A revisionist replicon model for higher eukaryotic genomes

Abstract

Summary The replicon model devised to explain replication control in bacteria has served as the guiding paradigm in the search for origins of replication in the more complex genomes of eukaryotes. In S. cerevisiae, this model has proved to be extremely useful, leading to the identification of specific genetic elements (replicators) and the interacting initiator proteins that activate them. However, replication control in organisms ranging from S. pombe to mammals is far more fluid: only a small number of origins seem to represent classic replicators, while the majority correspond to zones of inefficient, closely-spaced start sites none of which are indispensable for origin activity. In addition, it is apparent that the epigenetic state of a given sequence largely determines its ability to be used as a replication initiation site. These conclusions were arrived at over a period of three decades, and required the development of several novel replicon mapping techniques, as well as new ways of examining the chromatin architecture of any sequence of interest. Recently, methods have been elaborated for isolating all of the active origins in the genomes of higher eukaryotes en masse. Microarray analyses and more recent high-throughput sequencing technology will allow all the origins to be mapped onto the chromosomes of any organism whose genome has been sequenced. With the advent of whole-genome studies on gene expression and chromatin composition, the field is now positioned to define both the genetic and epigenetic rules that govern origin activity.

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

“…Fragment numbers range from two to 11 in log-phase HeLa cells, with zonal lengths from 3.1 to 84.6 kb (mean of ;18.1 kb). These findings are consistent with results for most of the origins that have been studied on an individual basis (;2-55 kb in length; for review, see Hamlin et al 2008). Interestingly, the signal strengths of clustered fragments are higher on average than those from isolated fragments.…”

“…Of the few dozen mammalian origins that have been identified by molecular biological approaches, most fire in early S-phase, in many cases because they were identified as early replicating segments in synchronized cells (for review, see Aladjem et al 2006;Hamlin et al 2008). To determine the extent to which these origins are representative, we compared origin distributions between the early S-phase and log-phase HeLa libraries in the ENCODE regions.…”

“…Several origin mapping methods have been developed, most of which rely on prior characterization of the locus in question (usually because of prior interest in the local gene), and each is extremely challenging when applied to mammalian cells. In fact, only a few dozen potential origins have been localized so far, and then often by only one approach (for review, see Aladjem et al 2006;Hamlin et al 2008). A few of these (e.g., human lamin B2 [Abdurashidova et al 2000] and DBF4 [Romero and Lee 2008]) appear to correspond to very fixed initiation sites analogous to yeast ARS elements, while the majority represent zones of closely spaced inefficient sites ranging from ;2 kb to >55 kb in length (for review, see Aladjem and Fanning 2004;Gilbert 2005;Hamlin et al 2008).…”

Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment

“…Gene expression data obtained early with the RNA-Seq technique (Mortazavi et al 2008; The ENCODE Project Consortium 2011) have been intensively used to address the question of the role of epigenetic modifications in transcription regulation and genome activity during development and differentiation or in response to the environment (Zhou et al 2011). In contrast, progress in elucidating the chromatin-mediated control of replication origin usage and efficiency as well as of the maintenance of the spatio-temporal replication program in higher eukaryotes has been rather slow (Berezney et al 2000;Bogan et al 2000;Gilbert 2001Gilbert , 2010Méchali 2001Méchali , 2010Bell & Dutta 2002;McNairn & Gilbert 2003;Aladjem 2007;Courbet et al 2008;Hamlin et al 2008). Only very recently nascent DNA strands synthesized at origins were purified by various methods to map replication origins genome-wide in mouse (Sequeira-Mendes et al 2009;Cayrou et al 2011) and human (Lucas et al 2007;Cadoret et al 2008;Karnani et al 2010;Martin et al 2011;Mesner et al 2011;Valenzuela et al 2011).…”

Replication Origin Selection and Pre-Replication Complex Assembly

“…to-cell heterogeneity in origin selection (Hamlin et al, 2008). Recent development of genome-scale methods for identifying hundreds or thousands of new origins may compensate for this lack of data and thus provide information regarding the recognition features of complex origins (Eaton et al, 2010;MacAlpin et al, 2010).…”