Identification of MicroRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data

Methods in Molecular Biology

Volumn 883, Issue , 2012, Pages 221-227

  Zhang, Weixiong ^a,b,c   Zhou, Xuefeng ^b   Xia, Jing ^b   Zhou, Xiang ^b  

^a FUDAN UNIVERSITY   (China)

^b WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^c WASHINGTON UNIVERSITY   (United States)

Author keywords

MicroRNA; nat siRNA; Next generation deep sequencing

Indexed keywords

COMPLEMENTARY RNA; MICRORNA; RIBOSOME RNA; RNA; SMALL INTERFERING RNA; SMALL NUCLEOLAR RNA; SMALL UNTRANSLATED RNA; TRANSFER RNA;

ARTICLE; GENE EXPRESSION; GENE LOCUS; INTERSPERSED REPEAT; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SEQUENCE ANALYSIS; TRANSPOSON; COMPUTER PROGRAM; CONTIG MAPPING; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY;

CONTIG MAPPING; GENE EXPRESSION PROFILING; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84865695005     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-839-9_17     Document Type: Article

References (26)

1. Baulcombe D (2004) RNA silencing in plants. Nature 431:356-363
2. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94-108
3. Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656-668
4. Moazed D (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457:413-420
5. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
6. Kim VN, Nam J-W (2006) Genomics of microRNA. Trends Genet 22:165-173
7. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis Cell 123: 1279-1291
8. Zhou X, Sunkar R, Jin H, Zhu J-K, Zhang W (2009) Genome-wide identifi cation and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa Genome Res 19:70-78
9. Okamura K, Lai EC (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 9:673-678
10. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453: 539-543
11. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J-K (2008) Identifi cation of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8:25
12. Jagadeeswaran G, Zheng Y, Li Y-F, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R (2009) Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specifi c microRNA families. New Phytol 184:85-98
13. Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, Soulages JL, Zhang W, Sunkar R (2010) Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 11:52
14. Reddy AM, Zheng Y, Jagadeeswaran G, Macmil SL, Graham WB, Roe BA, Desilva U, Zhang W, Sunkar R (2009) Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics 10:65
15. Zhang W, Gao S, Zhou X, Xia J, Chellappan P, Zhou X, Zhang X, Jin H (2010) Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 11:R81
16. Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38:6883-6894
17. Reese TA, Xia J, Johnson LS, Zhou X, Zhang W, Virgin HW (2010) Identifi cation of novel microRNA-like molecules generated from Herpesvirus and host tRNA transcripts. J Virol 84:10344-10353
18. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-effi cient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
19. Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatshefte f Chemie 125:167-188
20. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J (2010) Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res 39:675-686
21. Morin RD, O'Connor MD, Griffi th M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008) Application of massively parallel sequencing to microRNA profi ling and discovery in human embryonic stem cells. Genome Res 18:610-621
22. MacRae IJ, Doudna JA (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol 17: 138-145
23. Tusher VG, Tibshirani R, Chu G (2001) Signifi cance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116-5121
24. Breitling R, Armengaud P, Amtmann A, Herzyk P (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573:83-92
25. Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33:W577-W581
26. Dimitrov RA, Zuker M 2004 Prediction of hybridization and melting for double-stranded nucleic acids Biophys J 87:215-226