Location, location, location: it's all in the timing for replication origins

Abstract

The differential replication timing of eukaryotic replication origins has long been linked with epigenetic regulation of gene expression and more recently with genome stability and mutation rates; however, the mechanism has remained obscure. Recent studies have shed new light by identifying novel factors that determine origin timing in yeasts and mammalian cells and implicate the spatial organization of origins within nuclear territories in the mechanism. These new insights, along with recent findings that several initiation factors are limiting relative to licensed origins, support and shape an emerging model for replication timing control. The mechanisms that control the spatial organization of replication origins have potential impacts for genome regulation beyond replication.

Figure 1.

Yeast replication origins and factors regulating initiation timing. Structure models of origins regulated by Fkh1/2 (A), Taz1-Rif1 (B), or Rif1 (C). The left panels show regulation of Cdc45 recruitment in wild-type cells in G1/early S phase and resulting initiation timing, and the right panels show the effects of deleting indicated genes or protein-binding sites on Cdc45 recruitment and initiation timing. Arrows and blocking arrows regulating Cdc45 recruitment are not implied to act directly. DNA sequence elements and DNA-binding proteins are defined in the key. Rif1 is hypothesized to bind LCS directly or indirectly.

Figure 2.

Preferential recruitment and recycling of limiting initiation factors as a timing mechanism. Recruitment of Cdc45 requires Sld3 and DDK activities, which are not shown. Additional initiation factors and replisome components are also excluded for simplicity.

Figure 3.

Replication timing model based on spatial organization of origins and limiting factor accumulation. Licensed origins are represented by a single MCM hexamer for simplicity. In G1 phase, interactions between Fkh1/2-bound origins create clusters that localize with Cdc45 and likely other limiting factors (not shown), creating a high probability of Cdc45 recruitment (although not all clustered origins are expected to recruit Cdc45 early in every cell). A Cdc45 gradient may form due to cooperative recruitment by clustered origins or another mechanism but remains speculative. CEN localizes proximal origin (1) with Cdc45, perhaps with Rif1 involvement, and/or clustering with other CENs (not shown). At other loci, Rif1 anchors Taz1- and Rif1-bound sites to the nuclear membrane, thereby localizing proximal origins to the nuclear periphery, sequestered from Cdc45 accumulation. Local heterochromatin may also contribute to Cdc45 exclusion from these domains. The cluster of Cdc45-bound origins, likely including origins from other chromosomes (not shown), establishes a replication focus in early S phase comprising these multiple replisomes. Replication draws flanking origins (2) toward the focus, where they access Cdc45, possibly recycled from earlier replisomes, and fire or replicate passively. Eventually, peripheral origins (3) relocate and fire or replicate passively, although in mammalian cells, the replication factors instead relocate to the periphery.