Mature microRNAs identified in highly purified nuclei from HCT116 colon cancer cells

RNA Biology

Volumn 7, Issue 5, 2010, Pages 606-614

  Park, Chang Won ^a   Zeng, Yan ^a   Zhang, Xiaoxiao ^a   Subramanian, Subbaya ^a   Steer, Clifford J ^a  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

Author keywords

Cytoplasmic; Microarray; microRNA; Northern blot; Nucleus; RT PCR

Indexed keywords

MICRORNA;

ARTICLE; CELL NUCLEUS; CELL STRAIN HCT116; CELLULAR DISTRIBUTION; CONTROLLED STUDY; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NORTHERN BLOTTING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS;

EID: 78649357109     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.7.5.13215     Document Type: Article

References (33)

1. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001; 294:853-8.
2. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T. New microRNAs from mouse and human. RNA 2003; 9:175-9.
3. Zeng Y, Cullen BR. Sequence requirements for micro RNA processing and function in human cells. RNA 2003; 9:112-23.
4. Yekta S, Shih IH, Bartel DP. MicroRNA-directed cleavage of HOXB8 mRNA. Science 2004; 304:594-6.
5. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425:415-9.
6. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science 2004; 303:95-8.
7. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001; 293:834-8.
8. Lee Y, Jeon K, Lee J, Kim S, Kim VN. MicroRNA maturation: stepwise processing and sub-cellular localization. EMBO J 2002; 21:4663-70.
9. Sontheimer EJ. Assembly and function of RNA silencing complexes. Nature Rev Mol Cell Biol 2005; 6:127-38.
10. Hwang HW, Wentzel EA, Mendell JT. A hexanucleotide element directs microRNA nuclear import. Science 2007; 315:97-100.
11. Politz JC, Zhang F, Pederson T. MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proc Natl Acad Sci USA 2006; 103:18957-62.
12. Politz JC, Hogan EM, Pederson T. MicroRNAs with a nucleolar location. RNA 2009; 15:1705-15.
13. Ohrt T, Mutze J, Staroske W, Weinmann L, Hock J, Crell K, et al. Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Res 2008; 36:6439-49.
14. Castanotto D, Lingeman R, Riggs AD, Rossi JJ. CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs. Proc Natl Acad Sci USA 2009; 106:21655-9.
15. Wade RH, Hyman AA. Microtubule structure and dynamics. Curr Opin Cell Biol 1997; 9:12-7.
16. Bachman KE, Rountree MR, Baylin SB. Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J Biol Chem 2001; 276:32282-7.
17. Wada I, Rindress D, Cameron PH, Ou WJ, Doherty JJ 2nd, Louvard D, et al. SSRa and associated calnexin are major calcium binding proteins of the endoplasmic reticulum membrane. J Biol Chem 1991; 266:19599-610.
18. Blobel G, Potter VR. Nuclei from rat liver: isolation method that combines purity with high yield. Science 1966; 154:1662-5.
19. Shelton KR. Selective effects of nonionic detergent and salt solutions in dissolving nuclear envelope protein. Biochim Biophys Acta 1976; 455:973-82.
20. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005; 33:e179.
21. Hutvágner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002; 297:2056-60.
22. Barroso-delJesus A, Romero-López C, Lucena-Aguilar G, Melen GJ, Sanchez L, Ligero G, et al. Embryonic stem cell-specific miR302-367 cluster: human gene structure and functional characterization of its core promoter. Mol Cell Biol 2008; 28:6609-19.
23. Köhler A, Hurt E. Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 2007; 8:761-73.
24. Daneholt B. A look at messenger RNP moving through the nuclear pore. Cell 1997; 88:585-8.
25. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 2004; 432:235-40.
26. Fasanaro P, Greco S, Lorenzi M, Pescatori M, Brioschi M, Kulshreshtha R, et al. An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 2009; 284:35134-43.
27. Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HG. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992; 71:527-42.
28. Clemson C, McNeil JA, Willard HF, Lawrence JB. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996; 132:259-75.
29. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136:215-33.
30. Groudine M, Peretz M, Weintraub H. Transcriptional regulation of hemoglobin switching on chicken embryos. Mol Cell Biol 1981; 1:281-8.
31. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680-5.
32. Thomson JM, Parker J, Perou CM, Hammond SM. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 2004; 1:47-53.
33. Zeng Y, Wagner EJ, Cullen BR. Both natural and designed microRNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 2002; 9:1327-33.