Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE

Molecular Biology Reports

Volumn 39, Issue 2, 2012, Pages 1975-1987

  Zhang, Yanping ^a   Yu, Mingliang ^b   Yu, Huaping ^a   Han, Jian ^a   Song, Changnian ^a   Ma, Ruijuan ^b   Fang, Jinggui ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Computational prediction; MicroRNAs; MiR RACE; Prunus persica; QRT PCR

Indexed keywords

MICRORNA; MICRORNA 171; MICRORNA 171A; MICRORNA 171B; UNCLASSIFIED DRUG; COMPLEMENTARY DNA; PRIMER DNA;

ACCURACY; ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EXPRESSED SEQUENCE TAG; FLOWER; FRUIT; GENE EXPRESSION; NONHUMAN; PEACH; PLANT DEVELOPMENT; PLANT LEAF; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; TISSUE SPECIFICITY; VALIDATION STUDY; BIOLOGY; DNA SEQUENCE; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; PRUNUS; REAL TIME POLYMERASE CHAIN REACTION;

PRUNUS PERSICA;

BASE SEQUENCE; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; FLOWERS; FRUIT; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PLANT LEAVES; PRUNUS; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84860318099     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-011-0944-6     Document Type: Article

References (43)

1. Bartel DP (2004) MicroRNAs, genomics, biogenesis, mechanism, and function. Cell 116:281-297
2. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19-53 (Pubitemid 44061017)
3. Laufs P, Peaucelle A, Morin H, Traas J (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131:4311-4322 (Pubitemid 39276198)
4. Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregu-late auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376-1386 (Pubitemid 43138191)
5. Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, Izhaki A (2003) Radial patterning of Arabidopsis shoots by Class III HD-ZIP and KANADI genes. Curr Biol 13:1768-1774 (Pubitemid 37269117)
6. Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC (2004) MicroRNA-mediated repression of rolled leaf specifies maize leaf polarity. Nature 428:84-88 (Pubitemid 38332362)
7. Mallory AC, Dugas DV, Bartel DP, Bartel B (2004) MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14:1035-1046 (Pubitemid 38791565)
8. 0 region. EMBO J 23:3356-3364 (Pubitemid 39209159)
9. Carra A, Mica E, Gambino G, Pindo M, Moser C, Enrico MP, Schubert A (2009) Cloning and characterization of small non-coding RNAs from grape. Plant J 59:750-763
10. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18:1602-1609
11. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730-2741 (Pubitemid 37470672)
12. Mallory AC, Bartel DP, Bartel B (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17:1-16
13. Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxi-dative stress tolerance. Plant Cell 18:2051-2065 (Pubitemid 44260196)
14. Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272:59-73 (Pubitemid 40083067)
15. Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5:R65
16. Yin Z, Li C, Han X, Shen F (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon es-culentum). Gene 414:60-66
17. Zhang BH, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46:243-259 (Pubitemid 43773564)
18. Zhang BH, Pan XP, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229:161-182
19. Zhang J, Zeng R, Chen J, Liu X, Liao Q (2008) Identification of conserved microRNAs and their targets from Solanum lycoper-sicum Mill. Gene 423:1-7
20. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581:1464-1474 (Pubitemid 46452623)
21. Qiu CX, Xie FL, Zhu YY, Guo K, Huang SQ, Nie L, Yang ZM (2007) Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395:49-61 (Pubitemid 46680491)
22. Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Guo TL, Cobb GP, Anderson TA (2007) Identification of cotton microRNAs and their targets. Gene 397:26-37 (Pubitemid 46977130)
23. Gleave AP, Ampomah-Dwamena C, Berthold S, Dejnoprat S, Karunairetnam S, Nain B, Wang YY, Crowhurst RN, MacDiar-mid RM (2008) Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genet Genomes 4:343-358 (Pubitemid 351214679)
24. Song C, Fang J, Li X, Liu H, Thomas Chao C (2009) Identification and characterization of 27 conserved microRNAs in citrus. Planta 230:671-685
25. Song C, Jia Q, Fang J, Li F, Wang C, Zhang Z (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biol 12:927-934
26. Zeng C, Wang W, Zheng Y, Chen X, Bo W, Song S, Zhang W, Peng M (2010) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Res 38:981-995
27. Song C, Fang J, Wang C, Guo L, Nicholas KK, Ma Z (2010) miR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Pon-cirus trifoliata) microRNAs. PLoS One 5:e10861
28. Yu HP, Song CN, Jia QD, Wang C, Li F, Kibet KN, Zhang XY, Fang JG (2010) Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE. Physiol Plant 141:56-70
29. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109-D111 (Pubitemid 38081615)
30. Li W, Godzik A (2006) Cd-hit, a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioin-formatics 22:1658-1659 (Pubitemid 43985301)
31. Dsouz M, Larsen N, Overbeek R (1997) Searching for patterns in genomic data. Trends Genet 13:497-498 (Pubitemid 28004924)
32. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20 (Pubitemid 40094598)
33. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Gene Res 15:78-91
34. Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579:3849-3854 (Pubitemid 40903114)
35. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenort-habditis elegans. Science 294:858-862 (Pubitemid 33032104)
36. Aravin A, Tuschl T (2005) Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett 579:5830-5840 (Pubitemid 41484129)
37. Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH (2004) Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res 32:1688-1695 (Pubitemid 38832713)
38. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179
39. Shi R, Chiang VL (2005) Facile means for quantifying microR-NA expression by real-time PCR. Biotechniques 39:519-525
40. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339:62-66 (Pubitemid 36263221)
41. Zhang BH, Pan X, Anderson TA (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580:3753-3762 (Pubitemid 43902810)
42. 0 precision of both microRNAs and their miRNA strands in flies. Curr Biol 18:147-151
43. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of MicroRNA on the plant transcriptome. Dev Cell 8:517-527 (Pubitemid 40450741)