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Identification of lncRNA MEG3 Binding Protein Using MS2-Tagged RNA Affinity Purification and Mass Spectrometry

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Abstract

Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Recently in mammals, thousands of long noncoding RNAs have been identified and studied as key molecular players in different biological processes with protein complexes. As a long noncoding RNA, maternally expressed gene 3 (MEG3) plays an important role in many cellular processes. However, the mechanism underlying MEG3 regulatory effects remains enigmatic. By using the specific interaction between MS2 coat protein and MS2 RNA hairpin, we developed a method (MS2-tagged RNA affinity purification and mass spectrometry (MTRAP-MS)) to identify proteins that interact with MEG3. Mass spectrometry and gene ontology (GO) analysis showed that MEG3 binding proteins possess nucleotide binding properties and take part in transport, translation, and other biological processes. In addition, interleukin enhancer binding factor 3 (ILF3) and poly(A) binding protein, cytoplasmic 3 (PABPC3) were validated for their interaction with MEG3. These findings indicate that the newly developed method can effectively enrich lncRNA binding proteins and provides a strong basis for studying MEG3 functions.

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Acknowledgments

This work was supported partially by the Chinese State Key Projects for Basic Research (2013CB910801), the National High Tech Research and Development Program (2012AA022501), and the Chinese National Natural Science Foundation projects (31370760, 31270836, and 31170713).

Conflict of Interest

The authors have no conflict of interest to declare.

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Authors and Affiliations

  1. Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, Jilin, People’s Republic of China

    Shanshan Liu & Yinghua Jin

  2. Beijing Institute of Radiation Medicine, Beijing, 100850, People’s Republic of China

    Shanshan Liu, Juanjuan Zhu, Taifeng Jiang, Yiran Zhong, Yi Tie, Xiaofei Zheng & Hanjiang Fu

  3. National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, People’s Republic of China

    Juanjuan Zhu & Yongge Wu

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  1. Shanshan Liu
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Correspondence to Yinghua Jin or Hanjiang Fu.

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Liu, S., Zhu, J., Jiang, T. et al. Identification of lncRNA MEG3 Binding Protein Using MS2-Tagged RNA Affinity Purification and Mass Spectrometry. Appl Biochem Biotechnol 176, 1834–1845 (2015). https://doi.org/10.1007/s12010-015-1680-5

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