Oscar Aparicio

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Swe1 regulation and transcriptional control restrict the activity of mitotic cyclins toward replication proteins in Saccharomyces cerevisiae
    Fangfang Hu
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    Proc Natl Acad Sci U S A 102:8910-5. 2005
  2. pmc Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics
    A Zachary Ostrow
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 9:e87647. 2014
  3. pmc The level of origin firing inversely affects the rate of replication fork progression
    Yuan Zhong
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
    J Cell Biol 201:373-83. 2013
  4. pmc Location, location, location: it's all in the timing for replication origins
    Oscar M Aparicio
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genes Dev 27:117-28. 2013
  5. pmc Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae
    Weihong Xu
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
    BMC Genomics 7:276. 2006
  6. pmc Strategies for analyzing highly enriched IP-chip datasets
    Simon R V Knott
    Molecular and Computational Biology Program, University of Southern California, Ray Irani Hall, University Park Campus, Los Angeles, CA 90089 2910, USA
    BMC Bioinformatics 10:305. 2009
  7. pmc Tackling an essential problem in functional proteomics of Saccharomyces cerevisiae
    Oscar M Aparicio
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1340, USA
    Genome Biol 4:230. 2003
  8. pmc The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae
    Jennifer G Aparicio
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS172, Los Angeles, CA 90089 1340, USA
    Mol Cell Biol 24:4769-80. 2004
  9. pmc Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae
    Shawn J Szyjka
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genes Dev 22:1906-20. 2008
  10. doi request reprint Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo
    Oscar Aparicio
    University of Southern California, Los Angeles, California, USA
    Curr Protoc Mol Biol . 2005

Collaborators

Detail Information

Publications22

  1. pmc Swe1 regulation and transcriptional control restrict the activity of mitotic cyclins toward replication proteins in Saccharomyces cerevisiae
    Fangfang Hu
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    Proc Natl Acad Sci U S A 102:8910-5. 2005
    ..Hence, Swe1 appears to reinforce the temporal activity of cyclins established through transcriptional control. The conserved nature of CDK function suggests that similar mechanisms regulate CDK specificity in multicellular organisms...
  2. pmc Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics
    A Zachary Ostrow
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 9:e87647. 2014
    ....
  3. pmc The level of origin firing inversely affects the rate of replication fork progression
    Yuan Zhong
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
    J Cell Biol 201:373-83. 2013
    ....
  4. pmc Location, location, location: it's all in the timing for replication origins
    Oscar M Aparicio
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genes Dev 27:117-28. 2013
    ..The mechanisms that control the spatial organization of replication origins have potential impacts for genome regulation beyond replication...
  5. pmc Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae
    Weihong Xu
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
    BMC Genomics 7:276. 2006
    ..However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites...
  6. pmc Strategies for analyzing highly enriched IP-chip datasets
    Simon R V Knott
    Molecular and Computational Biology Program, University of Southern California, Ray Irani Hall, University Park Campus, Los Angeles, CA 90089 2910, USA
    BMC Bioinformatics 10:305. 2009
    ..Array data from the latter studies typically have a high proportion of enriched probes whose signals vary considerably (due to heterogeneity in the cell population), and this makes their normalization and downstream analysis difficult...
  7. pmc Tackling an essential problem in functional proteomics of Saccharomyces cerevisiae
    Oscar M Aparicio
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1340, USA
    Genome Biol 4:230. 2003
    ..A new study has adapted a simple method for creating conditional alleles to allow large-scale analysis of essential genes in Saccharomyces cerevisiae and has identified a role in DNA replication for a newly identified protein complex...
  8. pmc The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae
    Jennifer G Aparicio
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS172, Los Angeles, CA 90089 1340, USA
    Mol Cell Biol 24:4769-80. 2004
    ..This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked...
  9. pmc Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae
    Shawn J Szyjka
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genes Dev 22:1906-20. 2008
    ..We propose a model for regulation of replication fork progression through damaged DNA involving a cycle of Rad53 activation and deactivation that coordinates replication restart with DNA repair...
  10. doi request reprint Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo
    Oscar Aparicio
    University of Southern California, Los Angeles, California, USA
    Curr Protoc Mol Biol . 2005
    ..in this unit describes the ChIP procedure for Saccharomyces cerevisiae; describes the corresponding steps for mammalian cells...
  11. pmc Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae
    Simon R V Knott
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genes Dev 23:1077-90. 2009
    ..Our results also reveal a novel and complementary genomic map of Rpd3L- and Rpd3S-regulated chromosomal loci...
  12. ncbi request reprint ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays
    Christopher J Viggiani
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
    Methods Mol Biol 521:255-78. 2009
    ..We also outline general protocols for data analysis; however, microarray data analyses usually must be tailored specifically for individual studies, depending on experimental design, microarray format, and data quality...
  13. pmc Diminished S-phase cyclin-dependent kinase function elicits vital Rad53-dependent checkpoint responses in Saccharomyces cerevisiae
    Daniel G Gibson
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1340, USA
    Mol Cell Biol 24:10208-22. 2004
    ..Together, our findings indicate that deregulation of S-CDK function has the potential to exacerbate genomic instability by reducing replication origin usage...
  14. ncbi request reprint Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae
    Daniel G Gibson
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 2910, USA
    Genes Cells 11:557-73. 2006
    ..We discuss the potential significance of these overlapping checkpoints and the impact of our findings on previously postulated role(s) of ORCs in other cell cycle functions...
  15. ncbi request reprint New vectors for simplified construction of BrdU-Incorporating strains of Saccharomyces cerevisiae
    Christopher J Viggiani
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089 2910, USA
    Yeast 23:1045-51. 2006
    ..These vectors ease strain construction and maintenance, thereby facilitating routine use of BrdU for analysis in yeast...
  16. ncbi request reprint Mrc1 is required for normal progression of replication forks throughout chromatin in S. cerevisiae
    Shawn J Szyjka
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Mol Cell 19:691-7. 2005
    ..These findings elucidate a central role for Mrc1 in normal replisome function, which is distinct from its role as a checkpoint mediator, but nevertheless critical to genome stability...
  17. pmc Identification of Clb2 residues required for Swe1 regulation of Clb2-Cdc28 in Saccharomyces cerevisiae
    Fangfang Hu
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089 2910, USA
    Genetics 179:863-74. 2008
    ....
  18. doi request reprint Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo
    Oscar Aparicio
    University of Southern California, Los Angeles, California, USA
    Curr Protoc Cell Biol . 2004
    ..This unit describes the ChIP protocol for Saccharomyces cerevisiae; however, it is also applicable to other organisms...
  19. ncbi request reprint To promote and protect: coordinating DNA replication and transcription for genome stability
    Simon R V Knott
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
    Epigenetics 4:362-5. 2009
    ..We also discuss future research directions that should lead to a better understanding of these mechanisms and their significance to faithful genome propagation and cellular differentiation...
  20. ncbi request reprint Functional annotation and network reconstruction through cross-platform integration of microarray data
    Xianghong Jasmine Zhou
    Nat Biotechnol 23:238-43. 2005
    ..Experiments reported in the literature and performed in our lab support a significant number of our predictions...
  21. pmc Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage
    Bryan M O'Neill
    Departments of Chemistry and Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:9290-5. 2007
    ..These findings suggest that Rad53 regulates replication fork restart and initiation of late firing origins independently and that regulation of these processes is mediated by specific Rad53 phosphatases...
  22. pmc H2A.Z functions to regulate progression through the cell cycle
    Namrita Dhillon
    Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, National Institutes of Health, Bldg 18T, Rm 106, 18 Library Dr, Bethesda, Maryland 20892, USA
    Mol Cell Biol 26:489-501. 2006
    ..We also found that H2A.Z localized to the promoters of cyclin genes, and cells lacking H2A.Z were delayed in the induction of these cyclin genes. Several different models are proposed to explain these observations...

Research Grants9

  1. Chromatin and Cell Cycle Regulation of ORC Function
    Oscar Aparicio; Fiscal Year: 2003
    ..abstract_text> ..
  2. Chromatin and Cell Cycle Regulation of ORC Function
    Oscar Aparicio; Fiscal Year: 2004
    ..abstract_text> ..
  3. Chromatin and Cell Cycle Regulation of ORC Function
    Oscar Aparicio; Fiscal Year: 2005
    ..abstract_text> ..
  4. Chromatin and Cell Cycle Regulation of ORC Function
    Oscar Aparicio; Fiscal Year: 2006
    ..abstract_text> ..
  5. Chromatin and Cell Cycle Regulation of ORC Function
    Oscar Aparicio; Fiscal Year: 2007
    ..abstract_text> ..
  6. Analysis of replication fork restart and checkpoint regulation after DNA damage
    Oscar Aparicio; Fiscal Year: 2009
    ..These checkpoint and DNA repair mechanisms are critical to the prevention of genome instabilities that can lead to the development of cancers and other genetic disorders. ..
  7. Analysis of replication fork restart and checkpoint regulation after DNA damage
    Oscar M Aparicio; Fiscal Year: 2010
    ..These checkpoint and DNA repair mechanisms are critical to the prevention of genome instabilities that can lead to the development of cancers and other genetic disorders. ..
  8. Analysis of replication fork restart and checkpoint regulation after DNA damage
    Oscar Aparicio; Fiscal Year: 2009
    ..These checkpoint and DNA repair mechanisms are critical to the prevention of genome instabilities that can lead to the development of cancers and other genetic disorders. ..