Diamonds in the rough: mRNA-like non-coding RNAs

Trends in Plant Science

Volumn 13, Issue 7, 2008, Pages 329-334

  Rymarquis, Linda A ^a   Kastenmayer, James P ^b   Hüttenhofer, Alexander G ^c   Green, Pamela J ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b Innsbruck Medical University ^*  (United States)

^c INNSBRUCK MEDICAL UNIVERSITY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; UNTRANSLATED RNA;

CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; REVIEW;

GENE EXPRESSION REGULATION, PLANT; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; RNA, UNTRANSLATED;

EID: 46149097613     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2008.02.009     Document Type: Review

References (77)

1. Lu C., et al. Elucidation of the small RNA component of the transcriptome. Science 309 (2005) 1567-1569
2. Nobuta K., et al. An expression atlas of rice mRNAs and small RNAs. Nat. Biotechnol. 25 (2007) 473-477
3. Yao Y., et al. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 8 (2007) R96
4. Katiyar-Agarwal S., et al. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev. 21 (2007) 3123-3134
5. Meyers B.C., et al. The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res. 14 (2004) 1641-1653
6. Yamada K., et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302 (2003) 842-846
7. Li L., et al. Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE 2 (2007) e294
8. Rajagopalan R., et al. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20 (2006) 3407-3425
9. Brown J.W., et al. Plant snoRNA database. Nucleic Acids Res. 31 (2003) 432-435
10. Hirotsune S., et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423 (2003) 91-96
11. Gray T.A., et al. The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 12039-12044
12. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
13. Lowe T.M., and Eddy S.R. A computational screen for methylation guide snoRNAs in yeast. Science 283 (1999) 1168-1171
14. He S., et al. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res. 36 (2008) D170-D172
15. Wuyts J., et al. The European ribosomal RNA database. Nucleic Acids Res. 32 (2004) D101-D103
16. Lu C., et al. Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs). Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 4951-4956
17. Vazquez F. Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci. 11 (2006) 460-468
18. Phillips J.R., et al. The role of small RNAs in abiotic stress. FEBS Lett. 581 (2007) 3592-3597
19. Sunkar R., et al. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 12 (2007) 301-309
20. Prasanth K.V., and Spector D.L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21 (2007) 11-42
21. Hirsch J., et al. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol. 140 (2006) 1192-1204
22. MacIntosh G.C., et al. Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol. 127 (2001) 765-776
23. Marker C., et al. Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr. Biol. 12 (2002) 2002-2013
24. Wen J., et al. In silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biology 7 (2007) 0034
25. Lukashin A.V., and Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26 (1998) 1107-1115
26. Burge C.B., and Karlin S. Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8 (1998) 346-354
27. Iseli C., et al. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. (1999) 138-148
28. Wutz A. Xist function: bridging chromatin and stem cells. Trends Genet. 23 (2007) 457-464
29. Bendtsen J.D., et al. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340 (2004) 783-795
30. Riano-Pachon D.M., et al. Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant J. 43 (2005) 205-212
31. Henz S.R., et al. Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol. 144 (2007) 1247-1255
32. Ma J., et al. Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biol. 7 (2006) R22
33. Osato N., et al. Antisense transcripts with rice full-length cDNAs. Genome Biol. 5 (2003) R5
34. Terryn N., and Rouze P. The sense of naturally transcribed antisense RNAs in plants. Trends Plant Sci. 5 (2000) 394-396
35. Jen C.H., et al. Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol. 6 (2005) R51
36. Burleigh S.H., and Harrison M.J. The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots. Plant Physiol. 119 (1999) 241-248
37. Martin A.C., et al. Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. Plant J. 24 (2000) 559-567
38. Franco-Zorrilla J.M., et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39 (2007) 1033-1037
39. Shin H., et al. Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation. Plant J. 45 (2006) 712-726
40. Wasaki J., et al. Expression of the OsPI1 gene, cloned from rice roots using cDNA microarray, rapidly responds to phosphorus status. New Phytol. 158 (2003) 239-248
41. Liu C., et al. Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol. Biol. 33 (1997) 867-874
42. Burleigh S.H., and Harrison M.J. A novel gene whose expression in Medicago truncatula roots is suppressed in response to colonization by vesicular-arbuscular mycorrhizal (VAM) fungi and to phosphate nutrition. Plant Mol. Biol. 34 (1997) 199-208
43. Childs K.L., et al. The TIGR Plant Transcript Assemblies database. Nucleic Acids Res. 35 (2007) D846-D851
44. Bari R., et al. PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol. 141 (2006) 988-999
45. Hore T.A., et al. Construction and evolution of imprinted loci in mammals. Trends Genet. 23 (2007) 440-448
46. Grant S., et al. Genetics of sex determination in flowering plants. Dev. Genet. 15 (1994) 214-230
47. Cho J., et al. Isolation and characterization of cDNA clones expressed under male sex expression conditions in a monoecious cucumber plant (Cucumis sativus L. cv. winter long). Euphytica 146 (2005) 271-281
48. Dai X., et al. Overexpression of Zm401, an mRNA-like RNA, has distinct effects on pollen development in maize. Plant Growth Regul. 52 (2007) 229-239
49. Sugiyama R., et al. CCLS96.1, a member of a multicopy gene family, may encode a non-coding RNA preferentially transcribed in reproductive organs of Silene latifolia. DNA Res. 10 (2003) 213-220
50. Teramoto H., et al. Noncoding RNA for CR20, a cytokinin-repressed gene of cucumber. Plant Mol. Biol. 32 (1996) 797-808
51. van Hoof A., et al. GUT 15 cDNAs from tobacco and Arabidopsis correspond to transcripts with unusual metabolism and a short conserved open reading frame. Plant Physiol. 113 (1997) 1004
52. Teramoto H., et al. Isolation of a cDNA clone for a cytokinin-repressed gene in excised cucumber cotyledons. Planta 193 (1994) 573-579
53. Ando S., et al. Cloning of ethylene responsive genes from the apices of cucumber plants (Cucumis sativus L.). Plant Biotechnol. 18 (2001) 163-167
54. Taylor C.B., and Green P.J. Identification and characterization of genes with unstable transcripts (GUTs) in tobacco. Plant Mol. Biol. 28 (1995) 27-38
55. Barbacar N., et al. Isolation of early genes expressed in reproductive organs of the dioecious white campion (Silene latifolia) by subtraction cloning using an asexual mutant. Plant J. 12 (1997) 805-817
56. Dai X.-Y., et al. Non-coding RNA for Zm401, a pollen-specific gene of Zea mays. Acta Bot. Sin. 46 (2004) 497-504
57. Qin F., et al. Co-suppression of Si401, a maize pollen specific Zm401 homologous gene, results in aberrant anther development in foxtail millet. Euphytica (2007). www.springerlink.com 10.1007/s10681-007-9610-4
58. Yang W.C., et al. Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J. 3 (1993) 573-585
59. Crespi M.D., et al. enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J. 13 (1994) 5099-5112
60. Girard G., et al. Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean. Nucleic Acids Res. 31 (2003) 5003-5015
61. Gultyaev A.P., and Roussis A. Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants. Nucleic Acids Res. 35 (2007) 3144-3152
62. Vleghels I., et al. Expression of ENOD40 during tomato plant development. Planta 218 (2003) 42-49
63. Kouchi H., et al. Rice ENOD40: isolation and expression analysis in rice and transgenic soybean root nodules. Plant J. 18 (1999) 121-129
64. Varkonyi-Gasic E., and White D.W. The white clover enod40 gene family. Expression patterns of two types of genes indicate a role in vascular function. Plant Physiol. 129 (2002) 1107-1118
65. Hardin S.C., et al. Phosphorylation of sucrose synthase at serine 170: occurrence and possible role as a signal for proteolysis. Plant J. 35 (2003) 588-603
66. Rohrig H., et al. Modification of soybean sucrose synthase by S-thiolation with ENOD40 peptide A. Biochem. Biophys. Res. Commun. 325 (2004) 864-870
67. Rohrig H., et al. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 1915-1920
68. Campalans A., et al. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16 (2004) 1047-1059
69. Sato M., et al. The fission yeast meiotic regulator Mei2p undergoes nucleocytoplasmic shuttling. FEBS Lett. 499 (2001) 251-255
70. Charon C., et al. Alteration of enod40 expression modifies Medicago truncatula root nodule development induced by Sinorhizobium meliloti. Plant Cell 11 (1999) 1953-1966
71. Ruttink T., et al. ENOD40 affects elongation growth in tobacco Bright Yellow-2 cells by alteration of ethylene biosynthesis kinetics. J. Exp. Bot. 57 (2006) 3271-3282
72. Symons R.H. Plant pathogenic RNAs and RNA catalysis. Nucleic Acids Res. 25 (1997) 2683-2689
73. Ferbeyre G., et al. Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank. Genome Res. 10 (2000) 1011-1019
74. Przybilski R., et al. Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell 17 (2005) 1877-1885
75. Wachter A., et al. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19 (2007) 3437-3450
76. Bocobza S., et al. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev. 21 (2007) 2874-2879
77. Kloc M., and Etkin L.D. Delocalization of Vg1 mRNA from the vegetal cortex in Xenopus oocytes after destruction of Xlsirt RNA. Science 265 (1994) 1101-1103