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  1. Article ; Online: Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.

    Riley, Kasandra J-L / Rabinowitz, Gabrielle S / Steitz, Joan A

    Journal of virology

    2010  Volume 84, Issue 10, Page(s) 5148–5157

    Abstract: Rhesus lymphocryptovirus (rLCV) and Epstein-Barr virus (EBV) are closely related gammaherpesviruses that infect and cause disease in rhesus monkeys and humans, respectively. Thus, rLCV is an important model system for EBV pathogenesis. Both rLCV and EBV ... ...

    Abstract Rhesus lymphocryptovirus (rLCV) and Epstein-Barr virus (EBV) are closely related gammaherpesviruses that infect and cause disease in rhesus monkeys and humans, respectively. Thus, rLCV is an important model system for EBV pathogenesis. Both rLCV and EBV express microRNAs (miRNAs), several conserved in sequence and genomic location. We have applied deep sequencing technology to obtain an inventory of rLCV miRNA expression in latently rLCV-infected monkey B cells. Our data confirm the presence of all previously identified mature rLCV miRNAs and have resulted in the discovery of 21 new mature miRNAs arising from previously identified precursor miRNAs (pre-miRNAs), as well as two novel pre-miRNAs (rL1-34 and rL1-35) that together generate four new mature miRNAs. Thus, the total number of rLCV-encoded pre-miRNAs is 35 and the total number of rLCV mature miRNAs is 68, the most of any virus examined. The exact 5' and 3' ends of all mature rLCV miRNAs were pinpointed, many showing marked sequence and length heterogeneity that could modulate function. We further demonstrate that rLCV mature miRNAs associate with Argonaute proteins in rLCV-infected B cells.
    MeSH term(s) Animals ; B-Lymphocytes/virology ; Cells, Cultured ; Gene Expression Profiling ; Lymphocryptovirus/physiology ; Macaca mulatta ; MicroRNAs/biosynthesis ; RNA, Viral/biosynthesis
    Chemical Substances MicroRNAs ; RNA, Viral
    Language English
    Publishing date 2010-03-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.00110-10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Analysis of p53-RNA interactions in cultured human cells.

    Riley, Kasandra J-L / James Maher, L

    Biochemical and biophysical research communications

    2007  Volume 363, Issue 2, Page(s) 381–387

    Abstract: Tumor suppressor p53 is a well-characterized transcription factor that binds DNA. More enigmatic are the RNA-binding properties of p53 and their physiological relevance. We used three sensitive co-immunoprecipitation methods in an attempt to detect RNAs ... ...

    Abstract Tumor suppressor p53 is a well-characterized transcription factor that binds DNA. More enigmatic are the RNA-binding properties of p53 and their physiological relevance. We used three sensitive co-immunoprecipitation methods in an attempt to detect RNAs that tightly associate with p53 in cultured human cells. Although recombinant p53 protein binds RNA in a sequence-nonspecific mode, we do not detect specific in vivo RNA binding by p53. These results suggest that RNA binding is prevented by post-translational p53 modifications. A ribonucleoprotein (not p53) is purified by multiple IgG monoclonal antibodies (including anti-p53 antibodies) from both p53 +/+ and p53 null cells. Caution is therefore required in interpreting RNA co-immunoprecipitation experiments. Though not formally excluded, these results do not support models in which p53 binds specific RNA partners in vivo.
    MeSH term(s) Binding Sites ; Breast Neoplasms ; Cell Line, Tumor ; Humans ; Protein Binding ; RNA/metabolism ; RNA-Binding Proteins/metabolism ; Tumor Suppressor Protein p53/metabolism
    Chemical Substances RNA-Binding Proteins ; Tumor Suppressor Protein p53 ; RNA (63231-63-0)
    Language English
    Publishing date 2007-11-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 205723-2
    ISSN 0006-291X ; 0006-291X
    ISSN (online) 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2007.08.181
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: p53 RNA interactions: new clues in an old mystery.

    Riley, Kasandra J-L / Maher, L James

    RNA (New York, N.Y.)

    2007  Volume 13, Issue 11, Page(s) 1825–1833

    Abstract: The p53 tumor suppressor protein is typically considered to be a sequence-specific DNA-binding transcription factor. However, reports over the last 15 years have described RNA binding by p53 in a variety of contexts, suggesting the possibility of new p53 ...

    Abstract The p53 tumor suppressor protein is typically considered to be a sequence-specific DNA-binding transcription factor. However, reports over the last 15 years have described RNA binding by p53 in a variety of contexts, suggesting the possibility of new p53 functions. It is clear that p53-RNA interactions are mediated by a nucleic acid-binding domain of p53 independent of the sequence-specific core domain responsible for DNA recognition. Reports disagree on several aspects of the putative RNA interaction, including sequence specificity and biological relevance. Here we review the history and recent advances in the study of p53-RNA interactions. We argue that p53-RNA interactions are sequence nonspecific and depend on incomplete post-translational modification of the p53 C-terminal domain when the protein is expressed in heterologous systems. It is unknown what fraction of p53 protein exists in a state competent for RNA binding in vivo. Thus, potential physiological roles of p53-RNA interactions remain mysterious.
    MeSH term(s) Amino Acid Sequence ; Animals ; Humans ; Models, Biological ; Molecular Sequence Data ; Protein Processing, Post-Translational ; RNA/chemistry ; RNA/metabolism ; Tumor Suppressor Protein p53/chemistry ; Tumor Suppressor Protein p53/metabolism
    Chemical Substances Tumor Suppressor Protein p53 ; RNA (63231-63-0)
    Language English
    Publishing date 2007-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1241540-6
    ISSN 1355-8382
    ISSN 1355-8382
    DOI 10.1261/rna.673407
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: RNA-p53 interactions in vitro.

    Riley, Kasandra J-L / Ramirez-Alvarado, Marina / Maher, L James

    Biochemistry

    2007  Volume 46, Issue 9, Page(s) 2480–2487

    Abstract: The tumor suppressor protein p53 is mutated in over half of human cancers. Despite 25 years of study, the complex regulation of this protein remains unclear. After serendipitously detecting RNA binding by p53 in the yeast three-hybrid system (Y3H), we ... ...

    Abstract The tumor suppressor protein p53 is mutated in over half of human cancers. Despite 25 years of study, the complex regulation of this protein remains unclear. After serendipitously detecting RNA binding by p53 in the yeast three-hybrid system (Y3H), we are exploring the specificity and function of this interaction. Electrophoretic mobility shift assays show that full-length p53 binds equally to RNAs that are strongly distinguished in the Y3H. RNA binding blocks sequence-specific DNA binding by p53. The C-terminus of p53 is necessary and sufficient for strong RNA interaction in vitro. Mouse and human C-terminal p53 peptides have different affinities for RNA, and an acetylated human p53 C-terminal peptide does not bind RNA. Circular dichroism spectroscopy of p53 peptides shows that RNA binding does not induce a structural change in the p53 C-terminal peptide, and C-terminal peptides do not detectably affect the structure of RNA. These results demonstrate that p53 binds RNA with little sequence specificity, RNA binding has the potential to regulate DNA binding, and RNA-p53 interactions can be regulated by acetylation of the p53 C-terminus.
    MeSH term(s) Animals ; Base Sequence ; Circular Dichroism ; Electrophoretic Mobility Shift Assay ; Humans ; Mice ; Molecular Sequence Data ; RNA/chemistry ; RNA/metabolism ; Spectrophotometry, Ultraviolet ; Tumor Suppressor Protein p53/metabolism ; Two-Hybrid System Techniques
    Chemical Substances Tumor Suppressor Protein p53 ; RNA (63231-63-0)
    Language English
    Publishing date 2007-03-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/bi061480v
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system.

    Riley, Kasandra J-L / Cassiday, Laura A / Kumar, Akash / Maher, L James

    RNA (New York, N.Y.)

    2006  Volume 12, Issue 4, Page(s) 620–630

    Abstract: The p53 tumor suppressor protein is a homotetrameric transcription factor whose gene is mutated in nearly half of all human cancers. In an unrelated screen of RNA/protein interactions using the yeast three-hybrid system, we inadvertently detected p53 ... ...

    Abstract The p53 tumor suppressor protein is a homotetrameric transcription factor whose gene is mutated in nearly half of all human cancers. In an unrelated screen of RNA/protein interactions using the yeast three-hybrid system, we inadvertently detected p53 interactions with several different RNAs. A literature review revealed previous reports of both sequence-specific and -non-specific interactions between p53 and RNA. Using yeast three-hybrid selections to identify preferred RNA partners for p53, we failed to identify primary RNA sequences or obvious secondary structures required for p53 binding. The cationic p53 C-terminus was shown to be required for RNA binding in yeast. We show that while p53 strongly discriminates between certain RNAs in the yeast three-hybrid assay, the same RNAs are bound equally by p53 in vitro. We further show that the p53 RNA-binding preferences in yeast are mirrored almost exactly by a recombinant tetrameric form of the HIV-1 nucleocapsid (NC) protein thought to be a sequence-nonspecific RNA-binding protein. However, the possibility of specific RNA binding by p53 could not be ruled out because p53 and HIV-1 NC displayed certain differences in RNA-binding preference. We conclude that (1) p53 binds RNA in vivo, (2) RNA binding by p53 is largely sequence-nonspecific in the yeast nucleus, (3) some structure-specific RNA binding by p53 cannot be ruled out, and (4) caution is required when interpreting results of RNA screens in the yeast three-hybrid system because sequence-dependent differences in RNA folding and display can masquerade as sequence-dependent differences in protein recognition.
    MeSH term(s) Base Sequence ; Blotting, Northern ; Electrophoretic Mobility Shift Assay ; Humans ; Molecular Sequence Data ; Protein Binding ; RNA/chemistry ; RNA/metabolism ; Sequence Homology, Nucleic Acid ; Tumor Suppressor Protein p53/metabolism ; Two-Hybrid System Techniques
    Chemical Substances Tumor Suppressor Protein p53 ; RNA (63231-63-0)
    Language English
    Publishing date 2006-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1355-8382
    ISSN 1355-8382
    DOI 10.1261/rna.2286706
    Database MEDical Literature Analysis and Retrieval System OnLINE

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