Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites

Genomics

Volumn 97, Issue 4, 2011, Pages 235-243

  Wang, Xiangfeng ^a,b   Laurie, John D ^a   Liu, Tao ^b   Wentz, Jacqueline ^c   Liu, X Shirley ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

High throughput sequencing; Principal component analysis; Small RNAs; TSS associated RNAs

Indexed keywords

ARGONAUTE 1 PROTEIN; ARGONAUTE 4 PROTEIN; ARGONAUTE PROTEIN; DICER LIKE ENDONUCLEASE 1; DICER LIKE ENDONUCLEASE 2; DICER LIKE ENDONUCLEASE 3; DICER LIKE ENDONUCLEASE 4; DOUBLE STRANDED RNA; ENDONUCLEASE; LONG HAIRPIN DOUBLE STRANDED RNA; MICRORNA; RNA DIRECTED RNA POLYMERASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARABIDOPSIS; ARTICLE; COMPUTER PREDICTION; GENE DUPLICATION; GENE LOCUS; GENETIC CODE; GENETIC DATABASE; PLANT GENETICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA SEQUENCE; RNA SYNTHESIS; STRUCTURAL GENOMICS; TRANSCRIPTION INITIATION SITE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; COMPUTATIONAL BIOLOGY; MICRORNAS; PRINCIPAL COMPONENT ANALYSIS; RNA REPLICASE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 79952899503     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.01.006     Document Type: Article

References (49)

1. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136(4):669-687.
2. Vaucheret H., Fagard M. Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet. 2001, 17(1):29-35.
3. Vazquez F., Vaucheret H., Rajagopalan R., Lepers C., Gasciolli V., Mallory A.C., Hilbert J.L., Bartel D.P., Crété P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 2004, 16(1):69-79.
4. Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D., Zilberman D., Jacobsen S.E., Carrington J.C. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004, 2(5):E104.
5. Zilberman D., Cao X., Jacobsen S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 2003, 299:716-719.
6. Kloc A., Zaratiegui M., Nora E., Martienssen R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 2008, 18(7):490-495.
7. Obbard D.J., Finnegan D.J. RNA interference: endogenous siRNAs derived from transposable elements. Curr. Biol. 2008, 18(13):R561-R563.
8. Chan S., Zilberman D., Xie Z., Johansen L.K., Carrington J.C., Jacobsen S.E. RNA silencing genes control de novo DNA methylation. Science 2004, 303:1336.
9. Ghildiyal M., Zamore P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 2009, 10(2):94-108.
10. Henderson I.R., Zhang X., Lu C., Johnson L., Meyers B.C., Green P.J., Jacobsen S.E. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 2006, 38:721-725.
11. Onodera Y., Haag J.R., Ream T., Nunes P.C., Pontes O., Pikaard C.S. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 2005, 120(5):613-622.
12. Pikaard C.S., Haag J.R., Ream T., Wierzbicki A.T. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci. 2008, 13(7):390-397.
13. Vaucheret H. Plant ARGONAUTES. Trends Plant Sci. 2008, 13(7):350-358.
14. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002, 16(13):1616-1626.
15. Allen E., Xie Z., Gustafson A.M., Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121(2):207-221.
16. Borsani O., Zhu J., Verslues P.E., Sunkar R., Zhu J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2009, 123(7):1279-1291.
17. Onodera Y., Haag J.R., Ream T., Nunes P.C., Pontes O., et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 2005, 120:613-622.
18. Wierzbicki A.T., Haag J.R., Pikaard C.S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008, 135(4):635-648.
19. Henderson Ian R., Jacobsen Steven E. Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev. 2008, 22:1597-1606.
20. Wang W.C., Lin F.M., Chang W.C., Lin K.Y., Huang H.D., Lin N.S. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinform. 2009, 10:328.
21. Huang P.J., Liu Y.C., Lee C.C., Lin W.C., Gan R.R., Lyu P.C., Tang P. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res. Jul 2010, 1:38.
22. Friedländer M.R., Chen W., Adamidi C., Maaskola J., Einspanier R., Knespel S., Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 2008, 26(4):407-415.
23. Yang J.H., Shao P., Zhou H., Chen Y.Q., Qu L.H. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010, 38:D123-D130. (Database issue).
24. Zhu E., Zhao F., Xu G., Hou H., Zhou L., Li X., Sun Z., Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res. 2010, 38:W392-W397. (Web Server issue).
25. Hackenberg M., Sturm M., Langenberger D., Falcón-Pérez J.M., Aransay A.M. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2009, 37:W68-W76. (Web Server issue).
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. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 2008, 133(1):116-127.
27. Lister R., O'Malley R.C., Tonti-Filippini J., Gregory B.D., Berry C.C., Millar A.H., Ecker J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133(3):523-536.
28. German M.A., Pillay M., Jeong D.H., Hetawal A., Luo S., Janardhanan P., Kannan V., Rymarquis L.A., Nobuta K., German R., De Paoli E., Lu C., Schroth G., Meyers B.C., Green P.J. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 2008, 26(8):941-946.
29. Kasschau K.D., Fahlgren N., Chapman E.J., Sullivan C.M., Cumbie J.S., Givan S.A., Carrington J.C. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007, 5(3):e57.
30. Fahlgren N., Sullivan C.M., Kasschau K.D., Chapman E.J., Cumbie J.S., Montgomery T.A., Gilbert S.D., Dasenko M., Backman T.W., Givan S.A., Carrington J.C. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 2009, 15(5):992-1002.
31. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10(3):R25.
32. Ringnér M. What is principal component analysis?. Nat. Biotechnol. 2008, 26(3):303-304.
33. Brodersen P., Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet. 2006, 22(5):268-280.
34. Meyers B.C., Axtell M.J., Bartel B., Bartel D.P., Baulcombe D., Bowman J.L., Cao X., Carrington J.C., Chen X., Green P.J., Griffiths-Jones S., Jacobsen S.E., Mallory A.C., Martienssen R.A., Poethig R.S., Qi Y., Vaucheret H., Voinnet O., Watanabe Y., Weigel D., Zhu J.K. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20(12):3186-3190.
35. Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 2003, 31(13):3429-3431.
36. Zhang X., Henderson I.R., Lu C., Green P.J., Jacobsen S.E. Role of RNA polymerase IV in plant small RNA metabolism. Proc. Natl Acad. Sci. USA 2007, 104(11):4536-4541.
37. Tam O.H., Aravin A.A., Stein P., Girard A., Murchison E.P., Cheloufi S., Hodges E., Anger M., Sachidanandam R., Schultz R.M., Hannon G.J. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453(7194):534-538.
38. K. Nobuta, C. Lu, R. Shrivastava, M. Pillay, E. De Paoli, M. Accerbi, M. Arteaga-Vazquez, L. Sidorenko, D.H. Jeong, Y. Yen, P.J. Green, V.L. Chandler, B.C. Meyers, Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc. Natl Acad. Sci. USA 105 (39) (2009) 14958-14963.
39. Wang X., Elling A.A., Li X., Li N., Peng Z., He G., Sun H., Qi Y., Liu X.S., Deng X.W. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009, 21(4):1053-1069.
40. http://emboss.bioinformatics.nl/cgi-bin/emboss/einverted/.
41. http://neomorph.salk.edu/epigenome/epigenome.html.
42. Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Schölkopf B., Weigel D., Lohmann J.U. A gene expression map of Arabidopsis thaliana development. Nat. Genet. 2005, 37(5):501-506.
43. Allen E., Xie Z., Gustafson A.M., Sung G.H., Spatafora J.W., Carrington J.C. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 2004, 36:1282-1290.
44. Taft R.J., Simons C., Nahkuri S., Oey H., Korbie D.J., Mercer T.R., Holst J., Ritchie W., Wong J.J., Rasko J.E., Rokhsar D.S., Degnan B.M., Mattick J.S. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat. Struct. Mol. Biol. 2010, 17(8):1030-1034.
45. Taft R.J., Glazov E.A., Cloonan N., Simons C., Stephen S., Faulkner G.J., Lassmann T., Forrest A.R., Grimmond S.M., Schroder K., Irvine K., Arakawa T., Nakamura M., Kubosaki A., Hayashida K., Kawazu C., Murata M., Nishiyori H., Fukuda S., Kawai J., Daub C.O., Hume D.A., Suzuki H., Orlando V., Carninci P., Hayashizaki Y., Mattick J.S. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 2009, 41(5):572-578.
46. Han J., Kim D., Morris K.V. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl Acad. Sci. USA 2007, 104(30):12422-12427.
47. Hawkins P.G., Santoso S., Adams C., Anest V., Morris K.V. Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res. 2009, 37(9):2984-2995.
48. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermüller J., Hofacker I.L., Bell I., Cheung E., Drenkow J., Dumais E., Patel S., Helt G., Ganesh M., Ghosh S., Piccolboni A., Sementchenko V., Tammana H., Gingeras T.R. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316(5830):1484-1488.
49. Seila A.C., Calabrese J.M., Levine S.S., Yeo G.W., Rahl P.B., Flynn R.A., Young R.A., Sharp P.A. Divergent transcription from active promoters. Science 2008, 322(5909):1849-1851.