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Gene clusters amplified in the ovarian follicle ceils of Drosophila serve as powerful models for metazoan DNA replication. In response to developmental signals, specific genomic regions undergo amplification by repeated firing of replication origins and bidirectional movement of replication forks for [approximately equal to] 50 kb in each direction. Previous work focused on initiation of amplification, defining replication origins, establishing the role of the prereplication complex and origin recognition complex (ORC), and uncovering regulatory functions for the Myb, E2F1, and Rb transcription factors. Here, we exploit follicle cell amplification to investigate the control of DNA replication fork progression and termination, poorly understood processes in metazoans. We identified a mutant in which, during gene amplification, the replication forks move twice as far from the origin compared with wild type. This phenotype is the result of an amino acid substitution mutation in the cyclinE gene, [cyclinE.sup.1f36]. The rate of oogenesis is normal in [cyclinE.sup.1f36]/[cyclinE.sup.Pz8] mutant ovaries, indicating that increased replication fork progression is due to increased replication fork speed, possibly from increased processivity. The increased amplification domains observed in the mutant imply that there are not replication fork barriers preventing replication forks from progressing beyond the normal 100-kb amplified region. These results reveal a previously unrecognized role for CyclinE in controlling replication fork movement. gene amplification | oogenesis | fork progression

We have combined standard micrococcal nuclease (MNase) digestion of nuclei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including the eviction of nucleosomes. To characterize DNA-binding features of transcription factors, we plotted the length of each fragment versus its position in the genome, which defined the minimal protected region of each factor. This process led to the precise mapping of protected and exposed regions at and around binding sites, and also determination of the degree to which they are flanked by phased nucleosomes and subnucleosome-sized particles. Our protocol and mapping method provide a general strategy for epigenome characterization, including nucleosome phasing and dynamics, ATP-dependent nucleosome remodelers, and transcription factors, from a single-sequenced sample. [ABSTRACT FROM AUTHOR]

The author discusses the genome-wide localization of a key replication initiation factor, origin recognition complex (ORC) and provide insight into genomic features which define distribution of human replication origins. Topics include correlations between chromatin state and DNA replication program; and chromatin immunoprecipitation coupled with genomic microarrays for identification of genomic loci associated with DNA binding factors and comprehensive identification of ORC binding sites.

Highlights a study which examined the impact of the Abf2P protein on the stability of mitochondrial DNA recombination. In-depth look at several high mobility group proteins (HMG); Identification of various HMG proteins in Saccharomyces cerevisiae; Methodology used to conduct the study; Results of the study.