Circadian Rhythms of Sense and Antisense Transcription in Sugarcane, a Highly Polyploid Crop

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Hotta, Carlos Takeshi ^a   Nishiyama, Milton Yutaka ^a   Souza, Glaucia Mendes ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; AUXIN; CARBOHYDRATE; CARBON DIOXIDE; CAROTENOID; CHLOROPHYLL; CITRIC ACID; FRUCTOKINASE; GLUCOSE 6 PHOSPHATE ISOMERASE; HEXOKINASE; HISTONE; LIPID; PHOSPHOGLUCOMUTASE; PHYTOHORMONE; PLANT RNA; PROTEIN ABA; RNA POLYMERASE; STARCH; SUCROSE; SUCROSE SYNTHASE; TRANSCRIPTOME; UNCLASSIFIED DRUG; URIDINE TRIPHOSPHATE GLUCOSE 1 PHOSPHATE URIDYLYLTRANSFERASE; VEGETABLE PROTEIN; XANTHOPHYLL;

AMINO ACID METABOLISM; ANTISENSE TRANSCRIPTION; ARABIDOPSIS THALIANA; ARTICLE; BIOGENESIS; CARBOHYDRATE SYNTHESIS; CARBON DIOXIDE FIXATION; CIRCADIAN RHYTHM; CITRIC ACID CYCLE; CONTROLLED STUDY; CULTIVAR; DNA REPLICATION; ELECTRON TRANSPORT; ENVIRONMENTAL CHANGE; ENZYME REGULATION; GENE CLUSTER; GENE EXPRESSION; GENETIC TRANSCRIPTION; GLUCONEOGENESIS; GLYCOLYSIS; HORMONAL REGULATION; HORMONE SYNTHESIS; LIGHT HARVESTING SYSTEM; LIPID METABOLISM; MAIZE; MOLECULAR HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARALOGY; PHOTORESPIRATION; PHOTOSYNTHESIS; PHOTOSYSTEM I; PHOTOSYSTEM II; PLANT GENETICS; PLANT METABOLISM; POLYPLOIDY; PROTEIN DEGRADATION; PROTEIN TRANSPORT; RIBOSOME; RICE; RNA DEGRADATION; RNA TRANSPORT; SENSE TRANSCRIPTION; SIGNAL TRANSDUCTION; SORGHUM; SPECIES DIFFERENCE; SPLICEOSOME; SUGARCANE; TRANSCRIPTION REGULATION;

ARABIDOPSIS THALIANA; SACCHARUM SP.; ZEA MAYS;

CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; CROPS, AGRICULTURAL; LIGHT; POLYPLOIDY; RNA, ANTISENSE; SACCHARUM; SEQUENCE HOMOLOGY, NUCLEIC ACID; SUCROSE; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84881139366     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071847     Document Type: Article

References (76)

1. Hotta CT, Gardner MJ, Hubbard KE, Baek SJ, Dalchau N, et al. (2007) Modulation of environmental responses of plants by circadian clocks. Plant, cell & environment 30: 333-349.
2. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
3. Pokhilko A, Fernandez AP, Edwards KD, Southern MM, Halliday KJ, et al. (2012) The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol 8: 574.
4. Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, et al. (2009) Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP J 3: 350-366.
5. Dixon LE, Knox K, Kozma-Bognar L, Southern MM, Pokhilko A, et al. (2011) Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Curr Biol 21: 120-125.
6. Nusinow DA, Helfer A, Hamilton EE, King JJ, Imaizumi T, et al. (2011) The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475: 398-402.
7. Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, et al. (2011) LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr Biol 21: 126-133.
8. Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, et al. (2012) Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proc Natl Acad Sci U S A 109: 3167-3172.
9. Huang W, Perez-Garcia P, Pokhilko A, Millar AJ, Antoshechkin I, et al. (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336: 75-79.
10. McClung CR, (2011) The genetics of plant clocks. Adv Genet 74: 105-139.
11. Imaizumi T, Tran HG, Swartz TE, Briggs WR, Kay SA, (2003) FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426: 302-306.
12. Lu SX, Knowles SM, Webb CJ, Celaya RB, Cha C, et al. (2011) The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiol 155: 906-915.
13. Harmer SL, (2000) Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock. Science 290: 2110-2113.
14. Filichkin SA, Mockler TC, (2012) Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes. Biol Direct 7: 20.
15. Staiger D, Green R, (2011) RNA-based regulation in the plant circadian clock. Trends Plant Sci 16: 517-523.
16. Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL, (2008) Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9: R130.
17. Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, et al. (2011) Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PloS one 6: e16907.
18. Khan S, Rowe SC, Harmon FG, (2010) Coordination of the maize transcriptome by a conserved circadian clock. BMC plant biology 10: 126.
19. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14.
20. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, et al. (2006) FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 18: 639-650.
21. Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, et al. (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17: 3257-3281.
22. D'Hont A, Glaszmann JC, (2005) Unravelling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res 109: 27-33.
23. D'Hont A, Glaszmann JC, (2001) Sugarcane genome analysis with molecular markers, a first decade of research. Proc Int Soc Sugar Cane Technol 24: 556-559.
24. Dal-Bianco M, Carneiro MS, Hotta CT, Chapola RG, Hoffmann HP, et al. (2012) Sugarcane improvement: how far can we go? Curr Opin Biotechnol 23: 265-270.
25. Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM, (2010) Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J 8: 263-276.
26. Hotta CT, Lembke CG, Domingues DS, Ochoa EA, Cruz GMQ, et al. (2010) The Biotechnology Roadmap for Sugarcane Improvement. Tropical Plant Biology 3: 75-87.
27. Rocha FR, Papini-Terzi FS, Nishiyama MY Jr, Vencio RZ, Vicentini R, et al. (2007) Signal transduction-related responses to phytohormones and environmental challenges in sugarcane. BMC genomics 8: 71.
28. Papini-Terzi F, Rocha F, Nicoliello R, (2005) Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Research 38: 27-38.
29. Lembke CG, Nishiyama MY Jr, Sato PM, de Andrade RF, Souza GM, (2012) Identification of sense and antisense transcripts regulated by drought in sugarcane. Plant Mol Biol 79: 461-477.
30. Lapidot M, Pilpel Y, (2006) Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep 7: 1216-1222.
31. Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, et al. (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30: 453-459.
32. Swiezewski S, Liu F, Magusin A, Dean C, (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799-802.
33. Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, et al. (2012) Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production. Plant J.
34. Helliwell CA, Robertson M, Finnegan EJ, Buzas DM, Dennis ES, (2011) Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PloS one 6: e21513.
35. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, et al. (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10: R17.
36. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, et al. (2009) Harmonics of circadian gene transcription in mammals. PLoS genetics 5: e1000442.
37. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, et al. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109: 307-320.
38. Hughes ME, Hogenesch JB, Kornacker K, (2010) JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms 25: 372-380.
39. Covington MF, Harmer SL, (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5: e222.
40. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, et al. (2003) Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane. Genome research 13: 2725-2735.
41. Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL, (2008) InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res 36: D263-266.
42. Alexeyenko A, Tamas I, Liu G, Sonnhammer EL, (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-15.
43. Herrero E, Kolmos E, Bujdoso N, Yuan Y, Wang M, et al. (2012) EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. Plant Cell 24: 428-443.
44. Kim J, Kim Y, Yeom M, Kim JH, Nam HG, (2008) FIONA1 is essential for regulating period length in the Arabidopsis circadian clock. Plant Cell 20: 307-319.
45. Pruneda-Paz JL, Breton G, Para A, Kay SA, (2009) A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323: 1481-1485.
46. Khanna R, Kikis EA, Quail PH, (2003) EARLY FLOWERING 4 functions in phytochrome B-regulated seedling de-etiolation. Plant Physiol 133: 1530-1538.
47. Murakami M, Tago Y, Yamashino T, Mizuno T, (2007) Comparative Overviews of Clock-Associated Genes of Arabidopsis thaliana and Oryza sativa. Plant and Cell Physiology 48: 110-121.
48. Rizzini L, Favory JJ, Cloix C, Faggionato D, O'Hara A, et al. (2011) Perception of UV-B by the Arabidopsis UVR8 protein. Science 332: 103-106.
49. Kim WY, Fujiwara S, Suh SS, Kim J, Kim Y, et al. (2007) ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature 449: 356-360.
50. Grivet L, Arruda P, (2002) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5: 122-127.
51. Higgins J, Magusin A, Trick M, Fraser F, Bancroft I, (2012) Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC genomics 13: 247.
52. Miller M, Zhang C, Chen ZJ, (2012) Ploidy and Hybridity Effects on Growth Vigor and Gene Expression in Arabidopsis thaliana Hybrids and Their Parents. G3 (Bethesda) 2: 505-513.
53. Ni Z, Kim ED, Ha M, Lackey E, Liu J, et al. (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
54. Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, et al. (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149: 171-180.
55. Perales M, Más P, (2007) A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. The Plant cell 19: 2111-2123.
56. Hong S, Song H-R, Lutz K, Kerstetter R, Michael TP, et al. (2010) Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 5: 1-6.
57. Sanchez SE, Petrillo E, Beckwith EJ, Zhang X, Rugnone ML, et al. (2010) A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature.
58. Wang X, Wu F, Xie Q, Wang H, Wang Y, et al. (2012) SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis. Plant Cell 24: 3278-3295.
59. Lidder P, Gutierrez RA, Salome PA, McClung CR, Green PJ, (2005) Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. Plant Physiol 138: 2374-2385.
60. Ietswaart R, Wu Z, Dean C, (2012) Flowering time control: another window to the connection between antisense RNA and chromatin. Trends Genet 28: 445-453.
61. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, et al. (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature.
62. Lu Y, Gehan JP, Sharkey TD, (2005) Daylength and circadian effects on starch degradation and maltose metabolism. Plant Physiol 138: 2280-2291.
63. Smith SM, Fulton DC, Chia T, Thorneycroft D, Chapple A, et al. (2004) Diurnal changes in the transcriptome encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol 136: 2687-2699.
64. Piques M, Schulze WX, Hohne M, Usadel B, Gibon Y, et al. (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol 5: 314.
65. Dowson-Day MJ, Millar AJ, (1999) Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. Plant J 17: 63-71.
66. Legnaioli T, Cuevas J, Mas P, (2009) TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. EMBO J 28: 3745-3757.
67. Robertson FC, Skeffington AW, Gardner MJ, Webb AA, (2009) Interactions between circadian and hormonal signalling in plants. Plant Mol Biol 69: 419-427.
68. Mizuno T, Yamashino T, (2008) Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in Arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants. Plant Cell Physiol 49: 481-487.
69. Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, et al. (2012) The fate of duplicated genes in a polyploid plant genome. Plant J.
70. Wang Y, Wang X, Paterson AH, (2012) Genome and gene duplications and gene expression divergence: a view from plants. Ann N Y Acad Sci 1256: 1-14.
71. Gibon Y, Pyl ET, Sulpice R, Lunn JE, Hohne M, et al. (2009) Adjustment of growth, starch turnover, protein content and central metabolism to a decrease of the carbon supply when Arabidopsis is grown in very short photoperiods. Plant Cell Environ 32: 859-874.
72. Cheadle C, Vawter MP, Freed WJ, Becker KG, (2003) Analysis of microarray data using Z score transformation. The Journal of molecular diagnostics: JMD 5: 73-81.
73. Castillo-Davis CI, Hartl DL, (2003) GeneMerge-post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19: 891-892.
74. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, et al. (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 13: 2725-2735.
75. Rohwer JM, Botha FC, (2001) Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem J 358: 437-445.
76. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, et al. (2007) The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 72: 353-363.