A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum

Molecular and Biochemical Parasitology

Volumn 144, Issue 2, 2005, Pages 149-158

  Upadhyay, Roopam ^a   Bawankar, Praveen ^a   Malhotra, Deepti ^a   Patankar, Swati ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

Bioinformatics; GC content; Malaria; Noncoding RNA; Plasmodium

Indexed keywords

MICRORNA; RNA; SELENOCYSTEINE; SMALL NUCLEAR RNA; TRANSFER RNA;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE EXPRESSION; GENE SEQUENCE; GENOME; MALARIA; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, INTERGENIC; GENOME, PROTOZOAN; MOLECULAR SEQUENCE DATA; PLASMODIUM FALCIPARUM; RNA, PROTOZOAN; RNA, UNTRANSLATED; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

PLASMODIUM FALCIPARUM;

EID: 27644468494     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbiopara.2005.08.012     Document Type: Article

References (30)

1. V. Ambros microRNAs: tiny regulators with great potential Cell 107 2001 823 826
2. J.S. Mattick RNA regulation: a new genetics? Nat Rev Genet 5 2004 316 323
3. M.J. Gardner, S.J. Shallom, and Carlton Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 Nature 419 2002 531 534
4. N. Hall, A. Pain, and M. Berriman Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13 Nature 419 2002 527 531
5. R.W. Hyman, E. Fung, and A. Conway Sequence of Plasmodium falciparum chromosome 12 Nature 419 2002 534 537
6. P. Horrocks, K. Dechering, and M. Lanzer Control of gene expression in Plasmodium falciparum Mol Biochem Parasitol 95 1998 171 181
7. S. Patankar, A. Munasinghe, A. Shoaibi, L.M. Cummings, and D.F. Wirth Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite Mol Biol Cell 12 2001 3114 3125
8. R.M. Coulson, N. Hall, and C.A. Ouzounis Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum Genome Res 14 2004 1548 1554
9. N. Hall, M. Karras, and J.D. Raine A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic and proteomic analyses Science 307 2005 82 86
10. S.R. Eddy Computational genomics of noncoding RNA genes Cell 109 2002 137 140
11. A. Huttenhofer, J. Cavaille, and J.P. Bachellerie Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms Methods Mol Biol 265 2004 409 428
12. L. Argaman, R. Hershberg, and J. Vogel Novel small RNA-encoding genes in the intergenic regions of Escherichia coli Curr Biol 11 2001 941 950
13. E. Rivas, and S.R. Eddy Noncoding RNA gene detection using comparative sequence analysis BMC Bioinformatics 2 2001 8
14. R.J. Klein, Z. Misulovin, and S.R. Eddy Noncoding RNA genes identified in A-T rich hyperthermophiles Proc Natl Acad Sci USA 99 2002 7542 7547
15. T. Mourier, A. Pain, B. Barrell, and S. Griffiths-Jones A selenocysteine tRNA and SECIS element in Plasmodium falciparum Rna 11 2005 119 122
16. W. Trager, and J.B. Jensen Human malaria parasites in continuous culture Science 193 1976 673 675
17. A. Bahl, B. Brunk, and J. Crabtree PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data Nucleic Acids Res 31 2003 212 215
18. P. Schattner Searching for RNA genes using base-composition statistics Nucleic Acids Research 30 2002 2076 2082
19. J.M. Carlton, S. Angiuoli, and B. Suh Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii Nature 419 2002 512 519
20. M. Verma, M.J. Olnes, R.N. Kurl, and E.A. Davidson Primary structure of the canine U1 snRNA Gene 154 1995 255 257
21. R.F. Weaver Post-transcriptional events: splicing Mol Biol 2002 430 439
22. E.S. Maxwell, and M.J. Fournier The small nucleolar RNAs Ann Rev Biochem 64 1995 897 934
23. T. Kiss Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions Cell 109 2002 145 148
24. Z. Bozdech, J. Zhu, M.P. Joachimiak, F.E. Cohen, B. Pulliam, and J.L. DeRisi Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray Genome Biol 4 2003 R9
25. K.G. Le Roch, Y. Zhou, and P.L. Blair Discovery of gene function by expression profiling of the malaria parasite life cycle Science 301 2003 1503 1508
26. J.A. Martens, L. Laprade, and F. Winston Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene Nature 429 2004 571 574
27. K.A. Frazer, L. Pachter, A. Poliakov, E.M. Rubin, and I. Dubchak VISTA: computational tools for comparative genomics Nucleic Acids Res 32 2004 273 279
28. K.M. Wassarman, F. Repoila, C. Rosenow, G. Storz, and S. Gottesman Identification of novel small RNAs using comparative genomics and microarrays Genes Dev 15 2001 1637 1651
29. K.T. Militello, M. Dodge, L. Bethke, and D.F. Wirth Identification of regulatory elements in the Plasmodium falciparum genome Mol Biochem Parasitol 134 2004 75 88
30. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. PLoS Biol 2003;1(1):E5.