Prediction of rho-independent transcriptional terminators in Escherichia coli

Nucleic Acids Research

Volumn 29, Issue 17, 2001, Pages 3583-3594

  Lesnik, Elena A ^a   Sampath, Rangarajan ^a   Levene, Harold B ^a   Henderson, Timothy J ^a   McNeil, John A ^a   Ecker, David J ^a  

^a Ibis Therapeutics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RHO FACTOR; RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION TERMINATION FACTOR; UNCLASSIFIED DRUG;

ALGORITHM; ANIMAL CELL; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; CORRELATION FUNCTION; ESCHERICHIA COLI; GENE ACTIVITY; GENETIC CODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; RECEIVER OPERATING CHARACTERISTIC; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; SCORING SYSTEM; SIGNAL TRANSDUCTION; THERMODYNAMICS; TRANSCRIPTION TERMINATION;

ALGORITHMS; BASE SEQUENCE; ESCHERICHIA COLI; GENOME, BACTERIAL; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, NUCLEIC ACID; RHO FACTOR; RNA, BACTERIAL; RNA, RIBOSOMAL; RNA, TRANSFER; TRANSCRIPTION, GENETIC;

ANIMALIA; BACTERIA (MICROORGANISMS); ESCHERICHIA; ESCHERICHIA COLI; ESCHERICHIA COLI K12; NEGIBACTERIA;

EID: 0035444240     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.17.3583     Document Type: Article

References (42)

1. An integrated model of the transcription complex in elongation, termination and editing
2. Rho-independent termination: Dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro
3. Transcription termination at intrinsic terminators: The role of the RNA hairpin
4. Parameters affecting transcription termination by Escherichia coli RNA polymerase. I. Analysis of 13 rho-independent terminators
5. The elongation-termination decision in transcription
6. Escherichia coli RNA polymerase terminates transcription efficiently at rho-independent terminators on single-stranded DNA templates
7. The mechanism of intrinsic transcription termination
8. Mechanism of intrinsic transcription termination and antitermination
9. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
10. A structural model of transcription elongation
11. DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
12. RNA polymerase slides home: Pause and termination site recognition
13. Spatial organization of transcription elongation complex in Escherichia coli
14. A computer algorithm for testing potential prokaryotic terminators
15. Terminators of transcription with RNA polymerase from Escherichia coli: What they look like and how to find them
16. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
17. Prediction of transcription terminators in bacterial genomes
18. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models
19. RNA Motif - A new RNA secondary structure definition and discovery algorithm
20. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
21. The complete genome sequence of Escherichia coli K-12
22. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
23. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
24. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
25. Transcription attenuation
26. Control of RNA chain elongation and termination
27. Control of transcription termination in prokaryotes
28. A thermodynamic study of unusually stable RNA and DNA hairpins
29. A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene
30. Transcription termination in the Escherichia coli ribosomal RNA operon rrnC
31. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli
32. Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli
33. Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organisms
34. Ribosomal RNA antitermination in vitro: Requirement for Nus factors and one or more unidentified cellular components
35. Antitermination of characterized transcriptional terminators by the Escherichia coli rrnG leader region
36. Processing of tRNA in prokaryotes and eukaryotes
37. Small RNAs in Escherichia coli
38. RegulonDB(version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12
39. Transcriptional termination sequence at the end of the Escherichia coli ribosomal RNA G operon: Complex terminators and antitermination
40. Role of the spacer boxA of Escherichia coli ribosomal RNA operons in efficient 23 S rRNA synthesis in vivo
41. Recognition of boxA antiterminator RNA by the E. coli antitermination factors NusB and ribosomal protein S10