A transcriptome-wide study on the microRNA- and the Argonaute 1-enriched small RNA-mediated regulatory networks involved in plant leaf senescence

Plant Biology

Volumn 18, Issue 2, 2016, Pages 197-205

  Qin, J ^a   Ma, X ^b   Yi, Z ^a   Tang, Z ^a   Meng, Y ^b  

^a HUNAN AGRICULTURAL UNIVERSITY   (China)

^b HANGZHOU NORMAL UNIVERSITY   (China)

Author keywords

Argonaute 1; Leaf senescence; MicroRNA; Protein interaction; Senescence associated gene; Small RNA

Indexed keywords

AGO1 PROTEIN, ARABIDOPSIS; ARABIDOPSIS PROTEIN; ARGONAUTE PROTEIN; MESSENGER RNA; MICRORNA; PLANT PROTEIN; PLANT RNA; TRANSCRIPTOME;

ARABIDOPSIS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ORYZA; PLANT LEAF; RNA STABILITY;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; ARGONAUTE PROTEINS; BASE SEQUENCE; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; ORYZA; PLANT LEAVES; PLANT PROTEINS; RNA STABILITY; RNA, MESSENGER; RNA, PLANT; TRANSCRIPTOME;

EID: 84957841348     PISSN: 14358603     EISSN: 14388677     Source Type: Journal    
DOI: 10.1111/plb.12373     Document Type: Article

References (39)

1. Balazadeh S., Siddiqui H., Allu A.D., Matallana-Ramirez L.P., Caldana C., Mehrnia M., Zanor M.I., Kohler B., Mueller-Roeber B. (2010) A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. The Plant Journal, 62, 250-264.
2. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Rudnev D., Evangelista C., Kim I.F., Soboleva A., Tomashevsky M., Marshall K.A., Phillippy K.H., Sherman P.M., Muertter R.N., Edgar R. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Research, 37, D885-D890.
3. Baumberger N., Baulcombe D.C. (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences, USA, 102, 11928-11933.
4. Dai X., Zhao P.X. (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39, W155-W159.
5. Dhondt S., Coppens F., De Winter F., Swarup K., Merks R.M., Inze D., Bennett M.J., Beemster G.T. (2010) SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiology, 154, 1183-1195.
6. Du Z., Zhou X., Ling Y., Zhang Z., Su Z. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research, 38, W64-W70.
7. Ellis C.M., Nagpal P., Young J.C., Hagen G., Guilfoyle T.J., Reed J.W. (2005) AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development, 132, 4563-4574.
8. Fan K., Bibi N., Gan S., Li F., Yuan S., Ni M., Wang M., Shen H., Wang X. (2015) A novel nap member ghnap is involved in leaf senescence in Gossypium hirsutum. Journal of Experimental Botany, 66, 4669-4682.
9. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Research, 36, D154-D158.
10. Guo Y., Gan S. (2006) Atnap, a nac family transcription factor, has an important role in leaf senescence. The Plant Journal, 46, 601-612.
11. Hickman R., Hill C., Penfold C.A., Breeze E., Bowden L., Moore J.D., Zhang P., Jackson A., Cooke E., Bewicke-Copley F., Mead A., Beynon J., Wild D.L., Denby K.J., Ott S., Buchanan-Wollaston V. (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. The Plant Journal, 75, 26-39.
12. Huala E., Dickerman A.W., Garcia-Hernandez M., Weems D., Reiser L., LaFond F., Hanley D., Kiphart D., Zhuang M., Huang W., Mueller L.A., Bhattacharyya D., Bhaya D., Sobral B.W., Beavis W., Meinke D.W., Town C.D., Somerville C., Rhee S.Y. (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Research, 29, 102-105.
13. Jones-Rhoades M.W., Bartel D.P., Bartel B. (2006) MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology, 57, 19-53.
14. Kim J.H., Woo H.R., Kim J., Lim P.O., Lee I.C., Choi S.H., Hwang D., Nam H.G. (2009) Trifurcate feed-forward regulation of age-dependent cell death involving mir164 in Arabidopsis. Science, 323, 1053-1057.
15. Lee S., Seo P.J., Lee H.J., Park C.M. (2012) A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. Plant Journal, 70, 831-844.
16. Li Z., Zhao Y., Liu X., Peng J., Guo H., Luo J. (2014) LSD 2.0: an update of the leaf senescence database. Nucleic Acids Research, 42, D1200-D1205.
17. Liang C., Wang Y., Zhu Y., Tang J., Hu B., Liu L., Ou S., Wu H., Sun X., Chu J., Chu C. (2014) Osnap connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice. Proceedings of the National Academy of Sciences, USA, 111, 10013-10018.
18. Lim P.O., Woo H.R., Nam H.G. (2003) Molecular genetics of leaf senescence in Arabidopsis. Trends in Plant Science, 8, 272-278.
19. Lim P.O., Kim H.J., Nam H.G. (2007) Leaf senescence. Annual Review of Plant Biology, 58, 115-136.
20. Lim P.O., Lee I.C., Kim J., Kim H.J., Ryu J.S., Woo H.R., Nam H.G. (2010) Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity. Journal of Experimental Botany, 61, 1419-1430.
21. Lin J.F., Wu S.H. (2004) Molecular events in senescing Arabidopsis leaves. The Plant Journal, 39, 612-628.
22. Lin M., Shen X., Chen X. (2011) PAIR: the predicted Arabidopsis interactome resource. Nucleic Acids Research, 39, D1134-D1140.
23. Liu L., Zhou Y., Zhou G., Ye R., Zhao L., Li X., Lin Y. (2008) Identification of early senescence-associated genes in rice flag leaves. Plant Molecular Biology, 67, 37-55.
24. Liu X., Li Z., Jiang Z., Zhao Y., Peng J., Jin J., Guo H., Luo J. (2011) LSD: a leaf senescence database. Nucleic Acids Research, 39, D1103-D1107.
25. Meng Y., Shao C., Chen M. (2011) Toward microRNA-mediated gene regulatory networks in plants. Briefings in Bioinformatics, 12, 645-659.
26. Mi S., Cai T., Hu Y., Chen Y., Hodges E., Ni F., Wu L., Li S., Zhou H., Long C., Chen S., Hannon G.J., Qi Y. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell, 133, 116-127.
27. Nakano M., Nobuta K., Vemaraju K., Tej S.S., Skogen J.W., Meyers B.C. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research, 34, D731-D735.
28. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498-2504.
29. Shao C., Chen M., Meng Y. (2013) A reversed framework for the identification of microRNA-target pairs in plants. Briefings in Bioinformatics, 14, 293-301.
30. Vaucheret H. (2008) Plant ARGONAUTES. Trends in Plant Science, 13, 350-358.
31. Voinnet O. (2009) Origin, biogenesis, and activity of plant microRNAs. Cell, 136, 669-687.
32. Wysocka-Diller J.W., Helariutta Y., Fukaki H., Malamy J.E., Benfey P.N. (2000) Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development, 127, 595-603.
33. Xu X., Bai H., Liu C., Chen E., Chen Q., Zhuang J., Shen B. (2014) Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice. PLoS ONE, 9, e114313.
34. Yang S.D., Seo P.J., Yoon H.K., Park C.M. (2011) The Arabidopsis NAC transcription factor vni2 integrates abscisic acid signals into leaf senescence via the cor/rd genes. The Plant Cell, 23, 2155-2168.
35. Yoshida S. (2003) Molecular regulation of leaf senescence. Current Opinion in Plant Biology, 6, 79-84.
36. Yuan Q., Ouyang S., Liu J., Suh B., Cheung F., Sultana R., Lee D., Quackenbush J., Buell C.R. (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Research, 31, 229-233.
37. Zhang Y. (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Research, 33, W701-W704.
38. Zhang K., Gan S.S. (2012) An abscisic acid-atNAP transcription factor-SAG113 protein phosphatase 2C regulatory chain for controlling dehydration in senescing Arabidopsis leaves. Plant Physiology, 158, 961-969.
39. Zhao D., Derkx A.P., Liu D.C., Buchner P., Hawkesford M.J. (2015) Overexpression of a nac transcription factor delays leaf senescence and increases grain nitrogen concentration in wheat. Plant Biology, 17, 904-913.