publications
Ferre-D'Amare AR, Winkler WC. 2011. The roles of metal ions in regulation by riboswitches. Met Ions Life Sci 9:141-73.
http://www.ncbi.nlm.nih.gov/pubmed/22010271
Ramesh A, Wakeman CA, Winkler WC. 2011. Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol 407:556-70.
http://www.ncbi.nlm.nih.gov/pubmed/22010271
Ramesh A, Wakeman CA, Winkler WC. 2011. Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol 407:556-70.
http://www.ncbi.nlm.nih.gov/pubmed/21315082
Irnov I, Sharma CM, Vogel, J, Winkler WC. 2010. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Research 38:6637-51.
http://www.ncbi.nlm.nih.gov/pubmed/20525796
Irnov I, Winkler WC. 2010. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol 76:559-75.
http://www.ncbi.nlm.nih.gov/pubmed/20374491
Ramesh A, Winkler WC. 2010. Magnesium-sensing riboswitches in bacteria. RNA Biol 7:77-83.
http://www.ncbi.nlm.nih.gov/pubmed/20023416
Wakeman CA, Ramesh A, Winkler WC. 2009. Multiple metal binding cores are required for metalloregulation by M box riboswitch RNAs. J Mol Biol 392:723-35.
http://www.ncbi.nlm.nih.gov/pubmed/19619558
Fox KA*, Ramesh A*, Stearns JE, Bourgogne A, Reyes A, Winkler WC*, Garsin DA*. 2008. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc Natl Acad Sci 106:4435-4440. (*equal contribution)
http://www.ncbi.nlm.nih.gov/pubmed/19246383
Wakeman CA, Winkler WC. 2009. Analysis of the RNA backbone: Structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension (SHAPE). Methods Mol Biol 540:173-191.
http://www.ncbi.nlm.nih.gov/pubmed/19381560
Brautigam CA, Wakeman CA, Winkler WC. 2009. Methods for analysis of ligand-induced RNA conformational changes. Methods Mol Biol 540:77-95.
http://www.ncbi.nlm.nih.gov/pubmed/19381554
Wakeman CA, Winkler WC. 2009. Structural probing techniques for natural aptamers. Methods Mol Biol 535:115-133.
http://www.ncbi.nlm.nih.gov/pubmed/19377977
Dambach M, Winkler WC. 2009. Expanding roles for metabolite-sensing RNAs. Curr Opin Microbiol 12:161-169.
http://www.ncbi.nlm.nih.gov/pubmed/19250859
Attia AS, Sedillo JL, Wang W, Liu W, Brautigam CA, Winkler WC, Hansen EJ. 2008. Moraxella catarrhalis expresses an unusual Hfq protein. Infect Immun 76:2520-2530.
Collins JA, Irnov I, Baker SC, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes & Dev 21:3356-3368.
http://www.ncbi.nlm.nih.gov/pubmed/18079181
Dann CE*, Wakeman CA*, Sieling CL, Baker SC, Irnov I, Winkler WC. 2007. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130:878-892. (*equal contribution)
http://www.ncbi.nlm.nih.gov/pubmed/17803910
Wakeman CA, Winkler WC, Dann CE. 2007. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci 32:415-424.
http://www.ncbi.nlm.nih.gov/pubmed/17764952
Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwick A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. 2007. A riboswitch selective for the queuosine precursor preQ(1) contains an unusually small aptamer. Nat Struct Mol Biol 14:308-317.
Irnov, Kertsburg A, Winkler WC. 2006. Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: General principles and prospects for discovery. Cold Spring Harb Quant Biol 71:239-249.
http://www.ncbi.nlm.nih.gov/pubmed/17381303
Winkler WC, Dann CE. 2006. RNA allostery glimpsed. Nat Struct Mol Biol 13:569-571.
Winkler WC. 2005. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 9:594-602.
Winkler WC, Breaker RR. 2005. Regulation of bacterial gene expression by riboswitches. Ann Rev Microbiol 59:487-517.
Wickiser JK, Winkler WC, Breaker RR, Crothers D. 2005. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell 18:49-60.
Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. 2005. Molecular-recognition characteristics of SAM-binding riboswitches. Agnew Chem Int Ed Engl 34:964-968.
Winkler WC. 2005. Metabolic monitoring by bacterial mRNAs. Archives in Microbiol 183:151-159.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. 2004. RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci 101:6421-6426.
Winkler WC*, Nahvi A*, Roth A*, Collins JA*, Breaker RR. 2004. Control of bacterial gene expression by a natural metabolite-responsive ribozyme. Nature. 428:281-286.
Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 10:701-707.
Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. 2003. Metabolite-sensing riboswitches control fundamental biochemical pathways, in bacteria. Cell 113:577-586.
Winkler WC, Breaker RR. 2003. Genetic control by metabolite-binding riboswitches. ChemBioChem 4:1024-1032.
Winkler WC, Cohen-Chalamish S, Breaker RR. 2002. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci 99:15908-15913.
Winkler W, Nahvi A, Breaker RR. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956.
Grundy FJ, Winkler WC, Henkin TM. 2002. tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome. Proc Natl Acad Sci 99:11121-11126.
Winkler WC, Grundy FJ, Murphy BA, Henkin TM. 2001. The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 7:1165-1172.
Curnow AW, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin TM, Soll D. 1997. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc Natl Acad Sci 94:11819-11826.
Winkler WC, Gonzalez G, Wittenberg JB, Hille R, Dakappagari N, Jacob A, Gonzalez LA, Gilles-Gonzalez MA. 1996. Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the Rhizobial heme-based oxygen sensor FixL. Chem and Biol 3:841-850.
http://www.ncbi.nlm.nih.gov/pubmed/20525796
Irnov I, Winkler WC. 2010. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol 76:559-75.
http://www.ncbi.nlm.nih.gov/pubmed/20374491
Ramesh A, Winkler WC. 2010. Magnesium-sensing riboswitches in bacteria. RNA Biol 7:77-83.
http://www.ncbi.nlm.nih.gov/pubmed/20023416
Wakeman CA, Ramesh A, Winkler WC. 2009. Multiple metal binding cores are required for metalloregulation by M box riboswitch RNAs. J Mol Biol 392:723-35.
http://www.ncbi.nlm.nih.gov/pubmed/19619558
Fox KA*, Ramesh A*, Stearns JE, Bourgogne A, Reyes A, Winkler WC*, Garsin DA*. 2008. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc Natl Acad Sci 106:4435-4440. (*equal contribution)
http://www.ncbi.nlm.nih.gov/pubmed/19246383
Wakeman CA, Winkler WC. 2009. Analysis of the RNA backbone: Structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension (SHAPE). Methods Mol Biol 540:173-191.
http://www.ncbi.nlm.nih.gov/pubmed/19381560
Brautigam CA, Wakeman CA, Winkler WC. 2009. Methods for analysis of ligand-induced RNA conformational changes. Methods Mol Biol 540:77-95.
http://www.ncbi.nlm.nih.gov/pubmed/19381554
Wakeman CA, Winkler WC. 2009. Structural probing techniques for natural aptamers. Methods Mol Biol 535:115-133.
http://www.ncbi.nlm.nih.gov/pubmed/19377977
Dambach M, Winkler WC. 2009. Expanding roles for metabolite-sensing RNAs. Curr Opin Microbiol 12:161-169.
http://www.ncbi.nlm.nih.gov/pubmed/19250859
Attia AS, Sedillo JL, Wang W, Liu W, Brautigam CA, Winkler WC, Hansen EJ. 2008. Moraxella catarrhalis expresses an unusual Hfq protein. Infect Immun 76:2520-2530.
Collins JA, Irnov I, Baker SC, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes & Dev 21:3356-3368.
http://www.ncbi.nlm.nih.gov/pubmed/18079181
Dann CE*, Wakeman CA*, Sieling CL, Baker SC, Irnov I, Winkler WC. 2007. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130:878-892. (*equal contribution)
http://www.ncbi.nlm.nih.gov/pubmed/17803910
Wakeman CA, Winkler WC, Dann CE. 2007. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci 32:415-424.
http://www.ncbi.nlm.nih.gov/pubmed/17764952
Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwick A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. 2007. A riboswitch selective for the queuosine precursor preQ(1) contains an unusually small aptamer. Nat Struct Mol Biol 14:308-317.
Irnov, Kertsburg A, Winkler WC. 2006. Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: General principles and prospects for discovery. Cold Spring Harb Quant Biol 71:239-249.
http://www.ncbi.nlm.nih.gov/pubmed/17381303
Winkler WC, Dann CE. 2006. RNA allostery glimpsed. Nat Struct Mol Biol 13:569-571.
Winkler WC. 2005. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 9:594-602.
Winkler WC, Breaker RR. 2005. Regulation of bacterial gene expression by riboswitches. Ann Rev Microbiol 59:487-517.
Wickiser JK, Winkler WC, Breaker RR, Crothers D. 2005. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell 18:49-60.
Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. 2005. Molecular-recognition characteristics of SAM-binding riboswitches. Agnew Chem Int Ed Engl 34:964-968.
Winkler WC. 2005. Metabolic monitoring by bacterial mRNAs. Archives in Microbiol 183:151-159.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. 2004. RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci 101:6421-6426.
Winkler WC*, Nahvi A*, Roth A*, Collins JA*, Breaker RR. 2004. Control of bacterial gene expression by a natural metabolite-responsive ribozyme. Nature. 428:281-286.
Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 10:701-707.
Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. 2003. Metabolite-sensing riboswitches control fundamental biochemical pathways, in bacteria. Cell 113:577-586.
Winkler WC, Breaker RR. 2003. Genetic control by metabolite-binding riboswitches. ChemBioChem 4:1024-1032.
Winkler WC, Cohen-Chalamish S, Breaker RR. 2002. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci 99:15908-15913.
Winkler W, Nahvi A, Breaker RR. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956.
Grundy FJ, Winkler WC, Henkin TM. 2002. tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome. Proc Natl Acad Sci 99:11121-11126.
Winkler WC, Grundy FJ, Murphy BA, Henkin TM. 2001. The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 7:1165-1172.
Curnow AW, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin TM, Soll D. 1997. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc Natl Acad Sci 94:11819-11826.
Winkler WC, Gonzalez G, Wittenberg JB, Hille R, Dakappagari N, Jacob A, Gonzalez LA, Gilles-Gonzalez MA. 1996. Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the Rhizobial heme-based oxygen sensor FixL. Chem and Biol 3:841-850.