The Activator/Dissociation transposable elements comprise a two-component gene regulatory switch that controls endogenous gene expression in maize

Genetics

Volumn 187, Issue 3, 2011, Pages 749-759

  Bai, Ling ^a   Brutnell, Thomas P ^a  

^a United States Department of Agriculture   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN PINK SCUTELLUM 1; TRANSPOSASE; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

5' UNTRANSLATED REGION; ALLELE; ARTICLE; BIOACCUMULATION; COPY NUMBER VARIATION; DISSOCIATION; GENE EXPRESSION REGULATION; GENE INSERTION; GENE LOCUS; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; LOSS OF FUNCTION MUTATION; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT GENETICS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY MECHANISM; SEEDLING; TRANSCRIPTION INITIATION SITE; TRANSPOSON; WILD TYPE;

ALLELES; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PHENOTYPE; PLANT PROTEINS; TRANSCRIPTION INITIATION SITE; TRANSPOSASES; ZEA MAYS;

ZEA MAYS;

EID: 79953218383     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.124149     Document Type: Article

References (74)

1. AHERN, K. R., P. DEEWATTHANAWONG, J. SCHARES, M. MUSZYNSKI, R. WEEKS et al., 2009 Regional mutagenesis using Dissociation in maize. Methods 49: 248-254.
2. BAI, L., M. SINGH, L. PITT, M. SWEENEY and T. P. BRUTNELL, 2007 Generating novel allelic variation through Activator insertional mutagenesis in maize. Genetics 175: 981-992.
3. BAI, L., E. H. KIM, D. DELLAPENNA and T. P. BRUTNELL, 2009 Novel lycopene epsilon cyclase activities in maize revealed through perturbation of carotenoid biosynthesis. Plant J. 59: 588-599.
4. BARKAN, A., and R. A. MARTIENSSEN, 1991 Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proc. Natl. Acad. Sci. USA 88: 3502-3506.
5. BRUTNELL, T. P., 1995 Epigenetic regulation of Activator (Ac) in maize, Ph.D. Thesis, Yale University, New Haven, CT.
6. BRUTNELL, T. P., and S. L. DELLAPORTA, 1994 Somatic inactivation and reactivation of Ac associated with changes in cytosine methylation and transposase expression. Genetics 138: 213-225.
7. BURKE, T. W., and J. T. KADONAGA, 1996 Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10: 711-724.
8. BURKE, T. W., and J. T. KADONAGA, 1997 The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 11: 3020-3031.
9. CARNINCI, P., A. SANDELIN, B. LENHARD, S. KATAYAMA, K. SHIMOKAWA et al., 2006 Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38: 626-635.
10. CHOMET, P., 1988 Characterization of stable and metastable changes of the maize transposable element, Activator. Ph.D. Thesis, State University of New York, Stony Brook, NY.
11. CHOMET, P. S., S. WESSLER and S. L. DELLAPORTA, 1987 Inactivation of the maize transposable element Activator (Ac) is associated with its DNA modification. EMBO J. 6: 295-302.
12. CONRAD, L. J., L. BAI, K. AHERN, K. DUSINBERRE, D. P. KANE et al., 2007 State II Dissociation element formation following Activator excision in maize. Genetics 177: 737-747.
13. CONRAD, L. J., and T. P. BRUTNELL, 2005 Ac-immobilized, a stable source of Activator transposase that mediates sporophytic and gametophytic excision of Dissociation elements in maize. Genetics 171: 1999-2012.
14. COUPLAND, G., C. PLUM, S. CHATTERJEE, A. POST and P. STARLINGER, 1989 Sequences near the termini are required for transposition of the maize transposon Ac in transgenic tobacco plants. Proc. Natl. Acad. Sci. USA 86: 9385-9388.
15. COURAGE-TEBBE, U., H. P. DORING, N. FEDOROFF and P. STARLINGER, 1983 The controlling element Ds at the Shrunken locus in Zea mays: structure of the unstable sh-m5933 allele and several revertants. Cell 34: 383-393.
16. DOONER, H. K., and J. L. KERMICLE, 1971 Structure of the R r tandem duplication in maize. Genetics 67: 427-436.
17. DOONER, H. K., and A. BELACHEW, 1991 Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize. Genetics 129: 855-862.
18. DORING, H. P., and P. STARLINGER, 1986 Molecular genetics of transposable elements in plants. Annu. Rev. Genet. 20: 175-200.
19. DORING, H. P., B. NELSEN-SALZ, R. GARBER and E. TILLMANN, 1989 Double Ds elements are involved in specific chromosome breakage. Mol. Gen. Genet. 219: 299-305.
20. DOWE, JR., M. F., G. W. ROMAN and A. S. KLEIN, 1990 Excision and transposition of two Ds transposons from the bronze mutable 4 derivative 6856 allele of Zea mays L. Mol. Gen. Genet. 221: 475-485.
21. DYNAN, W. S., 1986 Promoters for housekeeping genes. Trends Genet. 2: 196-197.
22. ELROUBY, N., and T. E. BUREAU, 2000 Molecular characterization of the Abp1 59-flanking region in maize and the teosintes. Plant Physiol. 124: 369-377.
23. ENGLISH, J. J., K. HARRISON and J. JONES, 1995 Aberrant transpositions of maize double Ds-like elements usually involve Ds ends on sister chromatids. Plant Cell 7: 1235-1247.
24. FEDOROFF, N., S. WESSLER and M. SHURE, 1983 Isolation of the transposable maize controlling elements Ac and Ds. Cell 35: 235-242.
25. FESCHOTTE, C., N. JIANG and S. R. WESSLER, 2002 Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329-341.
26. FRIDLENDER, M., Y. SITRIT, O. SHAUL, O. GILEADI and A. A. LEVY, 1998 Analysis of the Ac promoter: structure and regulation. Mol. Gen. Genet. 258: 306-314.
27. FUSSWINKEL, H., S. SCHEIN, U. COURAGE, P. STARLINGER and R. KUNZE, 1991 Detection and abundance of mRNA and protein encoded by transposable element activator (Ac) in maize. Mol. Gen. Genet. 225: 186-192.
28. GIERL, A., S. LUTTICKE and H. SAEDLER, 1988 TnpA product encoded by the transposable element En-1 of Zea mays is a DNA binding protein. EMBO J. 7: 4045-4053.
29. GROTEWOLD, E., P. ATHMA and T. PETERSON, 1991 Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors. Proc. Natl. Acad. Sci. USA 88: 4587-4591.
30. HEINLEIN, M., 1996 Excision patterns of Activator (Ac) and Dissociation (Ds) elements in Zea mays L.: implications for the regulation of transposition. Genetics 144: 1851-1869.
31. KIGER, A. A., S. GIGLIOTTI and M. T. FULLER, 1999 Developmental genetics of the essential Drosophila nucleoporin nup154: allelic differences due to an outward-directed promoter in the P-element 39 end. Genetics 153: 799-812.
32. KLEIN, A. S., M. CLANCY, L. PAJE-MANALO, D. B. FURTEK, L. C. HANNAH et al., 1988 The mutation bronze-mutable 4 derivative 6856 in maize is caused by the insertion of a novel 6.7-kilobase pair transposon in the untranslated leader region of the bronze-1 gene. Genetics 120: 779-790.
33. KOLESNIK, T., I. SZEVERENYI, D. BACHMANN, C. S. KUMAR, S. JIANG et al., 2004 Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J. 37: 301-314.
34. KUNZE, R., 1996 The maize transposable element Activator (Ac). Curr. Top. Microbiol. Immunol. 204: 161-194.
35. KUNZE, R., and P. STARLINGER, 1989 The putative transposase of transposable element Ac from Zea mays L. interacts with subterminal sequences of Ac. EMBO J. 8: 3177-3185.
36. KUNZE, R., and C. F. WEIL, 2002 The hAT and CACTA superfamily of plant transposons. Mobile DNA II: 565-610.
37. KUNZE, R., U. STOCHAJ, J. LAUFS and P. STARLINGER, 1987 Transcription of the transposable element Activator (Ac) of Zea mays L. EMBO J. 6: 1555-1563.
38. KUTACH, A. K., and J. T. KADONAGA, 2000 The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20: 4754-4764.
39. MARTIENSSEN, R., and A. BARON, 1994 Coordinate suppression of mutations caused by Robertson's Mutator transposons in maize. Genetics 136: 1157-1170.
40. MASSON, P., R. SUROSKY, J. A. KINGSBURY and N. V. FEDOROFF, 1987 Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus. Genetics 117: 117-137.
41. MAY, B. P., H. LIU, E. VOLLBRECHT, L. SENIOR, P. D. RABINOWICZ et al., 2003 Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. USA 100: 11541-11546.
42. MCCLINTOCK, B., 1946 Maize genetics. Carnegie Inst. Wash. Year Book 45: 176-186.
43. MCCLINTOCK, B., 1951 Chromosome organization and gene expression. Cold Spring Harb Symp. Quant. Biol. 16: 13-47.
44. MCCLINTOCK, B., 1954 Mutations in maize and chromosomal aberrations in Neurospora. Carnegie Inst. Wash. Year Book 53: 254-260.
45. MCCLINTOCK, B., 1962 Topographical relations between elements of control systems in maize. Carnegie Inst. Wash. Year Book 61: 448-461.
46. MCCLINTOCK, B., 1965 Components of action of the regulators Spm and Ac. Carnegie Inst. Wash. Year Book 64: 527-534.
47. MENSSEN, A., S. HOHMANN, W. MARTIN, P. S. SCHNABLE, P. A. PETERSON et al., 1990 The En/Spm transposable element of Zea mays contains splice sites at the termini generating a novel intron from a dSpm element in the A2 gene. EMBO J. 9: 3051-3057.
48. MORENO, M. A., J. CHEN, I. GREENBLATT and S. L. DELLAPORTA, 1992 Reconstitutional mutagenesis of the maize P gene by short-range Ac transpositions. Genetics 131: 939-956.
49. MULLER-NEUMANN, M., J. I. YODER and P. STARLINGER, 1984 The DNA sequence of the transposable element Ac of Zea mays L. Mol. Gen. Genet. 198: 9-24.
50. NAITO, K., F. ZHANG, T. TSUKIYAMA, H. SAITO, C. N. HANCOCK et al., 2009 Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134.
51. O'SHEA-GREENFIELD, A., and S. T. SMALE, 1992 Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription. J. Biol. Chem. 267: 1391-1402.
52. POHLMAN, R. F., N. V. FEDOROFF and J. MESSING, 1984a Correction: nucleotide sequence of Ac. Cell 39: 417.
53. POHLMAN, R. F., N. V. FEDOROFF and J. MESSING, 1984b The nucleotide sequence of the maize controlling element Activator. Cell 37: 635-643.
54. RALSTON, E., J. ENGLISH and H. K. DOONER, 1989 Chromosome-breaking structure in maize involving a fractured Ac element. Proc. Natl. Acad. Sci. USA 86: 9451-9455.
55. RUDENKO, G. N., H. J. NIJKAMP and J. HILLE, 1994 Ds read-out transcription in transgenic tomato plants. Mol. Gen. Genet. 243: 426-433.
56. SCHIEFELBEIN, J. W., D. B. FURTEK, H. K. DOONER and O. E. NELSON, JR., 1988a Two mutations in a maize bronze-1 allele caused by transposable elements of the Ac-Ds family alter the quantity and quality of the gene product. Genetics 120: 767-777.
57. SCHIEFELBEIN, J. W., V. RABOY, H. Y. KIM and O. E. NELSON, 1988b Molecular characterization of suppressor-mutator (Spm)-induced mutations at the bronze-1 locus in maize: the bz-m13 alleles. Basic Life Sci. 47: 261-278.
58. SCHNABLE, P. S., D. WARE, R. S. FULTON, J. C. STEIN, F. WEI et al., 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
59. SCHWARZ-SOMMER, Z., A. GIERL, R. BERNDTGEN and H. SAEDLER, 1985 Sequence comparison of 'states' of a1-m1 suggests a model of Spm (En) action. EMBO J. 4: 2439-2443.
60. SIMON, R., and P. STARLINGER, 1987 Transposable element Ds2 of Zea mays influences polyadenylation and splice site selection. Mol. Gen. Genet. 209: 198-199.
61. SINGH, M., P. E. LEWIS, K. HARDEMAN, L. BAI, J. K. ROSE et al., 2003 Activator mutagenesis of the pink scutellum1/viviparous7 locus of maize. Plant Cell 15: 874-884.
62. SLOTKIN, R. K., M. FREELING and D. LISCH, 2005 Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat. Genet. 37: 641-644.
63. SLOTKIN, R. K., and R. MARTIENSSEN, 2007 Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8: 272-285.
64. SMALE, S. T., 1997 Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta 1351: 73-88.
65. SMALE, S. T., and D. BALTIMORE, 1989 The "initiator" as a transcription control element. Cell 57: 103-113.
66. SMALE, S. T., and J. T. KADONAGA, 2003 The RNA polymerase II core promoter. Annu. Rev. Biochem. 72: 449-479.
67. SULLIVAN, T. D., J. W. SCHIEFELBEIN, JR. and O. E. NELSON, JR., 1989 Tissue-specific effects of maize bronze gene promoter mutations induced by Ds1 insertion and excision. Dev. Genet. 10: 412-424.
68. SUNDARESAN, V., P. SPRINGER, T. VOLPE, S. HAWARD, J. D. JONES et al., 1995 Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9: 1797-1810.
69. VOLLBRECHT, E., L. REISER and S. HAKE, 2000 Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene, knotted1. Development 127: 3161-3172.
70. VOLLBRECHT, E., J. DUVICK, J. P. SCHARES, K. R. AHERN, P. DEEWATTHANAWONG et al., 2010 Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 22: 1667-1685.
71. WEIL, C. F., and S. R. WESSLER, 1990 The effects of plant transposable element insertion on transcription initiation and RNA processing. Annu. Rev. Plant Physiol. Plant Mol. Biol. 41: 527-552.
72. WESSLER, S. R., 1988 Phenotypic diversity mediated by the maize transposable elements Ac and Spm. Science 242: 399-405.
73. WESSLER, S. R., G. BARAN and M. VARAGONA, 1987 The maize transposable element Ds is spliced from RNA. Science 237: 916-918.
74. ZHANG, J., C. YU, V. PULLETIKURTI, J. LAMB, T. DANILOVA et al., 2009 Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize. Genes Dev. 23: 755-765.