Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Mullapudi, Nandita ^a   Lancto, Cheryl A ^b   Abrahamsen, Mitchell S ^b   Kissinger, Jessica C ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; CRYPTOSPORIDIUM PARVUM; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; HUMAN; HUMAN CELL; MULTIGENE FAMILY; NONHUMAN; PROMOTER REGION; PROTEIN MOTIF; PROTOZOAL GENETICS; REAL TIME POLYMERASE CHAIN REACTION;

ALGORITHMS; ANIMALS; CRYPTOSPORIDIUM PARVUM; GENE EXPRESSION PROFILING; GENOME, PROTOZOAN; GENOMICS; PATTERN RECOGNITION, AUTOMATED; POLYMERASE CHAIN REACTION; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

APICOMPLEXA; CRYPTOSPORIDIUM PARVUM; PROTISTA;

EID: 33846837277     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-13     Document Type: Article

References (31)

1. Spano F Crisanti A Cryptosporidium parvum: The many secrets of a small genome Int J Parasitol 2000 30 4 553 565 10.1016/S0020-7519(99)00188-5 10731576
2. Abrahamsen M Schroeder AA Analysis of intracellular Cryptosporidium parvum gene expression Mol Biochem Parasitol 1999 10589988
3. Girouard D Gallant J Akiyoshi DE Nunnari J Tzipori S Failure to propagate Cryptosporidium spp. in cell-free culture J Parasitol 2006 92 2 399 400 10.1645/GE-661R.1 16729703
4. Abrahamsen MS Templeton TJ Enomoto S Abrahante JE Zhu G Lancto CA Deng M Liu C Widmer G Tzipori S Buck GA Xu P Bankier AT Dear PH Konfortov BA Spriggs HF Iyer L Anantharaman V Aravind L Kapur V Complete Genome Sequence of the Apicomplexan, Cryptosporidium parvum Science 2004 304 441 445 10.1126/science.1094786 15044751
5. Xu P Widmer G Wang Y Ozaki LS Alves JM Serrano MG Puiu D Manque P Akiyoshi D Mackey AJ Pearson WR Dear PH Bankier AT Peterson DL Abrahamsen MS Kapur V Tzipori S Buck GA The genome of Cryptosporidium hominis Nature 2004 431 7012 1107 1112 10.1038/nature02977 15510150
6. Mercier C Lefebvre-Van Hende S Garber GE Lecordier L Capron A Cesbron-Delauw MF Common cis-acting elements critical for the expression of several genes of Toxoplasma gondii Mol Microbiol 1996 21 2 421 428 10.1046/j.1365-2958.1996.6501361.x 8858595
7. NF VANP Welagen J Vermeulen AN Schaap D The complete set of Toxoplasma gondii ribosomal protein genes contains two conserved promoter elements Parasitology 2006 133 Pt 1 19 31 16674839
8. Kibe MK Coppin A Dendouga N Oria G Meurice E Mortuaire M Madec E Tomavo S Transcriptional regulation of two stage-specifically expressed genes in the protozoan parasite Toxoplasma gondii Nucleic Acids Res 2005 33 5 1722 1736 10.1093/nar/gki314 15784612
9. Bailey TL Elkan C Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proc Int Conf Intell Syst Mol Biol 1994 2 28 36 7584402
10. Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J Mol Biol 2000 296 5 1205 1214 10.1006/jmbi.2000.3519 10698627
11. Templeton TJ Lancto CA Vigdorovich V Liu C London NR Hadsall KZ Abrahamsen MS The Cryptosporidium oocyst wall protein is a member of a multigene family and has a homolog in Toxoplasma Infect Immun 2004 72 2 980 987 321576 14742544 10.1128/IAI.72.2.980-987.2004
12. Striepen B Pruijssers AJP Huang J Li C Gubbels MJ Umejiego NN Hedstrom L Kissinger JC Gene transfer in the evolution of parasite nucleotide biosynthesis Proc Natl Acad Sci U S A 2004 101 9 3154 3159 10.1073/ pnas.0304686101 14973196 365759
13. Bell SP Dutta A DNA replication in eukaryotic cells Annu Rev Biochem 2002 71 333 374 10.1146/annurev.biochem.71.110601.135425 12045100
14. Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998 9 12 3273 3297 25624 9843569
15. Keithly JS Langreth SG Buttle KF Mannella CA Electron tomographic and ultrastructural analysis of the Cryptosporidium parvum relict mitochondrion, its associated membranes, and organelles J Eukaryot Microbiol 2005 52 2 132 140 10.1111/j.1550-7408.2005.04-3317.x 15817118
16. Entrala E Mascaro C Glycolytic enzyme activities in Cryptosporidium parvum oocysts FEMS Microbiol Lett 1997 151 1 51 57 10.1111/ j.1574-6968.1997.tb10393.x 9198281
17. Struhl K Fundamentally different logic of gene regulation in eukaryotes and prokaryotes Cell 1999 98 1 1 4 10.1016/S0092-8674(00)80599-1 10412974
18. Day DA Tuite MF Post-transcriptional gene regulatory mechanisms in eukaryotes: An overview J Endocrinol 1998 157 3 361 371 10.1677/ joe.0.1570361 9691970
19. Kozak M Regulation of translation via mRNA structure in prokaryotes and eukaryotes Gene 2005 361 13 37 10.1016/j.gene.2005.06.037 16213112
20. 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 Genome Biol 2003 4 2 R9 151308 12620119 10.1186/gb-2003-4-2-r9
21. Le Roch KG Johnson JR Florens L Zhou Y Santrosyan A Grainger M Yan SF Williamson KC Holder AA Carucci DJ Yates JR 3rd Winzeler EA Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle Genome Res 2004 14 11 2308 2318 525690 15520293 10.1101/gr.2523904
22. Radke JR Behnke MS Mackey AJ Radke JB Roos DS White MW The transcriptome of Toxoplasma gondii BMC Biol 2005 3 26 1325263 16324218 10.1186/ 1741-7007-3-26
23. Sullivan WJ Jr. Hakimi MA Histone mediated gene activation in Toxoplasma gondii Mol Biochem Parasitol 2006 16644030
24. Stamatoyannopoulos JA The genomics of gene expression Genomics 2004 84 3 449 457 10.1016/j.ygeno.2004.05.002 15498452
25. Deng M Templeton TJ London NR Bauer C Schroeder AA Abrahamsen MS Cryptosporidium parvum genes containing thrombospondin type 1 domains Infect Immun 2002 70 12 6987 6995 132954 12438378 10.1128/ IAI.70.12.6987-6995.2002
26. Coulson RM Hall N Ouzounis CA Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum Genome Res 2004 14 8 1548 1554 509263 15256513 10.1101/gr.2218604
27. Callebaut I Prat K Meurice E Mornon JP Tomavo S Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: Conserved features and differences relative to other eukaryotes BMC Genomics 2005 6 100 1199594 16042788 10.1186/ 1471-2164-6-100
28. Meissner M Soldati D The transcription machinery and the molecular toolbox to control gene expression in Toxoplasma gondii and other protozoan parasites Microbes Infect 2005 7 13 1376 1384 10.1016/ j.micinf.2005.04.019 16087378
29. Balaji S Babu MM Iyer LM Aravind L Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains Nucleic Acids Res 2005 33 13 3994 4006 1178005 16040597 10.1093/nar/gki709
30. Salzberg SL Pertea M Delcher AL Gardner MJ Tettelin H Interpolated Markov models for eukaryotic gene finding Genomics 1999 59 1 24 31 10.1006/geno.1999.5854 10395796
31. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004 14 6 1188 1190 419797 15173120 10.1101/ gr.849004