Experts and Doctors on rna binding proteins in Boulder, Colorado, United States

Summary

Locale: Boulder, Colorado, United States
Topic: rna binding proteins

Top Publications

  1. Tsu C, Uhlenbeck O. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998;37:16989-96 pubmed
    ..Taken together with the tight, site-specific binding to naked, unmodified 23S rRNA, this suggests a role for DbpA in ribosome biogenesis rather than translation. ..
  2. Shtatland T, Gill S, Javornik B, Johansson H, Singer B, Uhlenbeck O, et al. Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res. 2000;28:E93 pubmed
    ..Such methods may be useful tools for both randomized sequence SELEX and genomic SELEX...
  3. Parma D, Bennett P, Boswell R. Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev Biol. 2007;308:507-19 pubmed
    ..On the other hand, Tsunagi/Y14 is essential for restricting oocyte fate to a single cell and may function with mago nashi in this process. ..
  4. Roberts E, Hammond K, Traish A, Resing K, Ahn N. Identification of G2/M targets for the MAP kinase pathway by functional proteomics. Proteomics. 2006;6:4541-53 pubmed
  5. Gawande B, Robida M, Rahn A, Singh R. Drosophila Sex-lethal protein mediates polyadenylation switching in the female germline. EMBO J. 2006;25:1263-72 pubmed
    ..The sex-specific poly(A) switching of e(r) provides a means for translational regulation in germ cells. We present a model for the SXL-dependent poly(A) site choice in the female germline. ..
  6. Hamady M, Peden E, Knight R, Singh R. Fast-Find: a novel computational approach to analyzing combinatorial motifs. BMC Bioinformatics. 2006;7:1 pubmed
    ..We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally. ..
  7. Kossen K, Uhlenbeck O. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res. 1999;27:3811-20 pubmed
    ..We propose that the C-terminus identifies a protein sub-family whose members bind 23S rRNA and that proteins of this family are likely to function in rRNA maturation/ribosome biogenesis or an unappreciated aspect of translation. ..
  8. Tsu C, Kossen K, Uhlenbeck O. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001;7:702-9 pubmed
    ..A model relating the RNA binding and ATPase activities of DbpA is presented. ..
  9. Diges C, Uhlenbeck O. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001;20:5503-12 pubmed
    ..This work indicates that certain RNA helicases require particular RNA structures in order for optimal unwinding activity to be observed. ..
  10. Luca F, Winey M. MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Mol Biol Cell. 1998;9:29-46 pubmed
    ..Perhaps in addition to, or as part of, its essential function in late mitosis, MOB1 is required for a cell cycle reset function necessary for the initiation of the spindle pole body duplication. ..

Detail Information

Publications21

  1. Tsu C, Uhlenbeck O. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998;37:16989-96 pubmed
    ..Taken together with the tight, site-specific binding to naked, unmodified 23S rRNA, this suggests a role for DbpA in ribosome biogenesis rather than translation. ..
  2. Shtatland T, Gill S, Javornik B, Johansson H, Singer B, Uhlenbeck O, et al. Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res. 2000;28:E93 pubmed
    ..Such methods may be useful tools for both randomized sequence SELEX and genomic SELEX...
  3. Parma D, Bennett P, Boswell R. Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev Biol. 2007;308:507-19 pubmed
    ..On the other hand, Tsunagi/Y14 is essential for restricting oocyte fate to a single cell and may function with mago nashi in this process. ..
  4. Roberts E, Hammond K, Traish A, Resing K, Ahn N. Identification of G2/M targets for the MAP kinase pathway by functional proteomics. Proteomics. 2006;6:4541-53 pubmed
  5. Gawande B, Robida M, Rahn A, Singh R. Drosophila Sex-lethal protein mediates polyadenylation switching in the female germline. EMBO J. 2006;25:1263-72 pubmed
    ..The sex-specific poly(A) switching of e(r) provides a means for translational regulation in germ cells. We present a model for the SXL-dependent poly(A) site choice in the female germline. ..
  6. Hamady M, Peden E, Knight R, Singh R. Fast-Find: a novel computational approach to analyzing combinatorial motifs. BMC Bioinformatics. 2006;7:1 pubmed
    ..We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally. ..
  7. Kossen K, Uhlenbeck O. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res. 1999;27:3811-20 pubmed
    ..We propose that the C-terminus identifies a protein sub-family whose members bind 23S rRNA and that proteins of this family are likely to function in rRNA maturation/ribosome biogenesis or an unappreciated aspect of translation. ..
  8. Tsu C, Kossen K, Uhlenbeck O. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001;7:702-9 pubmed
    ..A model relating the RNA binding and ATPase activities of DbpA is presented. ..
  9. Diges C, Uhlenbeck O. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001;20:5503-12 pubmed
    ..This work indicates that certain RNA helicases require particular RNA structures in order for optimal unwinding activity to be observed. ..
  10. Luca F, Winey M. MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Mol Biol Cell. 1998;9:29-46 pubmed
    ..Perhaps in addition to, or as part of, its essential function in late mitosis, MOB1 is required for a cell cycle reset function necessary for the initiation of the spindle pole body duplication. ..
  11. Fillman C, Lykke Andersen J. RNA decapping inside and outside of processing bodies. Curr Opin Cell Biol. 2005;17:326-31 pubmed
    ..Recent evidence suggests that the processing bodies may constitute specialized cellular compartments of mRNA turnover, which suggests that mRNA and protein localization may be integral to mRNA decay...
  12. Cui M, Allen M, Larsen A, MacMorris M, Han M, Blumenthal T. Genes involved in pre-mRNA 3'-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen. Proc Natl Acad Sci U S A. 2008;105:16665-70 pubmed publisher
    ..Furthermore, our results implicate a serine/arginine-rich (SR) protein, SRp20, in events following 3'-end cleavage, leading to termination of transcription. ..
  13. Clement S, Lykke Andersen J. A tethering approach to study proteins that activate mRNA turnover in human cells. Methods Mol Biol. 2008;419:121-33 pubmed publisher
  14. Singh G, Jakob S, Kleedehn M, Lykke Andersen J. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol Cell. 2007;27:780-92 pubmed
    ..Furthermore, retention of the NMD factor hUpf1 in the nucleus strongly impairs NMD. These observations suggest that the hUpf complex communicates with the EJC and triggers NMD in the cytoplasm...
  15. Pleshe E, Truesdell J, Batey R. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:722-8 pubmed
    ..The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the alpha/beta-knot superfamily, with alpha-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding. ..
  16. Kossen K, Karginov F, Uhlenbeck O. The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. J Mol Biol. 2002;324:625-36 pubmed
    ..These data support a model in which the carboxy-terminal domain binds hairpin 92 to target the protein to 23S rRNA. ..
  17. Lykke Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol. 2002;22:8114-21 pubmed
    ..These data suggest that a human decapping complex may be recruited to mRNAs containing premature termination codons by the hUpf proteins...
  18. Polach K, Uhlenbeck O. Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry. 2002;41:3693-702 pubmed
    ..This cooperativity is lost upon removal of helix 89 from R153, suggesting this helix is either the preferred target for DbpA's helicase activity or is a necessary structural element for organization of the target site within R153. ..
  19. Livengood A, Zaug A, Cech T. Essential regions of Saccharomyces cerevisiae telomerase RNA: separate elements for Est1p and Est2p interaction. Mol Cell Biol. 2002;22:2366-74 pubmed
    ..More generally, our results support a role for the telomerase RNA serving as a scaffold for binding key protein subunits. ..
  20. Mohr S, Dillon S, Boswell R. The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis. Genes Dev. 2001;15:2886-99 pubmed
  21. Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R. The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA. 2004;10:240-53 pubmed
    ..We propose that RRM3 has an unrecognized function that is possibly relevant for the splicing of only a subset of cellular introns. We discuss the implications of these observations on previous models of U2AF function. ..