The diversity of MicroRNAs in sequences and expression patterns

Progress in Biochemistry and Biophysics

Volumn 42, Issue 8, 2015, Pages 689-696

  Ding, Su Ping ^a   Liu, Li Li ^a,b   Huang, Ting ^a   Wang, Ying ^a   Yan, Ming Li ^a,b   Yuan, Zhi Dong ^a,b  

^a HUNAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b Key Laboratory of Integrated Management of the Pests and Diseases on Horticultural Crops in Hunan Province Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils   (China)

Author keywords

Arm switch; Diversity; IsomiR; MiRNA; MiRNA editing

Indexed keywords

ANIMALIA; METAZOA;

EID: 84939553446     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.16476/j.pibb.2015.0096     Document Type: Article

References (67)

1. Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281-297.
2. Newman M A, Hammond S M. Emerging paradigms of regulated microRNA processing. Genes Dev, 2010, 24(11): 1086-1092.
3. Slezak-Prochazka I, Durmus S, Kroesen B J, et al. MicroRNAs, macrocontrol: Regulation of miRNA processing. RNA, 2010, 16(6): 1087-1095.
4. Fernandez-Valverde S L, Taft R J, Mattick J S. Dynamic isomiR regulation in Drosophila development. RNA, 2010, 16 (10): 1881-1888.
5. Morin R D, O'Connor M D, Griffith M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res, 2008, 18 (4): 610-621.
6. Bizuayehu T T, Lanes C F, Furmanek T, et al. Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. BMC Genomics, 2012, 13: 11.
7. Xia J, Zhang W. A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species. Nucleic Acids Res, 2014, 42(3): 1427-1441.
8. Li J, Yang Z, Yu B, et al. Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol, 2005, 15(16): 1501-1507.
9. Landgraf P, Rusu M, Sheridan R, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 2007, 129(7): 1401-1414.
10. Ruby J G, Stark A, Johnston W K, et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res., 2007, 17(12): 1850-1864.
11. Zhang J, Zhang S, Li S, et al. A genome-wide survey of microRNA truncation and 3' nucleotide addition events in larch (Larix leptolepis). Planta, 2013, 237(4): 1047-1056.
12. Azuma-Mukai A, Oguri H, Mituyama T, et al. Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci USA, 2008, 105(23): 7964-7969.
13. Reid J G, Nagaraja A K, Lynn F C, et al. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res, 2008, 18(10): 1571-1581.
14. Seitz H, Ghildiyal M, Zamore P D. Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA∗ strands in flies. Curr Biol, 2008, 18(2): 147-151.
15. Lu S, Sun Y H, Chiang V L. Adenylation of plant miRNAs. Nucleic Acids Res, 2009, 37(6): 1878-1885.
16. Ebhardt H A, Tsang H H, Dai D C, et al. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNAmodifications. Nucleic Acids Res, 2009, 37(8): 2461-2470.
17. Reese T A, Xia J, Johnson L S, et al. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNAtranscripts. J Virol, 2010, 84(19): 10344-10353.
18. Xia J, Zhang W. Noncanonical microRNAs and endogenous siRNAs in lytic infection of murine gammaherpesvirus. PLoS ONE, 2012, 7(10): E47863.
19. Ruby J G, Jan C, Player C, et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 2006, 127(6): 1193-1207.
20. Burroughs A M, Ando Y, de Hoon M J, et al. A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res, 2010, 20(10): 1398-1410.
21. Starega-Roslan J, Witkos T M, Galka-Marciniak P, et al. Sequence features of drosha and dicer cleavage sites affect the complexity of isomiRs. Int J Mol Sci, 2015, 16(4): 8110-8127.
22. Ebhardt H A, Fedynak A, Fahlman R P. Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence, 2010, 1(1): 12.
23. Luciano D J, Mirsky H, Vendetti N J, et al. RNA editing of a miRNAprecursor. RNA, 2004, 10(8): 1174-1177.
24. Yang W, Chendrimada T P, Wang Q, et al. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol, 2006, 13(1): 13-21.
25. Kuchenbauer F, Morin R D, Argiropoulos B, et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res, 2008, 18(11): 1787-1797.
26. Chiang H R, Schoenfeld L W, Ruby J G, et al. Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes. Genes Dev, 2010, 24(10): 992-1009.
27. Berezikov E, Robine N, Samsonova A, et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res, 2011, 21(2): 203-215.
28. Ren G, Chen X, Yu B. Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis. Curr Biol, 2012, 22(8): 695-700.
29. Zhao Y, Yu Y, Zhai J, et al. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol, 2012, 22(8): 689-694.
30. Ibrahim F, Rymarquis L A, Kim E J, et al. Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc Natl Acad Sci USA, 2010, 107(8): 3906-3911.
31. Katoh T, Sakaguchi Y, Miyauchi K, et al. Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev, 2009, 23(4): 433-438.
32. Wyman S K, Knouf E C, Parkin R K, et al. Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res, 2011, 21(9): 1450-1461.
33. Bartel D P. MicroRNAs: Target recognition and regulatory functions. Cell, 2009, 136(2): 215-233.
34. Guo H, Ingolia N T, Weissman J S, et al. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 2010, 466(7308): 835-840.
35. Baek D, Villen J, Shin C, et al. The impact of microRNAs on protein output. Nature, 2008, 455(7209): 64-71.
36. Guo L, Yang Q, Lu J, et al. A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One, 2011, 6(6): E21072.
37. Borel C & Antonarakis S E. Functional genetic variation of human miRNAs and phenotypic consequences. Mamm Genome, 2008, 19(7-8): 503-509.
38. Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem, 2010, 79: 321-349.
39. Bass B L. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem, 2002, 71: 817-846.
40. Keegan L P, Leroy A, Sproul D, et al. Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes. Genome Biol, 2004, 5(2): 209.
41. Bass B L, Nishikura K, Keller W, et al. A standardized nomenclature for adenosine deaminases that act on RNA. RNA, 1997, 3(9): 947-949.
42. Li J B, Levanon E Y, Yoon J K, et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science, 2009, 324(5931): 1210-1213.
43. Kawahara Y, Zinshteyn B, Sethupathy P, et al. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science, 2007, 315(5815): 1137-1140.
44. Kawahara Y, Megraw M, Kreider E, et al. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res, 2008, 36(16): 5270-5280.
45. Ekdahl Y, Farahani H S, Behm M, et al. A-to-I editing of microRNAs in the mammalian brain increases during development. Genome Res, 2012, 22(8): 1477-1487.
46. Alon S, Mor E, Vigneault F, et al. Systematic identification of edited microRNAs in the human brain. Genome Res, 2012, 22(8): 1533-1540.
47. Vesely C, Tauber S, Sedlazeck F J, et al. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res, 2014, 42(19): 12155-12168.
48. Warnefors M, Liechti A, Halbert J, et al. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol, 2014, 15(6): R83.
49. Yuan Z, Ding S, Yan M, et al. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene, 2015, 569(2): 239-249.
50. Siddle K J, Tailleux L, Deschamps M, et al. Bacterial infection drives the expression dynamics of microRNAs and their isomiRs. PLoS Genet, 2015, 11(3): E1005064.
51. Loher P, Londin E R & Rigoutsos I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget, 2014, 5(18): 8790-8802.
52. Warf MB, Shepherd B A, JohnsonWE, et al. Effects of ADARs on small RNA processing pathways in C. elegans. Genome Res, 2012, 22(8): 1488-1498.
53. Hu H Y, Yan Z, Xu Y, et al. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics, 2009, 10: 413.
54. Cloonan N, Wani S, Xu Q, et al. MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol, 2011, 12(12): R126.
55. Ro S, Park C, Young D, et al. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res, 2007, 35(17): 5944-5953.
56. Li S C, Liao Y L, Ho MR, et al. miRNA arm selection and isomiR distribution in gastric cancer. BMC Genomics, 2012, 13(Suppl 1): S13.
57. Li S C, Tsai K W, Pan H W, et al. MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. BMC Syst Biol, 2012, 6(Suppl 2): S14.
58. Chang H T, Li S C, Ho M R, et al. Comprehensive analysis of microRNAs in breast cancer. BMC Genomics, 2012, 13(Suppl 7): S18.
59. Grimson A, Srivastava M, Fahey B, et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature, 2008, 455(7217): 1193-1197.
60. Marco A, Hui J H, Ronshaugen M, et al. Functional shifts in insect microRNA evolution. Genome Biol Evol, 2010, 2: 686-696.
61. Griffiths-Jones S, Hui J H, Marco A, et al. MicroRNA evolution by armswitching. EMBORep, 2011, 12(2): 172-177.
62. Li S C, Liao Y L, ChanWC, et al. Interrogation of rabbit miRNAs and their isomiRs. Genomics, 2011, 98(6): 453-459.
63. Li S C, ChanWC, HoMR, et al. Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics, 2010, 11(Suppl 4): S8.
64. Honda S, Kirino Y. Dumbbell-PCR: A method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences. Nucleic Acids Res, 2015, 43(12): E77.
65. HumphreysD T, Hynes C J, Patel H R, et al. Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function. PLoS ONE, 2012, 7(2): E30933.
66. Tan G C, Chan E, Molnar A, et al. 5' isomiR variation is of functional and evolutionary importance. Nucleic Acids Res, 2014, 42(14): 9424-9435.
67. Babapoor S, Fleming E, Wu R, et al. A novel miR-451a isomiR, associated with amelanotypic phenotype, acts as a tumor suppressor in melanoma by retarding cell migration and invasion. PLoS ONE, 2014, 9(9): E107502.