Eukaryotes duplicate their genomes using multiple replication origins, but the organization of origin firing along chromosomes and during S-phase is not well understood. Using fission yeast, we report the first genome-wide analysis of the spatial and temporal organization of replication origin firing, analyzed using single DNA molecules that can approach the full length of chromosomes. At S-phase onset, origins fire randomly and sparsely throughout the chromosomes. Later in S-phase, clusters of fired origins appear embedded in the sparser regions, which form the basis of nuclear replication foci. The formation of clusters requires proper histone methylation and acetylation, and their locations are not inherited between cell cycles. The rate of origin firing increases gradually, peaking just before mid S-phase. Toward the end of S-phase, nearly all the available origins within the unreplicated regions are fired, contributing to the timely completion of genome replication. We propose that the majority of origins do not fire as a part of a deterministic program. Instead, origin firing, both individually and as clusters, should be viewed as being mostly stochastic.

Mating-type switching in the fission yeast Schizosaccharomyces pombe is initiated by a strand-specific imprint located at the mating-type (mat1) locus. We show that the imprint corresponds to a single-strand DNA break (SSB), which is site-but not sequence-specific. We identified three novel cis-acting elements, involved in the formation and stability of the SSB. One of these elements is essential for a replication fork pause next to mat1 and interacts in vivo with the Swi1 protein. Another element is essential for maintaining the SSB during cell cycle progression. These results suggest that the DNA break appears during the S-phase and is actively protected against repair. Consequently, during the following round of replication, a polar double-strand break is formed. We show that when the replication fork encounters the SSB, the leading-strand DNA polymerase is able to synthesize DNA to the edge of the SSB, creating a blunt-ended recombination intermediate.

A strand-specific imprint (break) controls mating-type switching in fission yeast. By introducing a thiamine repressible promoter upstream of the mat1 locus, we can force transcription through the imprinted region, erasing the imprint and inhibiting further mating-type switching, in a reversible manner. Starting from a synchronized, virgin M-cell population, we show that the site-and strand-specific break is formed when DNA replication intermediates appear at mat1 during the first S phase. The formation of the break is concomitant with a replication fork pause and binding of the Swi1 protein at mat1 until early G 2 and then rapidly disappears. Upon its formation, the break remains stable throughout the cell cycle and triggers mating-type switching during the second S phase. Finally, we have recreated the mating-type switching pedigree at the molecular and single-cell levels, allowing for the first time separation between the establishment of imprinting and its developmental fate.The fission yeast Schizosaccharomyces pombe possesses a remarkable system for changing its mating type (MT) (reviewed in references 4 and 13). Homothallic MT switching in fission yeast, similar to that in budding yeast, is a genetically programmed event in haploid cells initiated by a site-specific lesion at the mat1 locus. This lesion is then repaired by homologous donor sequences, mat2-P and mat3-M, located on the same chromosome. These loci are maintained in a silent chromatin state, preventing their transcription or recombination, but they can serve as donors of genetic information at mat1 by recombination (7,15,25). The MT switching pattern, as determined several years ago by pedigree analyses at the single-cell level, follows two strict rules, as depicted in Fig. 1A (17, 28, 34). The first, termed the one-in-four rule, indicates that two consecutive divisions are necessary to produce one switched cell among four granddaughter cells. The first division produces two cells with identical MTs, but with different switching potentials, termed unswitchable (u) and switchable (s), such that only the s cell produces one switched cell after the second division. The second, termed the consecutive rule, indicates that the sister of this switched cell is able to switch during subsequent cell divisions. The newly switched cell is unswitchable, and will follow the same fate as the unswitchable (Mu or Pu) cells (where M stands for minus and P stands for plus). Therefore, an exponential culture-or well-grown colony contains not two but four cell types, with P or M MT information, and with two switching potentials, u and s, found in equal proportions (1 Pu:1 Mu:1 Ps:1 Ms). Cells from opposite MTs are able to conjugate in G 1 and sporulate when grown under sporulating conditions. The integrity of this pedigree and switching is conveniently verified by staining cells within a colony with iodine vapors, a marker of spore-containing colonies, such that wild-type homothallic cells stain darkly, whereas mutant cells exhibit a streaky or white phenotype (3...

The sexual locus mat1, in the fission yeast Schizosaccharomyces pombe, efficiently switches between the two mating types, P and M, by a process similar to gene conversion, using the silent mat2-P and mat3-M loci, respectively, as donors of the P and M genetic information . It has been proposed that an asymmetrically inherited, site- and strand-specific imprint at mat1 initiates the mating-type switching process . The molecular nature of the imprint is controversial; it was initially described as a double-strand break and then as a single-strand lesion or a strand-specific, alkali-labile modification . Here, we use E. coli DNA ligase in vitro to demonstrate that the imprint is a nick with no resection of nucleotides. By using ligation-mediated PCR, we show that the nick contains 3'OH and 5'OH unphosphorylated termini resistant to RNase treatments. This nonmutational mark on one of the DNA strands provides the first example of a novel type of imprint.

The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we use polymer models to examine the spatial organization of epigenetic marks, euchromatin and heterochromatin, and origins of replication within the Schizosaccharomyces pombe genome. These models incorporate data from microscopy and proximity-ligation experiments that inform on the positions of certain elements and contacts within and between chromosomes. Our results show a striking degree of compartmentalization of epigenetic and genomic features and lead to the proposal of a diffusion based mechanism, centred on the spindle pole body, for the coordination of DNA replication in S. pombe.