Immunoprecipitation of piRNPs and Directional, Next Generation Sequencing of piRNAs

Methods in Molecular Biology

Volumn 725, Issue , 2011, Pages 281-293

  Kirino, Yohei ^b   Vourekas, Anastassios ^b   Khandros, Eugene ^b   Mourelatos, Zissimos ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b NONE

Author keywords

Ago3; Argonaute; Aub; cDNA; Gene silencing; Illumina; Immunoprecipitation; Mili; Miwi; Miwi2; Next gen sequencing; PCR; piRNA; piRNP; Piwi; Polymerase Chain reaction; Posttranscriptional RNA processing; Reverse Transcriptase; RNA Immunoprecipitation; RNA IP; RT PCR; T4 RNA ligase; Xili; Xiwi; Y12

Indexed keywords

SMALL INTERFERING RNA;

ANIMAL; ARTICLE; DROSOPHILA MELANOGASTER; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; IMMUNOPRECIPITATION; ISOLATION AND PURIFICATION; MALE; METABOLISM; MOUSE; POLYMERASE CHAIN REACTION; XENOPUS LAEVIS;

ANIMALS; DROSOPHILA MELANOGASTER; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNOPRECIPITATION; MALE; MICE; POLYMERASE CHAIN REACTION; RNA, SMALL INTERFERING; XENOPUS LAEVIS;

MLCS; MLOWN;

EID: 80051567721     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-046-1_18     Document Type: Chapter

References (17)

1. Kuramochi-Miyagawa, S., Kimura, T., Ijiri, T. W., Isobe, T., Asada, N., Fujita, Y., Ikawa, M., Iwai, N., Okabe, M., Deng, W., Lin, H., Matsuda, Y., and Nakano, T. (2004) Mili, a mammalian member of piwi family gene, is essential for spermatogenesis, Development 131, 839–849.
2. Deng, W., and Lin, H. (2002) miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis, Dev Cell 2, 819–830.
3. Carmell, M. A., Girard, A., van de Kant, H. J., Bourc’his, D., Bestor, T. H., de Rooij, D. G., and Hannon, G. J. (2007) MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline, Dev Cell 12, 503–514.
4. Harris, A. N., and Macdonald, P. M. (2001) Aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C, Development 128, 2823–2832.
5. Cox, D. N., Chao, A., Baker, J., Chang, L., Qiao, D., and Lin, H. (1998) A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal, Genes Dev 12, 3715–3727.
6. Gunawardane, L. S., Saito, K., Nishida, K. M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H., and Siomi, M. C. (2007) A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila, Science 315, 1587–1590.
7. Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., and Hannon, G. J. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila, Cell 128, 1089–1103.
8. Li, C., Vagin, V. V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M. D., Syrzycka, M., Honda, B. M., Kittler, E. L., Zapp, M. L., Klattenhoff, C., Schulz, N., Theurkauf, W. E., Weng, Z., and Zamore, P. D. (2009) Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies, Cell 137, 509–521.
9. Kirino, Y., Kim, N., de Planell-Saguer, M., Khandros, E., Chiorean, S., Klein, P. S., Rigoutsos, I., Jongens, T. A., and Mourelatos, Z. (2009) Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability, Nat Cell Biol 11, 652–658.
10. Lau, N. C., Ohsumi, T., Borowsky, M., Kingston, R. E., and Blower, M. D. (2009) Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi, EMBO J 28, 2945–2958.
11. Thomson, T., and Lin, H. (2009) The biogenesis and function of PIWI proteins and piR-NAs: progress and prospect, Annu Rev Cell Dev Biol 25, 355–376.
12. Malone, C. D., and Hannon, G. J. (2009) Small RNAs as guardians of the genome, Cell 136, 656–668.
13. Lerner, M. R., and Steitz, J. A. (1979) Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus, Proc Natl Acad Sci USA 76, 5495–5499.
14. Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs, Genes Dev 16, 720–728.
15. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21-and 22-nucleotide RNAs, Genes Dev 15, 188–200.
16. Heo, I., and Kim, V. N. (2009) Regulating the regulators: posttranslational modifications of RNA silencing factors, Cell 139, 28–31.
17. Kirino, Y., Vourekas, A., Kim, N., de Lima Alves, F., Rappsilber, J., Klein, P. S., Jongens, T. A., and Mourelatos, Z (2010). Arginine methylation of vasa protein is conserved across phyla, J Biol Chem, 285, 8148–8154.