Analysis of Interaction Between Long Noncoding RNAs and Protein by RNA Immunoprecipitation in Arabidopsis

  • Jun Sung Seo
  • Nam-Hai ChuaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)


Long noncoding RNAs (lncRNAs) play important roles in several processes including control of gene expression. These RNAs function through binding to histone-modifying complexes and transcriptional machinery including transcription factor, mediator, and RNA polymerase II. We present methods for the discovery and characterization of lncRNAs. RNA immunoprecipitation (RIP) is a modified version of chromatin immunoprecipitation (ChIP), and it is now generally used in lncRNA study. The method allows for testing of lncRNA-protein interactions in vivo. RIP assay facilitates the identification of consensus sequences of preferred binding site for the RNA-binding protein under study, and identification of the binding sites can provide valuable information on the possible mechanism by which the RNA-binding protein functions.

Key words

Noncoding RNA ChIP RNA-protein interaction RIP lncRNA RNA immunoprecipitation 



This work was supported by Singapore NRF RSSS Grant (NRF-RSSS-002).


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Copyright information

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

Authors and Affiliations

  1. 1.Laboratory of Plant Molecular BiologyRockefeller UniversityNew YorkUSA
  2. 2.TEMASEK Life Sciences LaboratorySingaporeSingapore

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