The double-stranded transcriptome of Escherichia coli

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 8, 2014, Pages 3134-3139

  Lybecker, Meghan ^a   Zimmermann, Bob ^a   Bilusic, Ivana ^a   Tukhtubaeva, Nadezda ^a   Schroeder, Renée ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY RNA; DOUBLE STRANDED RNA; LDHA PROTEIN; LPTF PROTEIN; PEPA PROTEIN; RIBONUCLEASE III; RIBOSOME RNA; RNA ANTIBODY; UNCLASSIFIED DRUG; UNTRANSLATED RNA; YDBH PROTEIN; YNEM PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA LIBRARY; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; IMMUNOPRECIPITATION; IN VITRO STUDY; IN VIVO STUDY; MUTANT; NONHUMAN; NORTHERN BLOTTING; OPERON; PRIORITY JOURNAL; STEADY STATE;

BLOTTING, NORTHERN; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNOPRECIPITATION; MODELS, STATISTICAL; RIBONUCLEASE III; RNA, ANTISENSE; RNA, DOUBLE-STRANDED; TRANSCRIPTOME;

EID: 84896805416     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1315974111     Document Type: Article

References (29)

1. Georg J, Hess WR (2011) cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 75(2):286-300.
2. Thomason MK, Storz G (2010) Bacterial antisense RNAs: How many are there, and what are they doing? Annu Rev Genet 44:167-188.
3. Raghavan R, Sloan DB, Ochman H (2012) Antisense transcription is pervasive but rarely conserved in enteric bacteria. mBio 3(4):e00156-12.
4. Brantl S (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10(2):102-109.
5. Wagner EG, Simons RW (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48:713-742.
6. Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P (2013) The excludon: A new concept in bacterial antisense RNA-mediated gene regulation. Nat Rev Microbiol 11(2):75-82.
7. Stead MB, et al. (2011) Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res 39(8):3188 -3203.
8. Durand S, Gilet L, Bessières P, Nicolas P, Condon C (2012) Three essential ribonu-cleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet 8(3):e1002520.
9. Lasa I, et al. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci USA 108(50):20172-20177.
10. Arraiano CM, et al. (2010) The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 34(5):883-923.
11. Lioliou E, et al. (2012) Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet 8(6):e1002782.
12. Bonin M, et al. (2000) Determination of preferential binding sites for anti-dsRNA antibodies on double-stranded RNA by scanning force microscopy. RNA 6(4):563-570. (Pubitemid 30212234)
13. Schönborn J, et al. (1991) Monoclonal antibodies to double-stranded RNA as probes of RNA structure in crude nucleic acid extracts. Nucleic Acids Res 19(11):2993-3000. (Pubitemid 21896939)
14. Lukács N (1994) Detection of virus infection in plants and differentiation between coexisting viruses by monoclonal antibodies to double-stranded RNA. J Virol Methods 47(3):255-272.
15. Mueller S, et al. (2010) RNAi-mediated immunity provides strong protection against the negative-strand RNA vesicular stomatitis virus in Drosophila. Proc Natl Acad Sci USA 107(45):19390-19395.
16. Targett-Adams P, Boulant S, McLauchlan J (2008) Visualization of double-stranded RNA in cells supporting hepatitis C virus RNA replication. J Virol 82(5):2182-2195. (Pubitemid 351293519)
17. Wang H, Vaheri A, Weber F, Plyusnin A (2011) Old World hantaviruses do not produce detectable amounts of dsRNA in infected cells and the 5′ termini of their genomic RNAs are monophosphorylated. J Gen Virol 92(Pt 5):1199-1204.
18. Overby AK, Popov VL, Niedrig M, Weber F (2010) Tick-borne encephalitis virus delays interferon induction and hides its double-stranded RNA in intracellular membrane vesicles. J Virol 84(17):8470-8483.
19. Triantafilou K, et al. (2012) Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses. J Cell Sci 125(Pt 20):4761-4769.
20. Zangger H, et al. (2013) Detection of Leishmania RNA virus in Leishmania parasites. PLoS Negl Trop Dis 7(1):e2006.
21. Benson DA, et al. (2013) GenBank. Nucleic Acids Res 41(Database issue):D36-D42.
22. Huerta AM, Collado-Vides J (2003) Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol 333(2):261-278. (Pubitemid 37188571)
23. Babitzke P, Granger L, Olszewski J, Kushner SR (1993) Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III. J Bacteriol 175(1):229-239. (Pubitemid 23016671)
24. +. Biochimie 72(11):791-802.
25. Wurtzel O, et al. (2012) Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8:583.
26. Gottesman S, Storz G (2011) Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3(12):a003798.
27. Ross JA, Ellis MJ, Hossain S, Haniford DB (2013) Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA 19(5):670-684.
28. Jahn CE, Charkowski AO, Willis DK (2008) Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J Microbiol Methods 75(2):318- 324.
29. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357-359.