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Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing

  • Pooja Gangras
  • Daniel M. Dayeh
  • Justin W. Mabin
  • Kotaro Nakanishi
  • Guramrit SinghEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1680)

Abstract

Argonaute proteins (AGOs) are loaded with small RNAs as guides to recognize target mRNAs. Since the target specificity heavily depends on the base complementarity between two strands, it is important to identify small guide and long target RNAs bound to AGOs. For this purpose, next-generation sequencing (NGS) technologies have extended our appreciation truly to the nucleotide level. However, the identification of RNAs via NGS from scarce RNA samples remains a challenge. Further, most commercial and published methods are compatible with either small RNAs or long RNAs, but are not equally applicable to both. Therefore, a single method that yields quantitative, bias-free NGS libraries to identify small and long RNAs from low levels of input will be of wide interest. Here, we introduce such a procedure that is based on several modifications of two published protocols and allows robust, sensitive, and reproducible cloning and sequencing of small amounts of RNAs of variable lengths. The method was applied to the identification of small RNAs bound to a purified eukaryotic AGO. Following ligation of a DNA adapter to RNA 3′-end, the key feature of this method is to use the adapter for priming reverse transcription (RT) wherein biotinylated deoxyribonucleotides specifically incorporated into the extended complementary DNA. Such RT products are enriched on streptavidin beads, circularized while immobilized on beads and directly used for PCR amplification. We provide a stepwise guide to generate RNA-Seq libraries, their purification, quantification, validation, and preparation for next-generation sequencing. We also provide basic steps in post-NGS data analyses using Galaxy, an open-source, web-based platform.

Key words

Small RNAs Argonaute Next-generation sequencing Biotinylated dNTPs Low RNA input 

Notes

Acknowledgements

Our research is supported by start-up funds from The Ohio State University (to G.S. and K.N.), a seed-grant from the Center for RNA Biology, OSU (to G.S. and K.N.), a Center for RNA Biology Fellowship, OSU (to D.M.D.) and a Graduate Student Pelotonia Fellowship (to D.M.D). We acknowledge Erin Heyer and Melissa Moore from University of Massachusetts Medical School, Worcester for their critical insights to streamline this procedure in our laboratory.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Pooja Gangras
    • 1
    • 5
  • Daniel M. Dayeh
    • 2
    • 3
  • Justin W. Mabin
    • 1
    • 5
  • Kotaro Nakanishi
    • 2
    • 3
    • 4
  • Guramrit Singh
    • 1
    • 3
    Email author
  1. 1.Department of Molecular GeneticsThe Ohio State UniversityColumbusUSA
  2. 2.Ohio State Chemistry ProgramThe Ohio State UniversityColumbusUSA
  3. 3.Center for RNA BiologyThe Ohio State UniversityColumbusUSA
  4. 4.Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusUSA
  5. 5.Center for RNA BiologyThe Ohio State UniversityColumbusUSA

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