Comparative genomic analysis of dinucleotide repeats in Tritryps

Gene

Volumn 487, Issue 1, 2011, Pages 29-37

  Duhagon, María Ana ^a,b   Smircich, Pablo ^a,b   Forteza, Diego ^a   Naya, Hugo ^c   Williams, Noreen ^d   Garat, Beatriz ^a  

^a Facultad de Ciencias   (Uruguay)

^b DEPARTAMENTO DE BIOQUÍMICA   (Uruguay)

^c INSTITUT PASTEUR DE MONTEVIDEO   (Uruguay)

^d UNIVERSITY AT BUFFALO   (United States)

Author keywords

DNA; Gene; Microsatellite; Polycistron; Regulation; Trypanosoma

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; DINUCLEOTIDE REPEAT; DNA STRAND; GENE CLUSTER; GENE FUNCTION; GENE STRUCTURE; GENETIC ANALYSIS; LEISHMANIA MAJOR; PRIORITY JOURNAL; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

ANIMALS; BASE SEQUENCE; DINUCLEOTIDE REPEATS; DNA, PROTOZOAN; GENOME, PROTOZOAN; HUMANS; LEISHMANIA MAJOR; PROTOZOAN INFECTIONS; SPECIES SPECIFICITY; TRYPANOSOMA BRUCEI BRUCEI; TRYPANOSOMA CRUZI;

EUKARYOTA; LEISHMANIA MAJOR; PROTOZOA; TRYPANOSOMA; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

EID: 84860422569     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.07.022     Document Type: Article

References (48)

1. Aguero F., Verdun R.E., Frasch A.C., Sanchez D.O. A random sequencing approach for the analysis of the Trypanosoma cruzi genome: general structure, large gene and repetitive DNA families, and gene discovery. Genome Res. 2000, 10:1996-2005.
2. Andersson B., Aslund L., Tammi M., Tran A.N., Hoheisel J.D., Pettersson U. Complete sequence of a 93.4-kb contig from chromosome 3 of Trypanosoma cruzi containing a strand-switch region. Genome Res. 1998, 8:809-816.
3. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27:573-580.
4. Berriman M., et al. The genome of the African trypanosome Trypanosoma brucei. Science 2005, 309:416-422.
5. Buschiazzo E., Gemmell N.J. The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays 2006, 28:1040-1050.
6. Campos P.C., Bartholomeu D.C., DaRocha W.D., Cerqueira G.C., Teixeira S.M. Sequences involved in mRNA processing in Trypanosoma cruzi. Int. J. Parasitol. 2008, 38:1383-1389.
7. Clayton C.E. Life without transcriptional control? From fly to man and back again. EMBO J. 2002, 21:1881-1888.
8. Clayton C., Shapira M. Post-transcriptional regulation of gene expression in trypanosomes and leishmanias. Mol. Biochem. Parasitol. 2007, 156:93-101.
9. Cribb P., Esteban L., Trochine A., Girardini J., Serra E. Trypanosoma cruzi TBP shows preference for C/G-rich DNA sequences in vitro. Exp. Parasitol. 2010, 124:346-349.
10. Di Noia J.M., D'Orso I., Sanchez D.O., Frasch A.C. AU-rich elements in the 3'-untranslated region of a new mucin-type gene family of Trypanosoma cruzi confers mRNA instability and modulates translation efficiency. J. Biol. Chem. 2000, 275:10218-10227.
11. Dokholyan N.V., Buldyrev S.V., Havlin S., Stanley H.E. Distributions of dimeric tandem repeats in non-coding and coding DNA sequences. J. Theor. Biol. 2000, 202:273-282.
12. D'Orso I., De Gaudenzi J.G., Frasch A.C. RNA-binding proteins and mRNA turnover in trypanosomes. Trends Parasitol. 2003, 19:151-155.
13. Duhagon M.A., Dallagiovanna B., Garat B. Unusual features of poly[dT-dG].[dC-dA] stretches in CDS-flanking regions of Trypanosoma cruzi genome. Biochem. Biophys. Res. Commun. 2001, 287:98-103.
14. Eckert K.A., Hile S.E. Every microsatellite is different: intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome. Mol. Carcinog. 2009, 48:379-388.
15. El-Sayed N.M., et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 2005, 309:409-415.
16. El-Sayed N.M., et al. Comparative genomics of trypanosomatid parasitic protozoa. Science 2005, 309:404-409.
17. Epplen J.T., Kyas A., Maueler W. Genomic simple repetitive DNAs are targets for differential binding of nuclear proteins. FEBS Lett. 1996, 389:92-95.
18. Frank A.C., Lobry J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238:65-77.
19. Green P., Ewing B., Miller W., Thomas P.J., Green E.D. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 2003, 33:514-517.
20. Haile S., Dupe A., Papadopoulou B. Deadenylation-independent stage-specific mRNA degradation in Leishmania. Nucleic Acids Res. 2008, 36:1634-1644.
21. Jeffreys A.J., Murray J., Neumann R. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol. Cell 1998, 2:267-273.
22. Jurka J., Pethiyagoda C. Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 1995, 40:120-126.
23. Kelkar Y.D., Strubczewski N., Hile S.E., Chiaromonte F., Eckert K.A., Makova K.D. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biol. Evol. 2010, 2:620-635.
24. Li Y.C., Korol A.B., Fahima T., Beiles A., Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 2002, 11:2453-2465.
25. Lowenhaupt K., Rich A., Pardue M.L. Nonrandom distribution of long mono- and dinucleotide repeats in Drosophila chromosomes: correlations with dosage compensation, heterochromatin, and recombination. Mol. Cell. Biol. 1989, 9:1173-1182.
26. Majewski J., Ott J. GT repeats are associated with recombination on human chromosome 22. Genome Res. 2000, 10:1108-1114.
27. Martinez-Calvillo S., Yan S., Nguyen D., Fox M., Stuart K., Myler P.J. Transcription of Leishmania major Friedlin chromosome 1 initiates in both directions within a single region. Mol. Cell 2003, 11:1291-1299.
28. Martinez-Calvillo S., Nguyen D., Stuart K., Myler P.J. Transcription initiation and termination on Leishmania major chromosome 3. Eukaryot. Cell 2004, 3:506-517.
29. McDonagh P.D., Myler P.J., Stuart K. The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes. Nucleic Acids Res. 2000, 28:2800-2803.
30. McKee A.E., Silver P.A. Systems perspectives on mRNA processing. Cell Res. 2007, 17:581-590.
31. Mugal C.F., Wolf J.B., von Grunberg H.H., Ellegren H. Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes. Genome Biol. Evol. 2010, 2:19-28.
32. Nilsson D., Andersson B. Strand asymmetry patterns in trypanosomatid parasites. Exp. Parasitol. 2005, 109:143-149.
33. Obado S.O., Taylor M.C., Wilkinson S.R., Bromley E.V., Kelly J.M. Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional â€oestrand-switch―domain as a major feature 2005, 36-43.
34. Palenchar J.B., Bellofatto V. Gene transcription in trypanosomes. Mol. Biochem. Parasitol. 2006, 146:135-141.
35. Plohl M., Luchetti A., Mestrovic N., Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2008, 409:72-82.
36. Respuela P., Ferella M., Rada-Iglesias A., Aslund L. Histone acetylation and methylation at sites initiating divergent polycistronic transcription in Trypanosoma cruzi. J. Biol. Chem. 2008, 283:15884-15892.
37. Rocha E.P., Danchin A. Ongoing evolution of strand composition in bacterial genomes. Mol. Biol. Evol. 2001, 18:1789-1799.
38. Sharma V.K., Brahmachari S.K., Ramachandran S. (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length. BMC Genomics 2005, 6:83.
39. Sharma P.C., Grover A., Kahl G. Mining microsatellites in eukaryotic genomes. Trends Biotechnol. 2007, 25:490-498.
40. Siegel T.N., et al. Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev. 2009, 23:1063-1076.
41. Sinden R.R. DNA Structure and Function 1994, Academic Press, San Diego.
42. Stallings R.L. CpG suppression in vertebrate genomes does not account for the rarity of (CpG)n microsatellite repeats. Genomics 1992, 13:890-891.
43. Stern M.Z., et al. Multiple roles for polypyrimidine tract binding (PTB) proteins in trypanosome RNA metabolism. RNA 2009, 15:648-665.
44. Tautz D., Trick M., Dover G.A. Cryptic simplicity in DNA is a major source of genetic variation. Nature 1986, 322:652-656.
45. Thomas S., Green A., Sturm N.R., Campbell D.A., Myler P.J. Histone acetylations mark origins of polycistronic transcription in Leishmania major. BMC Genomics 2009, 10:152.
46. Toth G., Gaspari Z., Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000, 10:967-981.
47. Wall L., Christiansen T., Orwant J. Programming Perl 2000, O'Reilly, Beijing; Cambridge, Mass. 3rd ed.
48. Zhang W., He L., Liu W., Sun C., Ratain M.J. Exploring the relationship between polymorphic (TG/CA)n repeats in intron 1 regions and gene expression. Hum. Genomics 2009, 3:236-245.