A non-radioactive method for small RNA detection by northern blotting

Rice

Volumn 7, Issue 1, 2014, Pages

  Huang, Qi ^a   Mao, Zhinang ^a   Li, Shaoqing ^a   Hu, Jun ^a   Zhu, Yingguo ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

Biotin labeled probe; Epigenetic; Non radioactive; Northern blot; Small RNA

Indexed keywords

ARABIDOPSIS THALIANA; ORYZA SATIVA;

EID: 84919754551     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1186/s12284-014-0026-1     Document Type: Article

References (24)

1. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221
2. Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44
3. Chen X (2012) Small RNAs in development - insights from plants. Curr Opin Genet Dev 22:361–367
4. Creighton CJ, Reid JG, Gunaratne PH (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10:490–497
5. Gao Z, Peng Y (2011) A highly sensitive and specific biosensor for ligation- and PCR-free detection of MicroRNAs. Biosens Bioelectron 26(9):3768–3773
6. He L, Hannon GJ (2004) MicroRNAs: Small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531
7. Hu J, Wang K, Huang W, Liu G, Gao Y, Wang J, Huang Q, Ji Y, Qin X, Wan L, Zhu R, Li S, Yang D, Zhu Y (2012) The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162. Plant Cell 24:109–122
8. Huang H, Gao Q, Peng X, Choi SY, Sarma K, Ren H, Morris AJ, Frohman MA (2011) piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. Dev Cell 20:376–387
9. Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B (2010) A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res 38:e98
10. Lopez-Gomollon S (2011) Detecting sRNAs by Northern blotting. Methods Mol Biol 732:25–38
11. Ramkissoon SH, Mainwaring LA, Sloand EM, Young NS, Kajigaya S (2006) Nonisotopic detection of microRNA using digoxigenin labeled RNA probes. Mol Cell Probes 20:1–4
12. Song X, Wang D, Ma L, Chen Z, Li P, Cui X, Liu C, Cao S, Chu C, Tao Y, Cao X (2012) Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development. Plant J 71:378–389
13. Studholme DJ (2012) Deep sequencing of small RNAs in plants: Applied bioinformatics. Brief Funct Genomics 11:71–85
14. Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, Havelda Z (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32:e175
15. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687
16. Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH (2004) Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res 32:1688–1695
17. Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM, Yang YG, Qi Y (2012) A role for small RNAs in DNA double-strand break repair. Cell 149:101–112
18. Williams L, Carles CC, Osmont KS, Fletcher JC (2005) A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc Natl Acad Sci U S A 102:9703–9708
19. Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol 142:280–293
20. Yang L, Liu Z, Lu F, Dong A, Huang H (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 47:841–850
21. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309:1519–1524
22. Zhan X, Wang B, Li H, Liu R, Kalia RK, Zhu JK, Chinnusamy V (2012) Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis. Proc Natl Acad Sci U S A 109:18198–18203
23. Zhong SH, Liu JZ, Jin H, Lin L, Li Q, Chen Y, Yuan YX, Wang ZY, Huang H, Qi YJ, Chen XY, Vaucheret H, Chory J, Li J, He ZH (2013) Warm temperatures induce transgenerational epigenetic release of RNA silencing by inhibiting siRNA biogenesis in Arabidopsis. Proc Natl Acad Sci U S A 110:9171–9176
24. Zhuang F, Fuchs RT, Robb GB (2012) Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. Nucleic Acids 2012:360358