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Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing

  • Samatha Mathew
  • Ambily Sivadas
  • Paras Sehgal
  • Kriti Kaushik
  • Shamsudheen K. Vellarikkal
  • Vinod ScariaEmail author
  • Sridhar SivasubbuEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)

Abstract

Long noncoding RNAs (lncRNAs) belong to a class of RNA transcripts that do not have the potential to code for proteins. LncRNAs were largely discovered in the transcriptomes of human and several model organisms, using next-generation sequencing (NGS) approaches, which have enabled a comprehensive genome scale annotation of transcripts. LncRNAs are known to have dynamic expression status and have the potential to orchestrate gene regulation at the epigenetic, transcriptional, and posttranscriptional levels. Here we describe the experimental methods involved in the discovery of lncRNAs from the transcriptome of a popular model organism zebrafish (Danio rerio). A structured and well-designed computational analysis pipeline subsequent to the RNA sequencing can be instrumental in revealing the diversity of the lncRNA transcripts. We describe one such computational pipeline used for the discovery of novel lncRNA transcripts in zebrafish. We also detail the validation of the putative novel lncRNA transcripts using qualitative and quantitative assays in zebrafish.

Key words

RNA sequencing Transcriptome Noncoding RNA Long noncoding RNA Zebrafish 

Notes

Acknowledgments

This work was funded by the Council of Scientific and Industrial Research (CSIR), India. S.M., A.S., P.S., and K.K. acknowledge Senior Research Fellowships from CSIR, India.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Samatha Mathew
    • 1
    • 2
  • Ambily Sivadas
    • 2
    • 3
  • Paras Sehgal
    • 1
    • 2
  • Kriti Kaushik
    • 1
    • 2
  • Shamsudheen K. Vellarikkal
    • 1
    • 2
  • Vinod Scaria
    • 2
    • 3
    Email author
  • Sridhar Sivasubbu
    • 1
    • 2
    Email author
  1. 1.Genomics and Molecular MedicineCSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)DelhiIndia
  2. 2.Academy of Scientific and Innovative Research (AcSIR)New DelhiIndia
  3. 3.G.N. Ramachandran Knowledge Centre for BioinformaticsCSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)DelhiIndia

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