Intronic regions of plant genes potentially encode RDR (RNA-dependent RNA polymerase)-dependent small RNAs

Journal of Experimental Botany

Volumn 66, Issue 7, 2015, Pages 1763-1768

  Qin, Jingping ^a   Ma, Xiaoxia ^b   Yi, Zili ^a   Tang, Zhonghai ^a   Meng, Yijun ^b  

^a HUNAN AGRICULTURAL UNIVERSITY   (China)

^b HANGZHOU NORMAL UNIVERSITY   (China)

Author keywords

Arabidopsis thaliana; double stranded RNA precursor; intron; phase distributed; RDR (RNA dependent RNA polymerase); small RNA

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

DOUBLE STRANDED RNA; MICRORNA; PLANT PROTEIN; PLANT RNA; RNA DIRECTED RNA POLYMERASE; SMALL INTERFERING RNA;

ARABIDOPSIS; BIOLOGICAL MODEL; DNA SEQUENCE; GENETICS; INTRON; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ARABIDOPSIS; BASE SEQUENCE; INTRONS; MICRORNAS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; RNA REPLICASE; RNA, DOUBLE-STRANDED; RNA, PLANT; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, DNA;

EID: 84928901980     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/eru542     Document Type: Review

References (18)

1. Barrett T, Troup DB, Wilhite SE, et al. (2009). NCBI GEO: archive for highthroughput functional genomic data. Nucleic Acids Research 37, D885-D890
2. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. (2007). Mammalian mirtron genes. Molecular Cell 28, 328-336
3. Chen D, Meng Y, Yuan C, Bai L, Huang D, Lv S, Wu P, Chen LL, Chen M. (2011). Plant siRNAs from introns mediate DNA methylation of host genes. RNA 17, 1012-1024
4. Huala E, Dickerman AW, Garcia-Hernandez M, et al. (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
5. Jones-Rhoades MW, Bartel DP, Bartel B. (2006). MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 57, 19-53
6. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. (2007). Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biology 5, e57
7. Ladewig E, Okamura K, Flynt AS, Westholm JO, Lai EC. (2012). Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Research 22, 1634-1645
8. Lorkovic ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. (2000). Pre-mRNA splicing in higher plants. Trends in Plant Science 5, 160-167
9. Lu C, Kulkarni K, Souret FF, et al. (2006). MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Research 16, 1276-1288
10. Meng Y, Shao C. (2012). Large-scale identification of mirtrons in Arabidopsis and rice. PLoS One 7, e31163
11. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. (2007). The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89-100
12. Reddy AS, Marquez Y, Kalyna M, Barta A. (2013). Complexity of the alternative splicing landscape in plants. The Plant Cell 25, 3657-3683
13. Rogers K, Chen X. (2013). Biogenesis, turnover, and mode of action of plant microRNAs. The Plant Cell 25, 2383-2399
14. Ruby JG, Jan CH, Bartel DP. (2007). Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83-86
15. Voinnet O. (2009). Origin, biogenesis, and activity of plant microRNAs. Cell 136, 669-687
16. Yang GD, Yan K, Wu BJ, Wang YH, Gao YX, Zheng CC. (2012). Genome-wide analysis of intronic microRNAs in rice and Arabidopsis. Journal of Genetics 91, 313-324
17. Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD. (2010). Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genetics 6, e1001141
18. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. (2008). A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research 18, 1456-1465