Experts and Doctors on genetic transcription in Boulder, Colorado, United States

Summary

Locale: Boulder, Colorado, United States
Topic: genetic transcription

Top Publications

  1. Olson A, Rosenblum E, Kuchta R. Regulation of influenza RNA polymerase activity and the switch between replication and transcription by the concentrations of the vRNA 5' end, the cap source, and the polymerase. Biochemistry. 2010;49:10208-15 pubmed publisher
    ..These data provide insights into the regulation of RdRp throughout the viral life cycle and how it synthesizes the appropriate amounts of viral mRNA and replication products (vRNA and cRNA). ..
  2. Eisenberg S, Hale K, Heimdal P, Thompson R. Location of the protease-inhibitory region of secretory leukocyte protease inhibitor. J Biol Chem. 1990;265:7976-81 pubmed
    ..Instead they suggest that leucine 72 is also the inhibitory site for trypsin, even though the amino acid residues at the inhibitory sites of other trypsin inhibitors are almost always either lysine or arginine. ..
  3. Zhao X, Raitt D, V Burke P, Clewell A, Kwast K, Poyton R. Function and expression of flavohemoglobin in Saccharomyces cerevisiae. Evidence for a role in the oxidative stress response. J Biol Chem. 1996;271:25131-8 pubmed
    ..This finding is consistent with the observation that conditions that promote oxidative stress also enhance expression of YHB1. Together, these findings suggest that YHb plays a role in the oxidative stress response in yeast. ..
  4. Hooper J, Perez Alonso M, Bermingham J, Prout M, Rocklein B, Wagenbach M, et al. Comparative studies of Drosophila Antennapedia genes. Genetics. 1992;132:453-69 pubmed
    ..The conservation of transcript complexity suggests functional requirements for the different protein forms. ..
  5. Ferguson H, Kugel J, Goodrich J. Kinetic and mechanistic analysis of the RNA polymerase II transcrption reaction at the human interleukin-2 promoter. J Mol Biol. 2001;314:993-1006 pubmed
    ..We present a kinetic model for a single round of basal transcription at the IL-2 promoter that provides insight into mechanisms by which the IL-2 gene is transcriptionally regulated. ..
  6. 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...
  7. Rosenzweig B, Imamura T, Okadome T, Cox G, Yamashita H, ten Dijke P, et al. Cloning and characterization of a human type II receptor for bone morphogenetic proteins. Proc Natl Acad Sci U S A. 1995;92:7632-6 pubmed
    ..Binding of OP-1/BMP-7 to BMPR-II was also observed in nontransfected cell lines. Moreover, a transcriptional activation signal was transduced by BMPR-II in the presence of type I receptors after stimulation by OP-1/BMP-7. ..
  8. Kahn N, Rea S, Moyle S, Kell A, Johnson T. Proteasomal dysfunction activates the transcription factor SKN-1 and produces a selective oxidative-stress response in Caenorhabditis elegans. Biochem J. 2008;409:205-13 pubmed
  9. Donner A, Szostek S, Hoover J, Espinosa J. CDK8 is a stimulus-specific positive coregulator of p53 target genes. Mol Cell. 2007;27:121-33 pubmed
    ..Furthermore, increased binding of CDK8 to p53 target genes correlates positively with transcriptional strength. RNAi experiments demonstrate that CDK8 functions as a coactivator within the p53 transcriptional program. ..
  10. Han A, Pan F, Stroud J, Youn H, Liu J, Chen L. Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2. Nature. 2003;422:730-4 pubmed
    ..Our studies of the ternary Cabin1/MEF2/DNA complex show a general mechanism by which MEF2 recruits transcriptional co-repressor Cabin1 and class II HDACs to specific DNA sites. ..

Detail Information

Publications40

  1. Olson A, Rosenblum E, Kuchta R. Regulation of influenza RNA polymerase activity and the switch between replication and transcription by the concentrations of the vRNA 5' end, the cap source, and the polymerase. Biochemistry. 2010;49:10208-15 pubmed publisher
    ..These data provide insights into the regulation of RdRp throughout the viral life cycle and how it synthesizes the appropriate amounts of viral mRNA and replication products (vRNA and cRNA). ..
  2. Eisenberg S, Hale K, Heimdal P, Thompson R. Location of the protease-inhibitory region of secretory leukocyte protease inhibitor. J Biol Chem. 1990;265:7976-81 pubmed
    ..Instead they suggest that leucine 72 is also the inhibitory site for trypsin, even though the amino acid residues at the inhibitory sites of other trypsin inhibitors are almost always either lysine or arginine. ..
  3. Zhao X, Raitt D, V Burke P, Clewell A, Kwast K, Poyton R. Function and expression of flavohemoglobin in Saccharomyces cerevisiae. Evidence for a role in the oxidative stress response. J Biol Chem. 1996;271:25131-8 pubmed
    ..This finding is consistent with the observation that conditions that promote oxidative stress also enhance expression of YHB1. Together, these findings suggest that YHb plays a role in the oxidative stress response in yeast. ..
  4. Hooper J, Perez Alonso M, Bermingham J, Prout M, Rocklein B, Wagenbach M, et al. Comparative studies of Drosophila Antennapedia genes. Genetics. 1992;132:453-69 pubmed
    ..The conservation of transcript complexity suggests functional requirements for the different protein forms. ..
  5. Ferguson H, Kugel J, Goodrich J. Kinetic and mechanistic analysis of the RNA polymerase II transcrption reaction at the human interleukin-2 promoter. J Mol Biol. 2001;314:993-1006 pubmed
    ..We present a kinetic model for a single round of basal transcription at the IL-2 promoter that provides insight into mechanisms by which the IL-2 gene is transcriptionally regulated. ..
  6. 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...
  7. Rosenzweig B, Imamura T, Okadome T, Cox G, Yamashita H, ten Dijke P, et al. Cloning and characterization of a human type II receptor for bone morphogenetic proteins. Proc Natl Acad Sci U S A. 1995;92:7632-6 pubmed
    ..Binding of OP-1/BMP-7 to BMPR-II was also observed in nontransfected cell lines. Moreover, a transcriptional activation signal was transduced by BMPR-II in the presence of type I receptors after stimulation by OP-1/BMP-7. ..
  8. Kahn N, Rea S, Moyle S, Kell A, Johnson T. Proteasomal dysfunction activates the transcription factor SKN-1 and produces a selective oxidative-stress response in Caenorhabditis elegans. Biochem J. 2008;409:205-13 pubmed
  9. Donner A, Szostek S, Hoover J, Espinosa J. CDK8 is a stimulus-specific positive coregulator of p53 target genes. Mol Cell. 2007;27:121-33 pubmed
    ..Furthermore, increased binding of CDK8 to p53 target genes correlates positively with transcriptional strength. RNAi experiments demonstrate that CDK8 functions as a coactivator within the p53 transcriptional program. ..
  10. Han A, Pan F, Stroud J, Youn H, Liu J, Chen L. Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2. Nature. 2003;422:730-4 pubmed
    ..Our studies of the ternary Cabin1/MEF2/DNA complex show a general mechanism by which MEF2 recruits transcriptional co-repressor Cabin1 and class II HDACs to specific DNA sites. ..
  11. Weaver J, Good K, Walters R, Kugel J, Goodrich J. Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter. Mol Immunol. 2007;44:2813-9 pubmed
    ..Although long considered an enhancer, our studies indicate that the regulatory region in the IL-2 promoter is better considered as a proximal regulatory element, since it lacks multiple properties associated with enhancer elements. ..
  12. Carroll S, DiNardo S, O Farrell P, White R, Scott M. Temporal and spatial relationships between segmentation and homeotic gene expression in Drosophila embryos: distributions of the fushi tarazu, engrailed, Sex combs reduced, Antennapedia, and Ultrabithorax proteins. Genes Dev. 1988;2:350-60 pubmed
    ..Finally, some cells contain a single homeotic product, whereas other cells simultaneously contain several, suggesting that certain cells may be determined by the combinatorial action of homeotic genes. ..
  13. 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. ..
  14. Wagner S, Kugel J, Goodrich J. TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain. Mol Cell Biol. 2010;30:91-7 pubmed publisher
    ..These studies also identify a new function for ncRNA repression domains: they stabilize interactions of ncRNAs with Pol II in the presence of TFIIF. ..
  15. Allen D, Weber J, Sycuro L, Leinwand L. Myocyte enhancer factor-2 and serum response factor binding elements regulate fast Myosin heavy chain transcription in vivo. J Biol Chem. 2005;280:17126-34 pubmed
    ..Together, these data demonstrate that the quantitative differences in MyHC expression in mouse skeletal muscle have evolved at least in part through the elimination of positive-acting transcription factor binding sites. ..
  16. Powell Coffman J, Knight J, Wood W. Onset of C. elegans gastrulation is blocked by inhibition of embryonic transcription with an RNA polymerase antisense RNA. Dev Biol. 1996;178:472-83 pubmed
    ..These results indicate that embryonically transcribed gene products are required for gastrulation initiation. They also demonstrate the efficacy of a method for blocking embryonic transcription that may be useful in other organisms. ..
  17. Riquelme C, Barthel K, Liu X. SUMO-1 modification of MEF2A regulates its transcriptional activity. J Cell Mol Med. 2006;10:132-44 pubmed
    ..Our results suggest that protein sumoylation could play a pivotal role in controlling MEF2 transcriptional activity. ..
  18. Wang W, Ungermannova D, Jin J, Harper J, Liu X. Negative regulation of SCFSkp2 ubiquitin ligase by TGF-beta signaling. Oncogene. 2004;23:1064-75 pubmed
  19. Mozdy A, Podell E, Cech T. Multiple yeast genes, including Paf1 complex genes, affect telomere length via telomerase RNA abundance. Mol Cell Biol. 2008;28:4152-61 pubmed publisher
    ..This report establishes that a subset of telomere length genes act by modulating telomerase RNA abundance. ..
  20. Barthel K, Liu X. A transcriptional enhancer from the coding region of ADAMTS5. PLoS ONE. 2008;3:e2184 pubmed publisher
    ..Thus, we report the identification and detailed characterization of an exonic enhancer. Ultimately, this leads to the interesting question of why evolution would be so parsimonious in the functional assignment of sequence. ..
  21. Dennehey B, Leinwand L, Krauter K. Diversity in transcriptional start site selection and alternative splicing affects the 5'-UTR of mouse striated muscle myosin transcripts. J Muscle Res Cell Motil. 2006;27:559-75 pubmed
    ..These findings indicate that alternative TSS usage and alternative splicing in the 5'-UTR are a general feature of murine Myh gene expression and that Myh gene regulation is more complex than previously appreciated. ..
  22. Batey R. Structures of regulatory elements in mRNAs. Curr Opin Struct Biol. 2006;16:299-306 pubmed
    ..Another highly structured mRNA element, the viral internal ribosomal entry site, is able to manipulate the ribosome and replace the function of initiation factors to promote gene expression. ..
  23. Taatjes D. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci. 2010;35:315-22 pubmed publisher
  24. Kapulkin W, Kapulkin V, Hiester B, Link C. Compensatory regulation among ER chaperones in C. elegans. FEBS Lett. 2005;579:3063-8 pubmed
    ..We show that this compensatory regulation is specific for ER chaperones, not dependent on RNA interference, and required for maintaining viability in worms containing a deletion of the hsp-3 gene. ..
  25. Trent C, Purnell B, Gavinski S, Hageman J, Chamblin C, Wood W. Sex-specific transcriptional regulation of the C. elegans sex-determining gene her-1. Mech Dev. 1991;34:43-55 pubmed
    ..This mode of regulation contrasts with that found for the Drosophila sex-determining genes, whose sex-specific expression is controlled by differential splicing in males and females. ..
  26. Bermingham J, Martinez Arias A, Petitt M, Scott M. Different patterns of transcription from the two Antennapedia promoters during Drosophila embryogenesis. Development. 1990;109:553-66 pubmed
    ..In addition, we have examined the regulation of each of the Antp promoters by genes of the bithorax complex (BX-C). We show that in BX-C- embryos both promoters are derepressed in the abdomen. ..
  27. Allen D, Uyenishi J, Cleary A, Mehan R, Lindsay S, Reed J. Calcineurin activates interleukin-6 transcription in mouse skeletal muscle in vivo and in C2C12 myotubes in vitro. Am J Physiol Regul Integr Comp Physiol. 2010;298:R198-210 pubmed publisher
    ..Together, these results suggest that IL-6 transcription in skeletal muscle cells can be activated by a calcineurin-MEF-2 axis which is antagonized by NFAT. ..
  28. Garst A, Batey R. A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta. 2009;1789:584-91 pubmed publisher
  29. Murakami S, Johnson T. The OLD-1 positive regulator of longevity and stress resistance is under DAF-16 regulation in Caenorhabditis elegans. Curr Biol. 2001;11:1517-23 pubmed
    ..This study reveals a new system for specifying longevity and stress resistance and suggests possible mechanisms for mediating life extension by dietary restriction and hormesis. ..
  30. Browning H, Hayles J, Mata J, Aveline L, Nurse P, McIntosh J. Tea2p is a kinesin-like protein required to generate polarized growth in fission yeast. J Cell Biol. 2000;151:15-28 pubmed
    ..These results suggest that this kinesin promotes microtubule growth, possibly through interactions with the microtubule end, and that it is important for establishing and maintaining polarized growth along the long axis of the cell. ..
  31. Tuerk C, Gauss P, Thermes C, Groebe D, Gayle M, Guild N, et al. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A. 1988;85:1364-8 pubmed
    ..The stability of CUUCGG hairpins is also utilized in the RNAs of many organisms besides T4. ..
  32. Roecklein B, Kuempel P. In vivo characterization of tus gene expression in Escherichia coli. Mol Microbiol. 1992;6:1655-61 pubmed
    ..We have also demonstrated that a minority of tus transcripts are initiated from an upstream region that contains two additional open reading frames. This readthrough transcription into tus is reduced in the presence of Tus protein. ..
  33. Mariner P, Walters R, Espinoza C, Drullinger L, Wagner S, Kugel J, et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 2008;29:499-509 pubmed publisher
    ..These studies provide an explanation for why mouse cells harbor two major classes of SINEs, whereas human cells contain only one. ..
  34. Yakovchuk P, Goodrich J, Kugel J. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A. 2009;106:5569-74 pubmed publisher
    ..In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB. ..
  35. Peterson E, Uhlenbeck O. Determination of recognition nucleotides for Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry. 1992;31:10380-9 pubmed
    ..However, recognition of the tRNA central core nucleotides is unique to E. coli FRS.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  36. Winslow G, Hayashi S, Krasnow M, Hogness D, Scott M. Transcriptional activation by the Antennapedia and fushi tarazu proteins in cultured Drosophila cells. Cell. 1989;57:1017-30 pubmed
    ..The results demonstrate that homeodomain proteins are transcriptional regulators in vivo and that in cultured cells, different homeodomain-containing proteins can act upon a common sequence to modulate gene transcription. ..
  37. Dynan W, Gilman M. Transcriptional control and signal transduction: of soap-operas and reductionism. Trends Genet. 1993;9:154-6 pubmed
  38. Weickert M, Adhya S. The galactose regulon of Escherichia coli. Mol Microbiol. 1993;10:245-51 pubmed
    ..The gal regulon has the potential to coordinate galactose metabolism and transport in a highly efficient manner, under a wide variety of conditions of galactose availability. ..
  39. Donner A, Ebmeier C, Taatjes D, Espinosa J. CDK8 is a positive regulator of transcriptional elongation within the serum response network. Nat Struct Mol Biol. 2010;17:194-201 pubmed publisher
    ..Furthermore, CDK8-Mediator specifically interacts with positive transcription elongation factor b. Thus, we have uncovered a role for CDK8 in transcriptional regulation that may contribute to its oncogenic effects. ..
  40. Marcora E, Gowan K, Lee J. Stimulation of NeuroD activity by huntingtin and huntingtin-associated proteins HAP1 and MLK2. Proc Natl Acad Sci U S A. 2003;100:9578-83 pubmed
    ..We propose that Htt, together with HAP1, may function as a scaffold for the activation of ND by MLK2. ..