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  • 1
    Publication Date: 2012-01-18
    Description: shRNAs can trigger effective silencing of gene expression in mammalian cells, thereby providing powerful tools for genetic studies, as well as potential therapeutic strategies. Specific shRNAs can interfere with the replication of pathogenic viruses and are currently being tested as antiviral therapies in clinical trials. However, this effort is hindered by our inability to systematically and accurately identify potent shRNAs for viral genomes. Here we apply a recently developed highly parallel sensor assay to identify potent shRNAs for HIV, hepatitis C virus (HCV), and influenza. We observe known and previously unknown sequence features that dictate shRNAs efficiency. Validation using HIV and HCV cell culture models demonstrates very high potency of the top-scoring shRNAs. Comparing our data with the secondary structure of HIV shows that shRNA efficacy is strongly affected by the secondary structure at the target RNA site. Artificially introducing secondary structure to the target site markedly reduces shRNA silencing. In addition, we observe that HCV has distinct sequence features that bias HCV-targeting shRNAs toward lower efficacy. Our results facilitate further development of shRNA based antiviral therapies and improve our understanding and ability to predict efficient shRNAs.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, John H -- Elledge, Stephen J -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1822-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; BRCA1 Protein/metabolism ; BRCA2 Protein/*chemistry/*metabolism ; Binding Sites ; Breast Neoplasms/genetics ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Damage ; *DNA Repair ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Humans ; Mice ; Ovarian Neoplasms/genetics ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rad51 Recombinase ; Rats ; Recombination, Genetic ; Replication Protein A
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 1999-11-05
    Description: The Brca1 (breast cancer gene 1) tumor suppressor protein is phosphorylated in response to DNA damage. Results from this study indicate that the checkpoint protein kinase ATM (mutated in ataxia telangiectasia) was required for phosphorylation of Brca1 in response to ionizing radiation. ATM resides in a complex with Brca1 and phosphorylated Brca1 in vivo and in vitro in a region that contains clusters of serine-glutamine residues. Phosphorylation of this domain appears to be functionally important because a mutated Brca1 protein lacking two phosphorylation sites failed to rescue the radiation hypersensitivity of a Brca1-deficient cell line. Thus, phosphorylation of Brca1 by the checkpoint kinase ATM may be critical for proper responses to DNA double-strand breaks and may provide a molecular explanation for the role of ATM in breast cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cortez, D -- Wang, Y -- Qin, J -- Elledge, S J -- GM44664/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 5;286(5442):1162-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Mars McLean Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10550055" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ataxia Telangiectasia/genetics ; Ataxia Telangiectasia Mutated Proteins ; BRCA1 Protein/*metabolism ; Breast Neoplasms/genetics ; Cell Cycle Proteins ; Cell Line ; *DNA Damage ; *DNA Repair ; DNA, Complementary ; DNA-Binding Proteins ; Female ; Gamma Rays ; Genes, BRCA1 ; Genetic Predisposition to Disease ; HeLa Cells ; Heterozygote ; Humans ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Tumor Suppressor Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2001-09-05
    Description: Cyclin E binds and activates the cyclin-dependent kinase Cdk2 and catalyzes the transition from the G1 phase to the S phase of the cell cycle. The amount of cyclin E protein present in the cell is tightly controlled by ubiquitin-mediated proteolysis. Here we identify the ubiquitin ligase responsible for cyclin E ubiquitination as SCFFbw7 and demonstrate that it is functionally conserved in yeast, flies, and mammals. Fbw7 associates specifically with phosphorylated cyclin E, and SCFFbw7 catalyzes cyclin E ubiquitination in vitro. Depletion of Fbw7 leads to accumulation and stabilization of cyclin E in vivo in human and Drosophila melanogaster cells. Multiple F-box proteins contribute to cyclin E stability in yeast, suggesting an overlap in SCF E3 ligase specificity that allows combinatorial control of cyclin E degradation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koepp, D M -- Schaefer, L K -- Ye, X -- Keyomarsi, K -- Chu, C -- Harper, J W -- Elledge, S J -- R01 AG011085/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):173-7. Epub 2001 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11533444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Breast Neoplasms/genetics/metabolism ; *CDC2-CDC28 Kinases ; *Cell Cycle ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cyclin E/*metabolism ; Cyclin-Dependent Kinase 2 ; Cyclin-Dependent Kinases/metabolism ; Drosophila Proteins ; Drosophila melanogaster ; *F-Box Proteins ; Humans ; Mice ; Molecular Sequence Data ; Peptide Synthases/chemistry/genetics/*metabolism ; Phosphorylation ; Protein-Serine-Threonine Kinases/metabolism ; RNA, Double-Stranded ; Recombinant Fusion Proteins/metabolism ; SKP Cullin F-Box Protein Ligases ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Transfection ; Tumor Cells, Cultured ; *Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 1999-04-24
    Description: Control of cyclin levels is critical for proper cell cycle regulation. In yeast, the stability of the G1 cyclin Cln1 is controlled by phosphorylation-dependent ubiquitination. Here it is shown that this reaction can be reconstituted in vitro with an SCF E3 ubiquitin ligase complex. Phosphorylated Cln1 was ubiquitinated by SCF (Skp1-Cdc53-F-box protein) complexes containing the F-box protein Grr1, Rbx1, and the E2 Cdc34. Rbx1 promotes association of Cdc34 with Cdc53 and stimulates Cdc34 auto-ubiquitination in the context of Cdc53 or SCF complexes. Rbx1, which is also a component of the von Hippel-Lindau tumor suppressor complex, may define a previously unrecognized class of E3-associated proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Skowyra, D -- Koepp, D M -- Kamura, T -- Conrad, M N -- Conaway, R C -- Conaway, J W -- Elledge, S J -- Harper, J W -- AG11085/AG/NIA NIH HHS/ -- GM41628/GM/NIGMS NIH HHS/ -- GM54137/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 23;284(5414):662-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs McLean Department of Biochemistry, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10213692" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anaphase-Promoting Complex-Cyclosome ; Animals ; Carrier Proteins/chemistry/*metabolism ; Cell Cycle Proteins/metabolism ; Cell Line ; *Cullin Proteins ; Cyclins/*metabolism ; F-Box Proteins ; Fungal Proteins/*metabolism ; Ligases/metabolism ; Molecular Sequence Data ; Peptide Synthases/*metabolism ; Phosphorylation ; Recombinant Fusion Proteins/metabolism ; S-Phase Kinase-Associated Proteins ; SKP Cullin F-Box Protein Ligases ; Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Ubiquitin-Conjugating Enzymes ; *Ubiquitin-Protein Ligase Complexes ; Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 1999-04-24
    Description: The von Hippel-Lindau (VHL) tumor suppressor gene is mutated in most human kidney cancers. The VHL protein is part of a complex that includes Elongin B, Elongin C, and Cullin-2, proteins associated with transcriptional elongation and ubiquitination. Here it is shown that the endogenous VHL complex in rat liver also includes Rbx1, an evolutionarily conserved protein that contains a RING-H2 fingerlike motif and that interacts with Cullins. The yeast homolog of Rbx1 is a subunit and potent activator of the Cdc53-containing SCFCdc4 ubiquitin ligase required for ubiquitination of the cyclin-dependent kinase inhibitor Sic1 and for the G1 to S cell cycle transition. These findings provide a further link between VHL and the cellular ubiquitination machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kamura, T -- Koepp, D M -- Conrad, M N -- Skowyra, D -- Moreland, R J -- Iliopoulos, O -- Lane, W S -- Kaelin, W G Jr -- Elledge, S J -- Conaway, R C -- Harper, J W -- Conaway, J W -- AG-11085/AG/NIA NIH HHS/ -- GM41628/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 23;284(5414):657-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10213691" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Cycle ; Cell Cycle Proteins/metabolism ; Cell Line ; *Cullin Proteins ; Cyclin-Dependent Kinase Inhibitor Proteins ; *F-Box Proteins ; Fungal Proteins/metabolism ; *Ligases ; Liver ; Male ; Molecular Sequence Data ; Peptide Synthases/*metabolism ; Proteins/*metabolism ; Rats ; Rats, Sprague-Dawley ; Recombinant Fusion Proteins/metabolism ; S-Phase Kinase-Associated Proteins ; SKP Cullin F-Box Protein Ligases ; Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Transcription Factors/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism ; Von Hippel-Lindau Tumor Suppressor Protein
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2001-11-27
    Description: The checkpoint kinases ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3 related) transduce genomic stress signals to halt cell cycle progression and promote DNA repair. We report the identification of an ATR-interacting protein (ATRIP) that is phosphorylated by ATR, regulates ATR expression, and is an essential component of the DNA damage checkpoint pathway. ATR and ATRIP both localize to intranuclear foci after DNA damage or inhibition of replication. Deletion of ATR mediated by the Cre recombinase caused the loss of ATR and ATRIP expression, loss of DNA damage checkpoint responses, and cell death. Therefore, ATR is essential for the viability of human somatic cells. Small interfering RNA directed against ATRIP caused the loss of both ATRIP and ATR expression and the loss of checkpoint responses to DNA damage. Thus, ATRIP and ATR are mutually dependent partners in cell cycle checkpoint signaling pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cortez, D -- Guntuku, S -- Qin, J -- Elledge, S J -- New York, N.Y. -- Science. 2001 Nov 23;294(5547):1713-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Mars McLean Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11721054" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Animals ; Ataxia Telangiectasia Mutated Proteins ; *Cell Cycle ; *Cell Cycle Proteins ; Cell Death ; Cell Line ; Cell Survival ; Conserved Sequence ; DNA Damage ; DNA-Binding Proteins ; *Exodeoxyribonucleases ; Exons/genetics ; Gene Deletion ; Genes, Essential/genetics ; HeLa Cells ; Humans ; Integrases/genetics/metabolism ; Molecular Sequence Data ; Molecular Weight ; Phosphoproteins/genetics/*metabolism ; Phosphorylation ; Precipitin Tests ; Protein Binding ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Sequence Alignment ; *Signal Transduction ; Viral Proteins/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 1999-11-05
    Description: In response to DNA damage, cells activate checkpoint pathways that prevent cell cycle progression. In fission yeast and mammals, mitotic arrest in response to DNA damage requires inhibitory Cdk phosphorylation regulated by Chk1. This study indicates that Chk1 is required for function of the DNA damage checkpoint in Saccharomyces cerevisiae but acts through a distinct mechanism maintaining the abundance of Pds1, an anaphase inhibitor. Unlike other checkpoint mutants, chk1 mutants were only mildly sensitive to DNA damage, indicating that checkpoint functions besides cell cycle arrest influence damage sensitivity. Another kinase, Rad53, was required to both maintain active cyclin-dependent kinase 1, Cdk1(Cdc28), and prevent anaphase entry after checkpoint activation. Evidence suggests that Rad53 exerts its role in checkpoint control through regulation of the Polo kinase Cdc5. These results support a model in which Chk1 and Rad53 function in parallel through Pds1 and Cdc5, respectively, to prevent anaphase entry and mitotic exit after DNA damage. This model provides a possible explanation for the role of Cdc5 in DNA damage checkpoint adaptation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Y -- Bachant, J -- Wang, H -- Hu, F -- Liu, D -- Tetzlaff, M -- Elledge, S J -- GM44664/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 5;286(5442):1166-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10550056" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase ; Anaphase-Promoting Complex-Cyclosome ; CDC2 Protein Kinase/metabolism ; Cell Cycle Proteins/genetics/metabolism ; Checkpoint Kinase 2 ; Cyclin B/genetics/metabolism ; *DNA Damage ; DNA, Fungal/metabolism ; Fungal Proteins/genetics/metabolism ; Intracellular Signaling Peptides and Proteins ; Ligases/metabolism ; *Mitosis ; Mutation ; Nuclear Proteins/metabolism ; Phosphorylation ; Protein Kinases/genetics/*metabolism ; *Protein-Serine-Threonine Kinases ; RNA-Binding Proteins ; Recombinant Fusion Proteins/metabolism ; S Phase ; Saccharomyces cerevisiae/*cytology/*enzymology/genetics ; *Saccharomyces cerevisiae Proteins ; Securin ; *Ubiquitin-Protein Ligase Complexes ; Ubiquitin-Protein Ligases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2000-03-10
    Description: Chk2 is a protein kinase that is activated in response to DNA damage and may regulate cell cycle arrest. We generated Chk2-deficient mouse cells by gene targeting. Chk2-/- embryonic stem cells failed to maintain gamma-irradiation-induced arrest in the G2 phase of the cell cycle. Chk2-/- thymocytes were resistant to DNA damage-induced apoptosis. Chk2-/- cells were defective for p53 stabilization and for induction of p53-dependent transcripts such as p21 in response to gamma irradiation. Reintroduction of the Chk2 gene restored p53-dependent transcription in response to gamma irradiation. Chk2 directly phosphorylated p53 on serine 20, which is known to interfere with Mdm2 binding. This provides a mechanism for increased stability of p53 by prevention of ubiquitination in response to DNA damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hirao, A -- Kong, Y Y -- Matsuoka, S -- Wakeham, A -- Ruland, J -- Yoshida, H -- Liu, D -- Elledge, S J -- Mak, T W -- GM44664/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 10;287(5459):1824-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Amgen Institute, Ontario Cancer Institute, and Departments of Medical Biophysics and Immunology, University of Toronto, 620 University Avenue, Suite 706, Toronto, Ontario, M5G 2C1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10710310" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins ; Checkpoint Kinase 2 ; *DNA Damage ; DNA-Binding Proteins ; G1 Phase ; G2 Phase ; Gamma Rays ; Gene Expression Regulation ; Gene Targeting ; Genes, Tumor Suppressor ; Genes, p53 ; Humans ; *Interphase ; Mice ; *Nuclear Proteins ; Phosphorylation ; Phosphoserine/metabolism ; *Protein Kinases ; Protein-Serine-Threonine Kinases/*metabolism ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Stem Cells/cytology/metabolism ; T-Lymphocytes/cytology ; Transcription, Genetic ; Tumor Suppressor Protein p53/*metabolism ; Tumor Suppressor Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2002-10-05
    Description: 53BP1 binds to the tumor suppressor protein p53 and has a potential role in DNA damage responses. We used small interfering RNA (siRNA) directed against 53BP1 in mammalian cells to demonstrate that 53BP1 is a key transducer of the DNA damage checkpoint signal. 53BP1 was required for p53 accumulation, G2-M checkpoint arrest, and the intra-S-phase checkpoint in response to ionizing radiation. 53BP1 played a partially redundant role in phosphorylation of the downstream checkpoint effector proteins Brca1 and Chk2 but was required for the formation of Brca1 foci in a hierarchical branched pathway for the recruitment of repair and signaling proteins to sites of DNA damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Bin -- Matsuoka, Shuhei -- Carpenter, Phillip B -- Elledge, Stephen J -- New York, N.Y. -- Science. 2002 Nov 15;298(5597):1435-8. Epub 2002 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Mars McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364621" target="_blank"〉PubMed〈/a〉
    Keywords: BRCA1 Protein/metabolism ; Carrier Proteins/genetics/*metabolism ; Cell Cycle Proteins/metabolism ; Checkpoint Kinase 2 ; DNA/biosynthesis ; *DNA Damage ; *G2 Phase ; Histones/metabolism ; Humans ; *Intracellular Signaling Peptides and Proteins ; *Mitosis ; Nuclear Proteins/metabolism ; *Phosphoproteins ; Phosphorylation ; Protein Kinases/metabolism ; *Protein-Serine-Threonine Kinases ; RNA, Small Interfering ; Radiation, Ionizing ; *S Phase ; Signal Transduction ; Tumor Suppressor Protein p53/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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