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Krol K, Jendrysek J, Debski J, Skoneczny M, Kurlandzka A, Kaminska J, Dadlez M, Skoneczna A. Ribosomal DNA status inferred from DNA cloud assays and mass spectrometry identification of agarose-squeezed proteins interacting with chromatin (ASPIC-MS). Oncotarget 2018; 8:24988-25004. [PMID: 28212567 PMCID: PMC5421904 DOI: 10.18632/oncotarget.15332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/23/2017] [Indexed: 11/25/2022] Open
Abstract
Ribosomal RNA-encoding genes (rDNA) are the most abundant genes in eukaryotic genomes. To meet the high demand for rRNA, rDNA genes are present in multiple tandem repeats clustered on a single or several chromosomes and are vastly transcribed. To facilitate intensive transcription and prevent rDNA destabilization, the rDNA-encoding portion of the chromosome is confined in the nucleolus. However, the rDNA region is susceptible to recombination and DNA damage, accumulating mutations, rearrangements and atypical DNA structures. Various sophisticated techniques have been applied to detect these abnormalities. Here, we present a simple method for the evaluation of the activity and integrity of an rDNA region called a “DNA cloud assay”. We verified the efficacy of this method using yeast mutants lacking genes important for nucleolus function and maintenance (RAD52, SGS1, RRM3, PIF1, FOB1 and RPA12). The DNA cloud assay permits the evaluation of nucleolus status and is compatible with downstream analyses, such as the chromosome comet assay to identify DNA structures present in the cloud and mass spectrometry of agarose squeezed proteins (ASPIC-MS) to detect nucleolar DNA-bound proteins, including Las17, the homolog of human Wiskott-Aldrich Syndrome Protein (WASP).
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Affiliation(s)
- Kamil Krol
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Warsaw, 02-106, Poland
| | - Justyna Jendrysek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Warsaw, 02-106, Poland
| | - Janusz Debski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Mass Spectrometry Laboratory, Warsaw, 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Warsaw, 02-106, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Warsaw, 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Warsaw, 02-106, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Mass Spectrometry Laboratory, Warsaw, 02-106, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of Mutagenesis and DNA Repair, Warsaw, 02-106, Poland
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Takahashi T, Nozawa M, Hara S, Mizoguchi H. High fidelity segregation of a YEp vector in [cir0] strains of the yeast Saccharomyces cerevisiae. J Biosci Bioeng 2005; 96:413-20. [PMID: 16233549 DOI: 10.1016/s1389-1723(03)70125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Accepted: 07/24/2003] [Indexed: 11/23/2022]
Abstract
YEp vectors carrying the GPD promoter and PGK terminator for constitutive expression showed high partition efficiencies specifically in [cir(0)] strains, when DNA fragments were inserted into the cloning site. These plasmids appeared to be more stable than yeast centromeric plasmids, being lost in less than 10(-2) cells after each generation, and more than 90% of the cells carried the plasmids after 20 generations of growth in the absence of selective pressure. The REP3 region was essential together with the GPD promoter and PGK terminator for plasmid equipartitioning in [cir0] strains. The present results suggest that this host-vector system would be useful for astute observation of the phenotype caused by gene overexpression, and for heterogeneous protein production using natural medium, because of efficient partitioning of the plasmid without selective pressure.
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Affiliation(s)
- Toshinari Takahashi
- General Research Laboratory, Kiku-Masamune Sake Brewing Co., Ltd., 1-8-6 Uozaki-nishimachi, Higashinada-ku, Kobe 658-0026, Japan
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Current Awareness. Yeast 2001. [DOI: 10.1002/yea.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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