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Isolation of Nuclear RNA-Associated Protein Complexes

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Book cover Promoter Associated RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1543))

Abstract

Noncoding RNAs, being at the center stage of the organismal development and homeostasis, warrant a detailed analysis to utilize their full therapeutic potential. They form complexes with various proteins that enable the noncoding RNAs to acquire specific cellular functions such as the transcriptional outcomes that are controlled in a spatio-temporal manner. In this protocol, we describe a method to isolate such known (and unknown) protein complexes bound to a nuclear noncoding RNA.

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References

  1. Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  3. Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352

    Article  CAS  PubMed  Google Scholar 

  4. Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9:e1003569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: Insights into functions. Nat Rev Genet 10:155–159

    Article  CAS  PubMed  Google Scholar 

  6. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629–641

    Article  CAS  PubMed  Google Scholar 

  7. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494–1504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ebert MS, Sharp PA (2012) Roles for microRNAs in conferring robustness to biological processes. Cell 149:515–524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Luteijn MJ, Ketting RF (2013) PIWI-interacting RNAs: From generation to transgenerational epigenetics. Nat Rev Genet 14:523–534

    Article  CAS  PubMed  Google Scholar 

  10. Napoli S, Pastori C, Magistri M et al (2009) Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. EMBO J 28:1708–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Li W, Lam MT, Notani D (2014) Enhancer RNAs. Cell Cycle 13:3151–3152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Li W, Notani D, Ma Q et al (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516–520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Sun K, Lai EC (2013) Adult-specific functions of animal microRNAs. Nat Rev Genet 14:535–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Surzycki S (2000) DNA cloning—Experimental procedures. In: Surzycki S (ed) Basic techniques in molecular biology. Springer, Heidelberg, pp. 320–373

    Chapter  Google Scholar 

  16. Purbey PK, Jayakumar PC, Patole MS et al (2006) pC6-2/caspase-6 system to purify glutathione-S-transferase-free recombinant fusion proteins expressed in Escherichia coli. Nat Protoc 1:1820–1827

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Dimple Notani .

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Jayani, R.S., Singh, A., Notani, D. (2017). Isolation of Nuclear RNA-Associated Protein Complexes. In: Napoli, S. (eds) Promoter Associated RNA. Methods in Molecular Biology, vol 1543. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6716-2_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6716-2_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6714-8

  • Online ISBN: 978-1-4939-6716-2

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