Primary microRNA processing assay reconstituted using recombinant drosha and DGCR8

Methods in Molecular Biology

Volumn 1095, Issue , 2014, Pages 73-86

  Barr, Ian ^a   Guo, Feng ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DiGeorge syndrome; Heme; Nucleic acid binding protein; Pasha; Ribonuclease III; RNA processing; RNA binding protein

Indexed keywords

DGCR8 PROTEIN; DROSHA PROTEIN; HEMOPROTEIN; MICRORNA; RECOMBINANT PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; DIMERIZATION; ESCHERICHIA COLI; HUMAN; IN VITRO STUDY; NONHUMAN; OXIDATION REDUCTION STATE; PHYSIOLOGY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; RNA PROCESSING; RNA TRANSCRIPTION;

ESCHERICHIA COLI; HEME; HUMANS; MICRORNAS; PROTEINS; RECOMBINANT PROTEINS; RIBONUCLEASE III; RNA CLEAVAGE; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 84934441129     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-703-7_5     Document Type: Article

References (37)

1. Lee Y, Ahn C, Han J et al (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415-419
2. Denli AM, Tops BB, Plasterk RH et al (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432: 231-235
3. Gregory RI, Yan KP, Amuthan G et al (2004) The microprocessor complex mediates the genesis of microRNAs. Nature 432:235-240
4. Faller M, Matsunaga M, Yin S et al (2007) Heme is involved in microRNA processing. Nat Struct Mol Biol 14:23-29
5. Barr I, Smith AT, Senturia R et al (2011) DiGeorge critical region 8 (DGCR8) is a double-cysteine-ligated heme protein. J Biol Chem 286:16716-16725
6. Barr I, Smith AT, Chen Y et al (2012) Ferric, not ferrous, heme activates RNA-binding protein DGCR8 for primary microRNA processing. Proc Natl Acad Sci USA 109:1919-1924
7. Wang Y, Medvid R, Melton C et al (2007) DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell selfrenewal. Nat Genet 39:380-385
8. Yi R, Pasolli HA, Landthaler M et al (2009) DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci USA 106:498-502
9. Faller M, Guo F (2008) MicroRNA biogenesis: there's more than one way to skin a cat. Biochim Biophys Acta 1779:663-667
10. Han J, Lee Y, Yeom KH et al (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18:3016-3027
11. Fukuda T, Yamagata K, Fujiyama S et al (2007) DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 9:604-611
12. Guil S, Caceres JF (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 14:591-596
13. Viswanathan SR, Daley GQ, Gregory RI (2008) Selective blockade of microRNA processing by Lin28. Science 320:97-100
14. Davis BN, Hilyard AC, Lagna G et al (2008) SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454:56-61
15. Trabucchi M, Briata P, Garcia-Mayoral M et al (2009) The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459:1010-1014
16. Suzuki HI, Yamagata K, Sugimoto K et al (2009) Modulation of microRNA processing by p53. Nature 460:529-533
17. Sakamoto S, Aoki K, Higuchi T et al (2009) The NF90-NF45 complex functions as a negative regulator in the microRNA processing pathway. Mol Cell Biol 29:3754-3769
18. Michlewski G, Caceres JF (2010) Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat Struct Mol Biol 17:1011-1018
19. Zeng Y, Cullen BR (2005) Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 280:27595-27603
20. Yeom KH, Lee Y, Han J et al (2006) Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res 34:4622-4629
21. Sohn SY, Bae WJ, Kim JJ et al (2007) Crystal structure of human DGCR8 core. Nat Struct Mol Biol 14:847-853
22. Faller M, Toso D, Matsunaga M et al (2010) DGCR8 recognizes primary transcripts of microRNAs through highly cooperative binding and formation of higher-order structures. RNA 16:1570-1583
23. Guo F (2012) Drosha and DGCR8 in microRNA biogenesis. In: Guo F, Tamanoi F (eds) The enzymes: eukaryotic RNases and their partners in RNA degradation and biogenesis, Part B, vol 32, 1st edn. Elsevier Academic Press, Amsterdam, Netherlands, pp. 101-121
24. Lee Y, Jeon K, Lee JT et al (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663-4670
25. Newman MA, Thomson JM, Hammond SM (2008) Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 14:1539-1549
26. Lee Y, Kim VN (2007) In vitro and in vivo assays for the activity of Drosha complex. Methods Enzymol 427:89-106
27. Zeng Y, Yi R, Cullen BR (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 24:138-148
28. Zhang X, Zeng Y (2010) The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res 38: 7689-7697
29. Senturia R, Faller M, Yin S et al (2010) Structure of the dimerization domain of DiGeorge Critical Region 8. Protein Sci 19: 1354-1365
30. Senturia R, Laganowsky A, Barr I et al (2012) Dimerization and heme binding are conserved in amphibian and starfish homologues of the microRNA processing protein DGCR8. PLoS One 7(7):e39688. doi:10.1371/journal. pone.0039688
31. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126-139
32. Morlando M, Ballarino M, Gromak N et al (2008) Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol Biol 15:902-909
33. Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26:775-783
34. Milligan JF, Uhlenbeck OC (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51-62
35. Pace CN, Vajdos F, Fee L et al (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci 4: 2411-2423
36. Cleland WW (1964) Dithiothreitol, a new protective reagent for SH groups. Biochemistry 3:480-482
37. Berry EA, Trumpower BL (1987) Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra. Anal Biochem 161:1-15