Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions

Nucleic Acids Research

Volumn 36, Issue 16, 2008, Pages

  Faridani, Omid R ^a   Mcinerney, Gerald M ^a   Gradin, Katarina ^a   Good, Liam ^a,b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b ROYAL VETERINARY COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; DOUBLE STRANDED RNA; ESCHERICHIA COLI PROTEIN; HOK PROTEIN; MESSENGER RNA; MICRORNA; PROTEIN TAR; RNA LIGASE; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; VIRUS PROTEIN; BACTERIAL TOXIN; HOK PROTEIN, E COLI; NUCLEASE S1; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; POLYNUCLEOTIDE 5' HYDROXYL KINASE;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; HUMAN IMMUNODEFICIENCY VIRUS; INTERACTIONS WITH RNA; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA INTERFERENCE; RNA METABOLISM; RNA SEQUENCE; RNA TRANSLATION; SENSITIVITY AND SPECIFICITY; CHEMISTRY; ENZYME SPECIFICITY; GENETIC PROCEDURES; GENETICS; LONG TERMINAL REPEAT; METABOLISM;

ESCHERICHIA COLI; HUMAN IMMUNODEFICIENCY VIRUS; MAMMALIA;

ASPERGILLUS NUCLEASE S1; BACTERIAL TOXINS; DNA LIGASES; ESCHERICHIA COLI PROTEINS; GENETIC TECHNIQUES; HIV LONG TERMINAL REPEAT; POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, DOUBLE-STRANDED; RNA, MESSENGER; SUBSTRATE SPECIFICITY;

EID: 52649110711     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn445     Document Type: Article

References (18)

1. Nicholson,A.W. (1996) Structure, reactivity, and biology of double-stranded RNA. Prog. Nucleic Acid. Res. Mol. Biol., 52 1-65.
2. Gullerova,M. and Proudfoot,N.J. (2008) Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell, 132, 983-995.
3. Tariq,M. and Paszkowski,J. (2004) DNA and histone methylation in plants. Trends Genet., 20, 244-251.
4. Kumar,M. and Carmichael,G.G. (1998) Antisense RNA: Function and fate of duplex RNA in cells of higher eukaryotes. Microbial. Mol. Biol. Rev. 62, 1415-1434.
5. Ott,M., Emiliani,S., Van Lint,C., Herbein,G., Lovett,J., Chirmule,N., McCloskey,T., Pahwa,S. and Verdin,E. (1997) Immune hyperactivation of HIV-1-infected T cells mediated by Tat and the CD28 pathway. Science 275, 1481-1485.
6. Dekker,N.H., Abels,J.A., Veenhuizen,P.T., Bruinink,M.M. and Dekker,C. (2004) Joining of long double-stranded RNA molecules through controlled overhangs. Nucleic Acids Res., 32, e140.
7. Imai,M., Richardson,M.A., Ikegami,N., Shatkin,A.J. and Furuichi,Y. (1983) Molecular cloning of double-stranded RNA virus genomes. Proc. Natl Acad. Sci. USA, 80, 373-377.
8. Lambden,P.R., Cooke,S.J., Caul,E.O. and Clarke,I.N. (1992) Cloning of noncultivatable human rotavirus by single primer amplification. J. Virol., 66, 1817-1822.
9. Higgins,N.P., Geballe,A.P. and Cozzarelli,N.R. (1979) Addition of oligonucleotides to the 5'-terminus of DNA by T4 RNA ligase. Nucleic Acids Res., 6, 1013-1024.
10. Lehman,R.I. (1981)Endonucleases specific for single-stranded polynucleotides. In Boyer,P.D. (ed.), The Enzymes, Vol. 4, 3rd edn. Academic Press Inc., New York, pp. 193-201.
11. Sakonju,S., Bogenhagen,D.F. and Brown,D.D. (1980) A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell, 19, 13-25.
12. Vogt,V.M. (1973) Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. Ear. J. Biochem., 33, 192-200.
13. Shishido,K. and Ando,T. (1981) Efficiency of T4 DNA ligase-catalyzed end joining after S1 endonuclease treatment on duplex DNA containing single-stranded portions. Biochim. Biophys. Acta, 656, 123-127.
14. Uchida,T., Rossignol,F., Matthay,M.A., Mounier,R., Couette,S., Clottes,E. and Clerici,C. (2004) Prolonged hypoxia differentially regulates hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha expression in lung epithelial cells: Implication of natural antisense HIF-1alpha. J. Biol. Chem., 279, 14871-14878.
15. Thrash-Bingham,C.A. and Tartof,K.D. (1999) aHIF: A natural antisense transcript overexpressed in human renal cancer and during hypoxia. J. Natl Cancer Inst., 91, 143-151.
16. Cayre,A., Rossignol,F., Clottes,E. and Penault-Llorea,F. (2003) aHIF but not HIF-1alpha transcript is a poor prognostic marker in human breast cancer. Breast Cancer Res., 5, R223-R230.
17. Munroe,S.H. and Zhu,J. (2006) Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective. Cell. Mol. Life Sci., 63, 2102-2118.
18. Jeang,K.T., Xiao,H. and Rich,E.A. (1999) Multifaceted activities of the HIV-1 transactivator of transcription, Tat. J. Biol. Chem., 274 28837-28840.