A single-base resolution map of an archaeal transcriptome

Genome Research

Volumn 20, Issue 1, 2010, Pages 133-141

  Wurtzel, Omri ^a   Sapra, Rajat ^b,c   Chen, Feng ^d   Zhu, Yiwen ^d,e   Simmons, Blake A ^b,c   Sorek, Rotem ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c JOINT BIOENERGY INSTITUTE   (United States)

^d U S DEPARTMENT OF ENERGY   (United States)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME; UNTRANSLATED RNA;

5' UNTRANSLATED REGION; ARCHAEAL GENE; ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA SEQUENCE; DNA TRANSCRIPTION; GENE MAPPING; GENE STRUCTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; RNA DEGRADATION; RNA ISOLATION; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; SULFOLOBUS SOLFATARICUS; TRANSCRIPTION INITIATION;

ARCHAEAL PROTEINS; BASE SEQUENCE; DNA, ARCHAEAL; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, ARCHAEAL; MOLECULAR SEQUENCE DATA; OPERON; RNA, MESSENGER; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, DNA; SULFOLOBUS SOLFATARICUS; TRANSCRIPTION INITIATION SITE;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 74949137952     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.100396.109     Document Type: Article

References (39)

1. Andersson AF, Lundgren M, Eriksson S, Rosenlund M, Bernander R, Nilsson P. 2006. Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol 7: R99. doi: 10.1186/gb-2006-7-10-r99.
2. Bejerano-Sagie M, Xavier KB. 2007. The role of small RNAs in quorum sensing. Curr Opin Microbiol 10: 189-198.
3. Bell SD, Jackson SP. 1998. Transcription and translation in Archaea: A mosaic of eukaryal and bacterial features. Trends Microbiol 6: 222-228.
4. Benelli D, Maone E, Londei P. 2003. Two different mechanisms for ribosome/mRNA interaction in archaeal translation initiation. Mol Microbiol 50: 635-643.
5. Brantl S. 2007. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10: 102-109.
6. Brenneis M, Hering O, Lange C, Soppa J. 2007. Experimental characterization of cis-acting elements important for translation and transcription in halophilic Archaea. PLoS Genet 3: e229. doi: 10.1371/ journal.pgen.0030229.
7. Brock TD, Brock KM, Belly RT, Weiss RL. 1972. Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84: 54-68.
8. Chen Q, Crosa JH. 1996. Antisense RNA, fur, iron, and the regulation of iron transport genes in Vibrio anguillarum. J Biol Chem 271: 18885-18891.
9. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004.WebLogo: A sequence logo generator. Genome Res 14: 1188-1190.
10. Evguenieva-Hackenberg E, Klug G. 2009. RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Prog Mol Biol Transl Sci 85: 275-317.
11. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. 2008. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18: 957-964.
12. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. 2008. The antisense transcriptomes of human cells. Science 322: 1855-1857.
13. Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, et al. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol 5: 285. doi: 10.1038/msb.2009.42.
14. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. 2004. In search of antisense. Trends Biochem Sci 29: 88-94.
15. Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM. 2009. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324: 1210-1213.
16. Masse E, Salvail H, Desnoyers G, Arguin M. 2007. Small RNAs controlling iron metabolism. Curr Opin Microbiol 10: 140-145.
17. McHardy AC, Goesmann A, Puhler A, Meyer F. 2004. Development of joint application strategies for two microbial gene finders. Bioinformatics 20: 1622-1631.
18. Moll I, Grill S, Gualerzi CO, Blasi U. 2002. Leaderless mRNAs in bacteria: Surprises in ribosomal recruitment and translational control. Mol Microbiol 43: 239-246.
19. Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M. 2007. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 392: 134-141.
20. Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH. 2009. The structure and complexity of a bacterial transcriptome. J Bacteriol 191: 3203-3211.
21. Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, et al. 2009. A strand-specific RNASeq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 5: e1000569. doi: 10.1371/journal.pgen.1000569.
22. Reiter WD, Hudepohl U, Zillig W. 1990. Mutational analysis of an archaebacterial promoter: Essential role of a TATA box for transcription efficiency and start-site selection in vitro. Proc Natl Acad Sci 87: 9509-9513.
23. Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ. 2009. Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci 106: 8605-8610.
24. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, et al. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci 98: 7835-7840.
25. Soppa J. 1999. Normalized nucleotide frequencies allow the definition of archaeal promoter elements for different archaeal groups and reveal base-specific TFB contacts upstream of the TATA box. Mol Microbiol 31: 1589-1592.
26. Sorek R, Kunin V, Hugenholtz P. 2008. CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6: 181-186.
27. Straub J, Brenneis M, Jellen-Ritter A, Heyer R, Soppa J, Marchfelder A. 2009. Small RNAs in haloarchaea: Identification, differential expression and biological function. RNA Biol 6: 281-292.
28. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, SeifertM, Borodina T, Soldatov A, Parkhomchuk D, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
29. Tang TH, Polacek N, Zywicki M, Huber H, Brugger K, Garrett R, Bachellerie JP, Huttenhofer A. 2005. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol 55: 469-481.
30. Toledo-Arana A, Repoila F, Cossart P. 2007. Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 10: 182-188.
31. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, et al. 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956.
32. Tolstrup N, Sensen CW, Garrett RA, Clausen IG. 2000. Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus. Extremophiles 4: 175-179.
33. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
34. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136: 615-628.
35. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846.
36. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al. 2003. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379-386.
37. Yoder-Himes DR, Chain PS, Zhu Y,Wurtzel O, Rubin EM, Tiedje JM, Sorek R. 2009. Mapping the Burkholderia cenocepacia niche response via highthroughput sequencing. Proc Natl Acad Sci 106: 3976-3981.
38. Zago MA, Dennis PP,Omer AD. 2005. The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 55: 1812-1828.
39. ZilligW, Palm P, Reiter WD, Gropp F, Puhler G, Klenk HP. 1988. Comparative evaluation of gene expression in archaebacteria. Eur J Biochem 173: 473-482.