HITS-CLIP (CLIP-Seq) for Mouse Piwi Proteins

Methods in Molecular Biology

Volumn 1093, Issue , 2014, Pages 73-95

  Vourekas, Anastassios ^a   Mourelatos, Zissimos ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Ago3; Argonaute; Aub; cDNA; CLIP Seq; Gene silencing; HITS CLIP; Illumina; Immunoprecipitation; Mili; Miwi; Miwi2; Next gen sequencing; PCR; piRNA; piRNP; Piwi; Polymerase chain reaction; Post transcriptional RNA processing; Reverse transcriptase; RNA IP; RT PCR; T4 RNA ligase

Indexed keywords

MILI PROTEIN; MIWI PROTEIN; PIWI PROTEIN; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; HIGH THROUGHPUT SEQUENCING AFTER IN VIVO CROSSLINKING AND IMMUNOPRECIPITATION; IN VIVO STUDY; MOUSE; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE;

ANIMALS; ARGONAUTE PROTEINS; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNOPRECIPITATION; MICE; PROTEIN DENATURATION; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA; ULTRAVIOLET RAYS; UREA;

EID: 84934435058     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-694-8_7     Document Type: Article

References (23)

1. Siomi MC, Sato K, Pezic D, Aravin AA (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12:246-258
2. Juliano C, Wang J, Lin H (2011) Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Ann Rev Genet 45:447-469
3. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specifi c class of small RNAs binds mammalian Piwi proteins. Nature 442:199-202
4. Aravin A, Gaidatzis D, Pfeffer S, Lagos- Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203-207
5. Lau NC, Seto AG, Kim J, Kuramochi- Miyagawa S, Nakano T, Bartel DP, Kingston RE (2006) Characterization of the piRNA complex from rat testes. Science 313:363-367
6. Kuramochi-Miyagawa S, Kimura T, Ijiri TW, Isobe T, Asada N, Fujita Y, Ikawa M, Iwai N, Okabe M, Deng W, Lin H, Matsuda Y, Nakano T (2004) Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131:839-849
7. Deng W, Lin H (2002) miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev Cell 2:819-830
8. Vagin VV, Wohlschlegel J, Qu J, Jonsson Z, Huang X, Chuma S, Girard A, Sachidanandam R, Hannon GJ, Aravin AA (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev 23:1749-1762
9. Kirino Y, Vourekas A, Sayed N, de Lima Alves F, Thomson T, Lasko P, Rappsilber J, Jongens TA, Mourelatos Z (2010) Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA 16:70-78
10. Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS (2009) Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profi le. Nat Struct Mol Biol 16:639-646
11. Mathioudakis N, Palencia A, Kadlec J, Round A, Tripsianes K, Sattler M, Pillai RS, Cusack S (2012) The multiple Tudor domain- containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. RNA 18:2056-2072
12. Tanaka SS, Toyooka Y, Akasu R, Katoh-Fukui Y, Nakahara Y, Suzuki R, Yokoyama M, Noce T (2000) The mouse homolog of Drosophila Vasa is required for the development of male germ cells. Genes Dev 14:841-853
13. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, Shiromoto Y, Asada N, Toyoda A, Fujiyama A, Totoki Y, Shibata T, Kimura T, Nakatsuji N, Noce T, Sasaki H, Nakano T (2010) MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev 24:887-892
14. Kotaja N, Sassone-Corsi P (2007) The chromatoid body: a germ-cell-specifi c RNAprocessing centre. Nat Rev Mol Cell Biol 8:85-90
15. Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNAmRNA interaction maps. Nature 460: 479-486
16. Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29:607-614
17. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464-469
18. Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD, Mourelatos Z (2012) Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat Struct Mol Biol 19:773-781
19. Kirino Y, Vourekas A, Khandros E, Mourelatos Z, Hobman TC, Duchaine TF (2011) Immunoprecipitation of piRNPs and directional, next generation sequencing of piRNAs. Methods Mol Biol 725:281-293
20. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31:785-799
21. Aravin AA, Sachidanandam R, Girard A, Fejes- Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316:744-747
22. Reuter M, Berninger P, Chuma S, Shah H, Hosokawa M, Funaya C, Antony C, Sachidanandam R, Pillai RS (2011) Miwi catalysis is required for piRNA amplifi cationindependent LINE1 transposon silencing. Nature 480:264-267
23. Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J (2012) Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 13:R67