Detection of novel human MiRNAs responding to X-ray irradiation

Journal of Radiation Research

Volumn 52, Issue 4, 2011, Pages 425-432

  Ding, Nan ^a,b,c   Wu, Xin ^a,c   He, Jinpeng ^a   Chang, Lei ^a,c   Hu, Wentao ^a,c   Li, Wenjian ^a   Wang, Jufang ^a   Wang, Tieshan ^b   Zhou, Guangming ^a  

^a INSTITUTE OF MODERN PHYSICS   (China)

^b LANZHOU UNIVERSITY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Ionizing radiation; Microrna; qRT PCR; Solexa

Indexed keywords

LANTHANUM COMPOUNDS; POLYMERASE CHAIN REACTION; PROTEINS; RADIATION SHIELDING; RNA;

CELL-BE; CELL/B.E; CELL/BE; HELA CELL; QRT-PCR; SMALL RNA; SOLEXUM; X RAY IRRADIATION;

IONIZING RADIATION;

EID: 79960887238     PISSN: 04493060     EISSN: 13499157     Source Type: Journal    
DOI: 10.1269/jrr.10158     Document Type: Article

References (50)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Ambros V (2004) The functions of animal microRNAs. Nature 431: 350-355.
3. Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
4. Nilsen TW (2007) Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet 23: 243-249.
5. Lee RC, Feinbaum RL and Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
6. Lagos-Quintana M, et al (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
7. Lau NC, et al (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
8. Berezikov E, et al (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
9. Miranda KC, et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
10. Berezikov E, et al (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 16: 1289-1298.
11. Stark MS, et al (2010) Characterization of the Melanoma miRNAome by Deep Sequencing. PLoS One 5: e9685.
12. Goff LA, et al (2009) Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors. PLoS One 4: e7192.
13. Chen CZ, et al (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
14. Kanellopoulou C, et al (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19: 489-501.
15. Wienholds E and Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579: 5911-5922.
16. Kusenda B, et al (2006) MicroRNA biogenesis, functionality and cancer relevance. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 150: 205-215.
17. Mattick JS and Makunin IV (2005) Small regulatory RNAs in mammals. Hum Mol Genet 14 Spec No 1: R121-132.
18. Creighton CJ, Reid JG and Gunaratne PH (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10: 490-497.
19. Calin GA and Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857-866.
20. Esquela-Kerscher A and Slack FJ (2006) Oncomirs - micro-RNAs with a role in cancer. Nat Rev Cancer 6: 259-269.
21. Negrini M, et al (2007) MicroRNAs in human cancer: from research to therapy. J Cell Sci 120: 1833-1840.
22. Marsit CJ, Eddy K and Kelsey KT (2006) MicroRNA responses to cellular stress. Cancer Res 66: 10843-10848.
23. Phillips JR, Dalmay T and Bartels D (2007) The role of small RNAs in abiotic stress. FEBS Lett 581: 3592-3597.
24. Sunkar R, et al (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301-309.
25. Babar IA, Slack FJ and Weidhaas JB (2008) miRNA modulation of the cellular stress response. Future Oncol 4: 289-298.
26. Kulshreshtha R, et al (2007) A microRNA signature of hypoxia. Mol Cell Biol 27: 1859-1867.
27. Trindade I, et al (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231: 705-716.
28. Zhang J, et al (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10: 449.
29. Hung JY, et al (2010) Oxidative and endoplasmic reticulum stress signaling are involved in dehydrocostuslactone-mediatedapoptosis in human non-small cell lung cancer cells. Lung Cancer 68: 355-365.
30. Li G, et al (2009) Alterations in microRNA expression in stress-induced cellular senescence. Mech Ageing Dev 130: 731-741.
31. Simone NL, et al (2009) Ionizing radiation-induced oxidative stress alters miRNA expression. PLoS One 4: e6377.
32. Maes OC, et al (2008) Changes in MicroRNA expression patterns in human fibroblasts after low-LET radiation. J Cell Biochem 105: 824-834.
33. Weidhaas JB, et al (2007) MicroRNAs as potential agents to alter resistance to cytotoxic anticancer therapy. Cancer Res 67: 11111-11116.
34. Koturbash I, et al (2010) Sex-specific radiation-induced microRNAome responses in the hippocampus, cerebellum and frontal cortex in a mouse model. Mutat Res.
35. Ilnytskyy Y, et al (2008) Altered microRNA expression patterns in irradiated hematopoietic tissues suggest a sex-specific protective mechanism. Biochem Biophys Res Commun 377: 41-45.
36. Ahmed FE, et al (2009) Differences in mRNA and microRNA microarray expression profiles in human colon adenocarcinoma HT-29 cells treated with either Intensity-modulated Radiation Therapy (IMRT), or Conventional Radiation Therapy (RT). Cancer Genomics Proteomics 6: 109-127.
37. Chaudhry MA, (2009) Real-time PCR analysis of micro-RNA expression in ionizing radiation-treated cells. Cancer Biother Radiopharm 24: 49-56.
38. Jian X, et al (2010) Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 95: 47-55.
39. Chen X, et al (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10: R78.
40. Creighton CJ, et al (2010) Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One 5: e9637.
41. Lewis BP, Burge CB and Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
42. Pawlik A, et al (2009) Changes in transcriptome after in vivoexposure to ionising radiation reveal a highly specialised liver response. Int J Radiat Biol 85: 656-671.
43. Wilson KD, et al (2010) Effects of ionizing radiation on self-renewal and pluripotency of human embryonic stem cells. Cancer Res 70: 5539-5548.
44. Hu ZZ, et al (2008) Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data. J Proteomics Bioinform 1: 47-60.
45. Xi Chen, et al (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biology 10: R78.
46. Huang J, et al (2009) Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach. PLoS One 4: e8206.
47. Yu X, et al (2009) A discovery of novel microRNAs in the silkworm (Bombyx mori) genome. Genomics 94: 438-444.
48. Chaudhry MA, Kreger B and Omaruddin RA (2010) Transcriptional modulation of micro-RNA in human cells differing in radiation sensitivity. Int J Radiat Biol 86: 569-583.
49. Chen G, et al (2010) MicroRNA-181a sensitizes human malignant glioma U87MG cells to radiation by targeting Bcl-2. Oncol Rep 23: 997-1003.
50. Ambros V, et al (2003) A uniform system for microRNA annotation. RNA. 9(3): 277-279.