate replication at all times in all cells; flexible origins (turquoise circles) initiate replication intermittently with initiation frequencies that vary from cell to cell; and dormant origins (dark red circles) are licensed to initiate replication but never, or very rarely, initiate during an unperturbed cell cycle. Dormant origins can be activated, however, if they reside next to a stalled or damaged replication fork (yellow triangle). a | Top: initiation from both constitutive and flexible origins shown on three hypothetical fibres, with each cell exhibiting a unique pattern of initiation. Experimentally, single-fibre analyses indicate the selection of initiation sites from the pool of flexible origins. Bottom: a population-based assay based on the abundance of nascent strands (nascent strand sequencing (NS-seq)) captures short, newly replicated DNA from all origins. Overall, the mean distances between population-based origin peaks are shorter than those measured on single fibres, indicating origin choice. b | Initiation rates can increase when DNA synthesis slows or when replication forks stall owing to DNA damage. Fast replication is associated with few origins on average because some potential initiation sites are passively replicated by adjacent replication forks before their own replication is actively initiated. Slow replication can increase the frequency of initiation from flexible origins, resulting in shorter inter-origin distances detected on single fibres. In addition, perturbed replication can activate dormant origins that do not normally initiate replication during unperturbed DNA synthesis.
Figure 5
Figure 5. Origin inhibition and activation in unperturbed cells and after replication stress.
a | Only approximately 10% of origins are typically used in an unperturbed cell cycle; most origins remain dormant and are replicated passively by replication forks emanating from adjacent origins. b | Stalled replication forks contain replication protein A (RPA)-coated single-stranded DNA that is sensed by the checkpoint kinase ataxia telangiectasia and RAD3-related protein (ATR), activating a signalling cascade (indicated by the beige star shape) that prevents initiation at late replication origins through checkpoint kinase 1 (CHK1)-mediated inhibition of phosphorylation events catalysed by cyclin-dependent kinases (CDKs) and DBF4-dependent kinase (DDK). Concomitantly, CHK1 activation permits replication initiation from origins (dormant or non-activated flexible origins) located near the stalled forks to complete DNA replication locally.
None
PCNA, proliferating cell nuclear antigen; RFC, replication factor C; tipin, TIMELESS-interacting protein.

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