Fox, C. A. & McConnell, K. H. Toward biochemical understanding of a transcriptionally silenced chromosomal domain in Saccharomyces cerevisiae. J. Biol. Chem. 280, 8629-8632

Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States
Journal of Biological Chemistry (Impact Factor: 4.57). 04/2005; 280(10):8629-32. DOI: 10.1074/jbc.R400033200
Source: PubMed

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    • "Transcriptional silencing at these loci relies on cisregulatory DNA elements called silencers and on a number of trans -acting gene products. Previous studies revealed that establishment of silencing involves a series of protein–DNA and protein–protein interactions (reviewed in Gasser and Cockell 2001; Rusche et al. 2003; Fox and Mcconnell 2005). The silencer elements flanking the HM loci recruit the DNA binding proteins "
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    ABSTRACT: In Saccharomyces cerevisiae, the two cryptic mating type loci, HML and HMR, are transcriptionally silent. Previous studies on the establishment of silencing at HMR identified a requirement for passage through S phase. However, the underlying mechanism for this requirement is still unknown. In contrast to HMR, we found that substantial silencing of HML could be established without passage through S phase. To understand this difference, we analyzed several chimeric HM loci and found that promoter strength determined the S phase requirement. To silence a locus with a strong promoter such as the a1/a2 promoter required passage through S phase while HM loci with weaker promoters such as the α1/α2 or TRP1 promoter did not show this requirement. Thus, transcriptional activity counteracts the establishment of silencing but can be overcome by passage through S phase.
    Full-text · Article · Oct 2010 · Genetics
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    • "The previously established role for the Saccharomyces cerevisiae Orc1BAH domain is to function in the process of transcriptional silencing via a direct physical interaction with the nonessential silencing protein Sir1 (Fox and McConnell 2005). Yeast cells lacking the Orc1BAH domain show no viability defects, and orc1bahD and sir1D mutations produce the same transcriptional silencing phenotypes alone and in combination, supporting the notion that the Orc1BAH domain of yeast functions in transcriptional silencing but not the essential process of DNA replication. "
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    ABSTRACT: The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan ORC shows no obvious DNA sequence specificity, whereas yeast ORC binds to a specific DNA sequence within all yeast origins. Thus, whereas chromatin must play an important role in metazoan ORC's ability to recognize origins, it is unclear whether chromatin plays a role in yeast ORC's recognition of origins. This study focused on the role of the conserved N-terminal bromo-adjacent homology domain of yeast Orc1 (Orc1BAH). Recent studies indicate that BAH domains are chromatin-binding modules. We show that the Orc1BAH domain was necessary for ORC's stable association with yeast chromosomes, and was physiologically relevant to DNA replication in vivo. This replication role was separable from the Orc1BAH domain's previously defined role in transcriptional silencing. Genome-wide analyses of ORC binding in ORC1 and orc1bahDelta cells revealed that the Orc1BAH domain contributed to ORC's association with most yeast origins, including a class of origins highly dependent on the Orc1BAH domain for ORC association (orc1bahDelta-sensitive origins). Orc1bahDelta-sensitive origins required the Orc1BAH domain for normal activity on chromosomes and plasmids, and were associated with a distinct local nucleosome structure. These data provide molecular insights into how the Orc1BAH domain contributes to ORC's selection of replication origins, as well as new tools for examining conserved mechanisms governing ORC's selection of origins within eukaryotic chromosomes.
    Full-text · Article · Jul 2010 · Genes & development
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    • "These two regions are found at both ends of chromosome III at a distance of about 280 kb. A nucleosome free region of each of these two sites is associated with a specific multiprotein complex (50). In spite of their distance in the chromosome, they may pair and form a loop (51). "
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    ABSTRACT: The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9–14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis.
    Full-text · Article · Dec 2009 · Nucleic Acids Research
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