Replication timing and transcriptional control: beyond cause and effect--part II

Abstract

Replication timing is frequently discussed superficially in terms of its relationship to transcriptional activity via chromatin structure. However, so little is known about what regulates where and when replication initiates that it has been impossible to identify mechanistic and causal relationships. Moreover, much of our knowledge base has been anecdotal, derived from analyses of a few genes in unrelated cell lines. Recent studies have revisited long-standing hypotheses using genome-wide approaches. In particular, the foundation of this field was recently shored up with incontrovertible evidence that cellular differentiation is accompanied by coordinated changes in replication timing and transcription. These changes accompany subnuclear repositioning, and take place at the level of megabase-sized domains that transcend localized changes in chromatin structure or transcription. Inferring from these results, we propose that there exists a key transition during the middle of S-phase and that changes in replication timing traversing this period are associated with subnuclear repositioning and changes in the activity of certain classes of promoters.

Figure 1. Relationship between isochore properties and replication timing regulation, subnuclear position, and transcription

(a) Isochores with unusual sequence properties are subject to replication timing regulation. The mammalian genome is partitioned into isochores with different GC content and gene density. Isochores that are high in both [(GC%, gene density)=(High, High)] are replicated early in S-phase, while those that are low in both [(GC%, gene density)=(Low, Low)] are replicated late in S-phase. Exceptional isochores in which the two properties are inversely related [(GC%, gene density)=(Mid, Low) or (Low, Mid)] are frequently subject to replication timing regulation during mouse ESC differentiation (speculatively labeled “Facultative Heterochromatin”) [8]. During neural differentiation of mouse ESCs, the former [(GC%, gene density)=(Mid, Low)] tend to change from late to early replication, while the latter [(GC%, gene density)=(Low, Mid)] show an opposite directionality. (b) Changes in replication timing that traverse the middle of S-phase accompany changes in subnuclear position and transcriptional potential. Replication early in S-phase (patterns I and II) takes place within the interior euchromatic compartment, while replication later in S-phase (patterns III, IV, and V) takes place at the nuclear periphery (pattern III), the nucleolar periphery (pattern III), and at internal blocks of heterochromatin (patterns IV and V) [19,57]. Note the dramatic transition from “euchromatic” to “heterochromatic” replication pattern during mid S-phase (from pattern II to III). In addition, a strong relationship between replication timing and transcription is observed for genes that replicate during mid to late stages of S-phase (“Strong Correlation”) [8]. In contrast, genes that are replicated in the first third of S-phase have equally high probability of being expressed (“No correlation”) and thus even large changes within this period may not accompany changes in subnuclear position or transcriptional competence. The figure illustrates how the durations of different spatial replication patterns (dotted lines) may relate to the probability of transcription [8,12]. These relationships imply that genome-wide replication timing analyses provide a means to infer changes in subnuclear position and transcriptional potential [8]. Photos are deconvolved images from Chinese hamster cells pulse-labeled with BrdU at different times during S-phase (J.L. and D.M.G., unpublished).