Characterizing viral MicroRNAs and its application on identifying new MicroRNAs in virus

Journal of Cellular Physiology

Volumn 211, Issue 1, 2007, Pages 10-18

  Pan, Xiaoping ^a   Zhang, Baohong ^a   San Francisco, Michael ^a   Cobb, George P ^a  

^a TEXAS TECH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA PRECURSOR; URACIL; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS GENOME; VIRUS IDENTIFICATION;

BASE COMPOSITION; BASE SEQUENCE; EXPRESSED SEQUENCE TAGS; GENOME, VIRAL; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA PRECURSORS; RNA, VIRAL; SOFTWARE; THERMODYNAMICS; VIRUSES;

ANIMALIA;

EID: 33847637633     PISSN: 00219541     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcp.20920     Document Type: Article

References (71)

1. Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, Horvitz HR, Ambros V. 2005. The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9:403-414.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
3. Alvarez-Garcia I, Miska EA. 2005. MicroRNA functions in animal development and human disease. Development 132:4653-4662.
4. Ambros V. 2001. microRNAs: Tiny regulators with great potential. Cell 107:823-826.
5. Ambros V. 2003. MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing. Cell 113:673-676.
6. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen XM, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. 2001. A uniform system for microRNA annotation. RNA 9:277-279.
7. Axtell MJ, Bartel DP. 2005. Antiquity of microRN As and their targets inland plants. Plant Cell 17:1658-1673.
8. Bartel DP. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116:281-297.
9. Bennasser Y, Le S-Y, Yeung ML, Jeang K-T. 2004. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1:43.
10. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37:766-770.
11. Berezikov E, Plasterk RHA. 2005. Camels and zebrafish, viruses and cancer: A microRNA update. Hum Mol Genet 14:R183-R190.
12. Boehm M, Slack F. 2005. A developmental timing microRNA and its target regulate life span in C. elegans. Science 310:1954-1957.
13. Bonnet E, Wuyts J, Rouze P, Van de Peer Y. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:2911-2917.
14. Cai XZ, Cullen BR. 2006. Transcriptional origin of Kaposi's sarcoma-associated herpesvirus MicroRNAs. J Virol 80:2234-2242.
15. Cai XZ, Lu SH, Zhang ZH, Gonzalez CM, Damania B, Cullen BR. 2005. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proceedings of the National Academy of Sciences of the United States of America, 102:5570-5575.
16. Cai XZ, Schafer A, Lu SH, Bilello JP, Desrosiers RC, Edwards R, Raab-traub N, Cullen BR. 2006. Epstein-Barr virus microRNAs are evolutionary conserved and differentially expressed. PLOS Pathogens 2:e23.
17. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, et al. 2002. Frequent deletions and down-regulation of micro-RN A genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America, 99:15524-15529.
18. Calin GA, Sevignani C, Dan Dumitru C, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, Croce CM. 2004. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences of the United States of America, 101:2999-3004.
19. Carrington JC, Ambros V. 2003. Role of microRNAs in plant and animal development. Science 301:336-338.
20. Chen XM. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022-2025.
21. Chen CZ, Li L, Lodish HF, Bartel DP. 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83-86.
22. Chen JF, Mandel EM, Thomson JM, Wu QL, Callis TE, Hammond SM, Conlon FL, Wang DZ. 2006. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38:228-233.
23. Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881-10890.
24. Cullen BR. 2006. Viruses and microRNAs. Nat Genet 38:525-530.
25. Dunn W, Trang P, Zhong Q, Yang E, van Belle C, Liu FY. 2005. Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol 7:1684-1695.
26. Esquela-Kerscher A, Slack FJ. 2006. Oncomirs-MicroRNAs with a role in cancer. Nat Rev Cancer 6:259-269.
27. Floyd SK, Bowman JL. 2004. Gene regulation: Ancient microRNA target sequences in plants. Nature 428:485-486.
28. Forstemann K, Tomari Y, Du TT, Vagin W, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE, Zamore PD. 2005. Normal microRNA maturation and germ-line stem cell maintenance requires loquacious, a double-stranded RNA-binding domain protein. Plos Biology 3:1187-1201.
29. Gerner CS, Dolan A, McGeoch DJ. 2004. Phylogenetic relationships in the Lymphocryptovirus genus of the Gammaherpesvirinae. Virus Res 99:187-192.
30. Grey F, Antoniewicz A, Allen E, Saugstad J, McShea A, Carrington JC, Nelson J. 2005. Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol 79:12095-12099.
31. Griffiths-Jones S. 2004. The microRNA registry. Nucleic Acids Res 32:D109-D111.
32. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. 2006. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140-D144.
33. Grun D, Wang Y-L, Langenberger D, Gunsalus KC, Rajewsky N. 2005. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1:e13.
34. Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, Ruohola-Baker H. 2005. Stem cell division is regulated by the microRNA pathway. Nature 435:974-978.
35. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM. 2005. A microRNA polycistron as a potential human oncogene. Nature 435:828-833.
36. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K. 2005. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19:489-501.
37. Karp X, Ambros V. 2005. Encountering microRNAs in cell fate signaling. Science 310:1288-1289.
38. Kwon C, Han Z, Olson EN, Srivastava D. 2005. MicroRNAI influences cardiac differentiation in Drosophila and regulates notch signaling. Proceedings of the National Academy of Sciences of the United States of America, 102:18986-18991.
39. Labourier E, Shingara J, Wolf I, Jeffers K, Brown D. 2004. MicroRNAs as potential diagnostic markers of disease. J Mol Diagn 6:433-433.
40. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294:853-858.
41. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-862.
42. Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862-864.
43. Lu SH, Cullen BR. 2004. Adenovirus VAI noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. J Virol 78:12868-12876.
44. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebet BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. 2005. MicroRNA expression profiles classify human cancers. Nature 435:834-838.
45. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911-940.
46. Miska EA. 2005. How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev 15:563-568.
47. Murchison EP, Partridge JF, Tam OH, Cheloufi S, Hannon GJ. 2005. Characterization of Dicer-deficient murine embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America, 102:12135-12140.
48. Nair V, Zavolan M. 2006. Virus-encoded microRNAs: Novel regulators of gene expression. Trends Microbiol 14:169-175.
49. Omoto S, Fujii YR. 2005. Regulation of human immunodeficiency virus I transcription by nef microRNA. J Gen Virol 86:751-755.
50. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86-89.
51. Pearce M, Matsumura S, Wilson AC. 2005. Transcripts encoding K12, v-FLIP, v-Cyclin, and the MicroRNA cluster of Kaposi's sarcoma-associated herpesvirus originate from a common promoter. J Virol 79:14457-14464.
52. Pfeffer S, Zavolan M, Grasser FA, Chien MC, Russo JJ, Ju JY, John B, Enright AJ, Marks D, Sander C, Tuschl T. 2004. Identification of virus-encoded microRNAs. Science 304:734-736.
53. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien MC, Russo JJ, Ju JY, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. 2005. Identification of microRNAs of the herpesvirus family. Nat Methods 2:269-276.
54. Rao M. 2004. Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells. Dev Biol 275:269-286.
55. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906.
56. Saetrom P, Snove O, Nedland M, Grunfeld TB, Lin Y, Bass MB, Cannon JR. 2006. Conserved microRNA characteristics in mammals. Oligonucleotides 16:115-144.
57. Samols MA, Hu JH, Skalsky RL, Renne R. 2005. Cloning and identification of a MicroRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol 79:9301-9305.
58. Seffens W, Digby D. 1999. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27:1578-1584.
59. Sunkar R, Zhu JK. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001-2019.
60. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, Croce CM. 2006. A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of Sciences of the United States of America, 103:2257-2261.
61. Weber MJ. 2005. New human and mouse microRNA genes found by homology search. FEBS J 272:59-73.
62. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. 2005. Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336-360.
63. Zhang BH, Pan XP, Anderson TA. 2006a. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580:3753-3762.
64. Zhang BH, Pan XP, Anderson TA. 2006b. MicroRNA: A new player in stem cells. Journal of Cellular Physiology 209:265-269.
65. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA. 2006c. Conservation and divergence of plant microRNA genes. Plant J 46:243-259.
66. Zhang BH, Pan XP, Cobb GP, Anderson TA. 2006d. microRNAs as oncogenes and tumor suppressors. Dev Biol DOI:10.1016/j.ydbio.2006.08.028.
67. Zhang BH, Pan XP, Cobb GP, Anderson TA. 2006e. Plant microRNA: A small regulatory molecule with big impact. Dev Biol 289:3-16.
68. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA. 2006f. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63:246-254.
69. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. 2006g. Computational identification of microRNAs and their targets. Comput Biol Chem 30:395-407.
70. Zhang BH, Wang QL, Pan XP. 2006h. MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol DOI:10.1002/icp.20869.
71. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415.