Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Liang, Chao ^a   Liu, Xuan ^a   Sun, Yuzhe ^a   Yiu, Siu Ming ^a   Lim, Boon L ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Chloroplasts; MiRNAs; Mitochondria; MORF; PPR; TasiRNAs and natsiRNAs

Indexed keywords

ADENOSINE TRIPHOSPHATE; APETALA 2 PROTEIN; CARBOHYDRATE; CIS ACTING ELEMENT; MICRORNA; SMALL INTERFERING RNA; TRANS ACTING FACTOR; TRANSFER RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; ZINC FINGER PROTEIN; APETALA2 PROTEIN, ARABIDOPSIS; ARABIDOPSIS PROTEIN; HOMEODOMAIN PROTEIN; NUCLEAR PROTEIN; PAP2 PROTEIN, ARABIDOPSIS; PLANT RNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS THALIANA; ARTICLE; CARBOHYDRATE ANALYSIS; CONTROLLED STUDY; GENE LIBRARY; GENE MAPPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PLANT GROWTH; PLANT LEAF; PLANT ROOT; PLANT STRESS; PREDICTION; PROTEIN EXPRESSION; PROTEIN INDUCTION; PROTEIN TARGETING; RNA ANALYSIS; SEQUENCE ANALYSIS; ANTAGONISTS AND INHIBITORS; ARABIDOPSIS; DRUG EFFECTS; ENERGY METABOLISM; GENETICS; METABOLISM;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

ADENOSINE TRIPHOSPHATE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CARBOHYDRATES; ENERGY METABOLISM; HOMEODOMAIN PROTEINS; MICRORNAS; NUCLEAR PROTEINS; PLANT LEAVES; PLANT PROTEINS; PLANT ROOTS; RNA, PLANT; RNA, SMALL INTERFERING; TRANSCRIPTION FACTORS;

EID: 84893690779     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-116     Document Type: Article

References (47)

1. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002, 16(13):1616-1626. 10.1101/gad.1004402, 186362, 12101121.
2. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 2007, 19(3):926-942. 10.1105/tpc.107.050062, 1867363, 17400893.
3. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20(24):3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
4. Allen E, Howell MD. miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin Cell Dev Biol 2010, 21(8):798-804. 10.1016/j.semcdb.2010.03.008, 20359543.
5. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121(2):207-221. 10.1016/j.cell.2005.04.004, 15851028.
6. Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, et al. AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci USA 2008, 105(51):20055-20062. 10.1073/pnas.0810241105, 2598728, 19066226.
7. Felippes FF, Weigel D. Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. Embo Rep 2009, 10(3):264-270. 10.1038/embor.2008.247, 2658565, 19180117.
8. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res 2010, 38(4):1382-1391. 10.1093/nar/gkp1128, 2831332, 19969544.
9. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A. miR390, Arabidopsis TAS3 tasiRNAs, and their Auxin response factor targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 2010, 22(4):1104-1117. 10.1105/tpc.109.072553, 2879756, 20363771.
10. Luo QJ, Mittal A, Jia F, Rock CD. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol 2012, 80(1):117-129. 10.1007/s11103-011-9778-9, 3272322, 21533841.
11. Baumberger N, Baulcombe DC. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA 2005, 102(33):11928-11933. 10.1073/pnas.0505461102, 1182554, 16081530.
12. Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 2008, 9:6. 10.1186/1471-2199-9-6, 2262095, 18194570.
13. Zhang X, Xia J, Lii YE, Barrera-Figueroa BE, Zhou X, Gao S, Lu L, Niu D, Chen Z, Leung C, et al. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol 2012, 13(3):R20. 10.1186/gb-2012-13-3-r20, 3439971, 22439910.
14. Sun F, Suen PK, Zhang Y, Liang C, Carrie C, Whelan J, Ward JL, Hawkins ND, Jiang L, Lim BL. A dual-targeted purple acid phosphatase in Arabidopsis thaliana moderates carbon metabolism and its overexpression leads to faster plant growth and higher seed yield. The New phytologist 2012, 194(1):206-219. 10.1111/j.1469-8137.2011.04026.x, 22269069.
15. Sun F, Carrie C, Law S, Murcha MW, Zhang R, Law YS, Suen PK, Whelan J, Lim BL. AtPAP2 is a tail-anchored protein in the outer membrane of chloroplasts and mitochondria. Plant signaling & behavior 2012, 7(8):927-932. 10.4161/psb.20769, 3474687, 22751362.
16. Sun F, Liang C, Whelan J, Yang J, Zhang P, Lim BL. Global transcriptome analysis of AtPAP2 - overexpressing Arabidopsis thaliana with elevated ATP. BMC Genomics 2013, 14(1):752. 10.1186/1471-2164-14-752, 3829102, 24180234.
17. Zhang Y, Yu L, Yung KF, Leung DY, Sun F, Lim BL. Over-expression of AtPAP2 in Camelina sativa leads to faster plant growth and higher seed yield. Biotechnol Biofuels 2012, 5:19. 10.1186/1754-6834-5-19, 3361479, 22472516.
18. Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant physiology 2009, 151(4):2120-2132. 10.1104/pp.109.147280, 2785986, 19854858.
19. Qiu D, Pan X, Wilson IW, Li F, Liu M, Teng W, Zhang B. High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis). Gene 2009, 436(1-2):37-44.
20. Sunkar R, Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 2008, 8:37. 10.1186/1471-2229-8-37, 2358906, 18416839.
21. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev cell 2005, 8(4):517-527. 10.1016/j.devcel.2005.01.018, 15809034.
22. Khraiwesh B, Zhu JK, Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica et biophysica acta 2012, 1819(2):137-148. 10.1016/j.bbagrm.2011.05.001, 3175014, 21605713.
23. Meng Y, Ma X, Chen D, Wu P, Chen M. MicroRNA-mediated signaling involved in plant root development. Biochem Biophys Res Commun 2010, 393(3):345-349. 10.1016/j.bbrc.2010.01.129, 20138828.
24. Achard P, Herr A, Baulcombe DC, Harberd NP. Modulation of floral development by a gibberellin-regulated microRNA. Development 2004, 131(14):3357-3365. 10.1242/dev.01206, 15226253.
25. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 2005, 17(8):2204-2216. 10.1105/tpc.105.033076, 1182483, 16006581.
26. Chen XM. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303(5666):2022-2025. 10.1126/science.1088060, 12893888.
27. Nag A, King S, Jack T. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc Natl Acad Sci USA 2009, 106(52):22534-22539. 10.1073/pnas.0908718106, 2799693, 20007771.
28. Palatnik JF, Allen E, Wu XL, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003, 425(6955):257-263. 10.1038/nature01958, 12931144.
29. Martin A, Adam H, Diaz-Mendoza M, Zurczak M, Gonzalez-Schain ND, Suarez-Lopez P. Graft-transmissible induction of potato tuberization by the microRNA miR172. Development 2009, 136(17):2873-2881. 10.1242/dev.031658, 19666819.
30. Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 2005, 15(22):2038-2043. 10.1016/j.cub.2005.10.016, 16303564.
31. Sunkar R, Kapoor A, Zhu JK. Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 2006, 18(8):2051-2065. 10.1105/tpc.106.041673, 1533975, 16861386.
32. Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004, 16(8):2001-2019. 10.1105/tpc.104.022830, 519194, 15258262.
33. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2007, 2(2):e219. 10.1371/journal.pone.0000219, 1790633, 17299599.
34. Jagadeeswaran G, Saini A, Sunkar R. Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis. Planta 2009, 229(4):1009-1014. 10.1007/s00425-009-0889-3, 19148671.
35. Kasschau KD, Xie ZX, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev cell 2003, 4(2):205-217. 10.1016/S1534-5807(03)00025-X, 12586064.
36. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. Rna 2008, 14(5):836-843. 10.1261/rna.895308, 2327369, 18356539.
37. Chen HM, Li YH, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci USA 2007, 104(9):3318-3323. 10.1073/pnas.0611119104, 1805617, 17360645.
38. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, et al. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 2004, 16(8):2089-2103. 10.1105/tpc.104.022236, 519200, 15269332.
39. Small ID, Peeters N. The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 2000, 25(2):46-47.
40. Takenaka M, Zehrmann A, Verbitskiy D, Kugelmann M, Hartel B, Brennicke A. Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proc Natl Acad Sci USA 2012, 109(13):5104-5109. 10.1073/pnas.1202452109, 3324002, 22411807.
41. Solfanelli C, Poggi A, Loreti E, Alpi A, Perata P. Sucrose-specific induction of the anthocyanin biosynthetic pathway in Arabidopsis. Plant physiology 2006, 140(2):637-646. 10.1104/pp.105.072579, 1361330, 16384906.
42. Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 2008, 44(1):3-12. 10.1016/j.ymeth.2007.09.009, 2847350, 18158127.
43. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
44. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127(6):1193-1207. 10.1016/j.cell.2006.10.040, 17174894.
45. Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R. Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biol 2011, 11:127. 10.1186/1471-2229-11-127, 3182138, 21923928.
46. Liu CM, Wong T, Wu E, Luo R, Yiu SM, Li Y, Wang B, Yu C, Chu X, Zhao K, et al. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 2012, 28(6):878-879. 10.1093/bioinformatics/bts061, 22285832.
47. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to cytoscape plugins. Nat Methods 2012, 9(11):1069-1076. 10.1038/nmeth.2212, 3649846, 23132118.