Transcriptional and post-transcriptional enhancement of gene expression by the 5′ UTR intron of rice rubi3 gene in transgenic rice cells

Molecular Genetics and Genomics

Volumn 279, Issue 4, 2008, Pages 429-439

  Samadder, Partha ^a,c   Sivamani, Elumalai ^a   Lu, Jianli ^a   Li, Xianggan ^b   Qu, Rongda ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b SYNGENTA BIOTECHNOLOGY INC   (United States)

^c UNIVERSITY OF ARIZONA COLLEGE OF MEDICINE   (United States)

Author keywords

EJC; Exon; Gene expression; IME; Nuclear run on

Indexed keywords

5' UNTRANSLATED REGION; ARTICLE; GENE ACTIVITY; GENE EXPRESSION; GENETIC TRANSCRIPTION; INTRON; NONHUMAN; PLANT CELL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REPORTER GENE; RICE; RNA ANALYSIS; RNA PROCESSING; STEADY STATE; SUSPENSION CELL CULTURE; TRANSGENICS;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; DNA PRIMERS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENES, REPORTER; INTRONS; ORYZA SATIVA; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; POLYUBIQUITIN; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, PLANT; TRANSCRIPTION, GENETIC;

ANIMALIA; DICOTYLEDONEAE; EUKARYOTA; LILIOPSIDA;

EID: 43349100430     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0323-8     Document Type: Article

References (61)

1. Azhakanandam K, McCabe MS, Power JB, Lowe KC, Cocking EC, Davey MR (2000) T-DNA transfer, integration, expression and inheritance in rice: effects of plant genotype and Agrobacterium super-virulence. J Plant Physiol 157:429-439
2. Belostotsky DA, Rose AB (2005) Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events. Trends Plant Sci 10:347-353
3. Blockland RV, Geest NV, Mol JNM, Kooter JM (1994) Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase RNA turnover. Plant J 6:861-877
4. Bourdon V, Harvey A, Lonsdale DM (2001) Introns and their positions affect the translational activity of mRNA in plant cells. EMBO Rep 2:394-398
5. Bousquet-Antonelli C, Presutti C, Tollervey D (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765-775
6. Buchman AR, Berg P (1988) Comparison of intron-dependent and intron-independent gene expression. Mol Cell Biol 8:4395-4405
7. Callis J, Fromm ME, Walbot V (1987) Introns increase gene expression in cultured maize cells. Genes Dev 1:1183-1200
8. Chekanova JA, Dutko JA, Mian IS, Belostotsky DA (2002) Arabidopsis thaliana exosome subuint AtRrp4p is a hydrolitic 3′→5′ exonuclease containing S1 and KH RNA binding domains. Nucleic Acids Res 30:695-700
9. Christensen AH, Quail PH (1996) Ubiquitin promoter-based vectors for high-level expression of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Res 5:213-218
10. Chung BYW, Simons C, Firth AE, Brown CM, Hellens RP (2006) Effect of 5′UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7:120
11. Clancy M, Hannah LC (2002) Splicing of the maize Sh1 first intron is essential for enhancement of gene expression, and a T-rich motif increases expression without affecting splicing. Plant Physiol 130:918-929
12. Clancy M, Vasil V, Hannah LC, Vasil IK (1994) Maize Shrunken-1 intron and exon regions increase gene expression in maize protoplasts. Plant Sci 98:151-161
13. Dean C, Favreau M, Bondnutter D, Bedbrook J, Dunsmuir P (1989) Sequences downstream of translation start regulate quantitative expression of 2 Petunia rbcs genes. Plant Cell 1:201-208
14. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 14:19-21
15. Egoavil C, Marton HA, Baynton CE, McCullough AJ, Schuler MA (1997) Structural analysis of elements contributing to 5′ splice site selection in plant pre-mRNA transcripts. Plant J 12:971-980
16. Eick D, Kohlhuber LF, Wolf DA, Strobl LJ (1994) Activation of pausing RNA polymerases by nuclear run-on experiments. Anal Biochem 218:347-351
17. Furger A, O'Sullivan JM, Binnie A, Lee BA, Proudfoot NJ (2002) Promoter proximal splice sites enhance transcription. Genes Dev 16:2792-2799
18. Gallagher SR (1992) GUS protocols: using the GUS gene as a reporter of gene expression quantitation of GUS activity by fluorometry. Academic press Inc., New York
19. Gallie DR (1993) Posttranscriptional regulation of gene-expression in plants. Annu Rev Plant Physiol Plant Mol Biol 44:77-105
20. Goodall GJ, Filipowicz W (1989) The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58:473-483
21. Goodall GJ, Kiss T, Filipowicz W (1991) Nuclear RNA splicing and small nuclear RNAs and their genes in higher plants. Oxf Surv Plant Mol Cell Biol 7:255-296
22. Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271-282
23. Huang MTF, Gorman CM (1990) Intervening sequences increase efficiency of RNA 3′ processing and accumulation of cytoplasmic RNA. Nucleic Acids Res 18:937-947
24. Ingelbrecht I, de Carvalho F (1992) Isolation of nuclei and in vivo run-off transcription. In: Inze D, Van der Straeten D, Van Montagu M (eds) EMBO practical course on plant molecular biology. Laboratorium voor Genetica, Gent, pp 117-132
25. Ingham DJ, Beer S, Money S, Hansen G (2001) Quantitative real-time PCR assay for determining transgene copy number in transformed plants. Biotechniques 31:132-140
26. Initiative AG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
27. Jefferson RA, Kavanagh TA, Bevan MW (1987) Gus fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901-3907
28. Kataoka N, Yong J, Kim VN, Velazquez F, Perkinson RA, Wang F, Dreyfuss G (2000) Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol Cell 6:673-682
29. Kataoka N, Diem MD, Kim VN, Yong J, Dreyfuss G (2001) Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing-dependent exon-exon junction complex. EMBO J 20:6424-6433
30. Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25:1869-1872
31. Klein TM, Gradziel T, Fromm ME, Sanford JC (1988) Factors influencing gene delivery into Zea mays cells by high-velocity microprojectiles. Biotechnology 6:559-563
32. Lambermon MHL, Simpson GG, Kirk DAW, Hemmings-Mieszczak M, Klahre U, Filipowicz W (2000) UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation. EMBO J 19:1638-1649
33. Le Hir H, Izaurralde E, Maquat LE, Moore MJ (2000) The spliceosome depositsmultiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J 19:6860-6869
34. Lu J (2006) Gene expression regulation by the 5′ regulatory sequences of the rice rubi3 gene in transgenic rice plants. Ph.D. thesis. North Carolina State University. http://www.lib.ncsu.edu/theses/available/etd- 04272006-145216/unrestricted/etd.pdf
35. Lu SH, Cullen BR (2003) Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9:618-630
36. Luehrsen KR, Walbot V (1991) Intron enhancement of gene-expression and the splicing efficiency of introns in maize cells. Mol Gen Genet 225:81-93
37. Luehrsen KR, Walbot V (1994) Addition of A-rich and U-rich sequence increases the splicing efficiency of a deleted form of a maize intron. Plant Mol Biol 24:449-463
38. Luehrsen KR, Taha S, Walbot V (1994) Nuclear pre-messenger RNA processing in higher plants. Nucleic Acid Res 47:149-193
39. Mascarenhas D, Mettler IJ, Pierce DA, Lowe HW (1990) Intron-mediated enhancement of heterologous gene expression in maize. Plant Mol Biol 15:913-920
40. McCullough AJ, Schuler MA (1997) Intronic and exonic sequences modulate 5' splice site selection in plant nuclei. Nucleic Acids Res 25:1071-1077
41. McElroy D, Zhang WG, Cao J, Wu R (1990) Isolation of an efficient actin promoter for use in rice transformation. Plant Cell 2:163-171
42. Nott A, Muslin SH, Moore MJ (2003) A quantitative analysis of intron effects on mammalian gene expression. RNA 9:607-617
43. Nott A, Le Hir H, Moore MJ (2004) Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Gene Dev 18:210-222
44. Okkema PG, Harrison SW, Plunger V, Aryana A, Fire A (1993) Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans. Genetics 135:385-404
45. Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JWS, Shaw PJ (2005) Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell 16:260-269
46. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating rnRNA processing with transcription. Cell 108:501-512
47. Reddy ASN (2001) Nuclear pre-mRNA splicing in plants. Crit Rev Plant Sci 20:523-571
48. Rethmeier N, Seurinck J, VanMontagu M, Cornelissen M (1997) Intron-mediated enhancement of transgene expression in maize is a nuclear, gene-dependent process. Plant J 12:895-899
49. Rethmeier N, Kramer E, van Montagu M, Cornelissen M (1998) Identification of cat sequences required for intron-dependent gene expression in maize cells. Plant J 13:833-835
50. Rose AB (2002) Requirements for intron-mediated enhancement of gene expression in Arabidopsis. RNA 8:1444-1453
51. Rose AB (2004) The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J 40:744-751
52. Rose AB, Beliakoff JA (2000) Intron-mediated enhancement of gene expression independent of unique intron sequence and splicing. Plant Physiol 122:535-542
53. Rose AB, Last RL (1997) Introns act post-transcriptionally to increase expression of the Arabidopsis thaliana tryptophan pathway gene PAT1. Plant J 11:455-464
54. Sanford JR, Gray NK, Beckmann K, Caceres JF (2004) A novel role for shuttling SR proteins in mRNA translation. Genes Dev 18:755-768
55. Simpson GG, Filipowicz W (1996) Splicing of precursors to mRNA in higher plants: Mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. Plant Mol Biol 32:1-41
56. Simpson CG, Simpson GG, Clark G, Leader DJ, Vaux P, Guerineau F, Waugh R, Brown JWS (1992) Splicing of plant pre-messenger RNAs. Proc R Soc Edinb B Biol Sci 99:31-50
57. Sivamani E, Qu R (2006) Expression enhancement of a rice polyubiquitin gene promoter. Plant Mol Biol 60:225-239
58. Sivamani E, Huet H, Shen P, Ong CA, de Kochko A, Fauquet C, Beachy RN (1999) Rice plant (Oryza sativa L.) containing Rice tungro spherical virus (RTSV) coat protein transgenes are resistant to virus infection. Mol Breed 5:177-185
59. Wiegand HL, Lu SH, Cullen BR (2003) Exon junction complexes mediate the enhancing effect of splicing on mRNA expression. Proc Natl Acad Sci USA 100:11327-11332
60. Yon J, Fried M (1989) Precise gene fusion by PCR. Nucleic Acids Res 17:4895-4895
61. Zhang S, Song W, Chen L, Ruan D, Taylor N, Ronald P, Beachy RN, Fauquet CM (1998) Transgenic elite Indica rice varieties, resistant to Xanthomonas oryzae pv. Oryzae. Mol Breed 4:551-558