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LIPRNAseq: a method to discover lipid interacting RNAs by sequencing

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Abstract

Background

Current biological research extensively describes the interactions of molecules such as RNA with other nucleic acids or proteins. However, the relatively recent discovery of nuclear phospholipids playing biologically relevant processes outside membranes, as well as, RNA-lipid interactions shows the need for new methods to explore the identity of these RNAs.

Methods and results

In this study, we describe the method for LIPID-RNA isolation followed by sequencing and analysis of the RNA that has the ability to interact with the selected lipids. Here we utilized specific phospholipid coated beads for selective RNA binding. We tested RNA from organisms belonging to different realms (human, plant, and yeast), and tested their ability to bind a specific lipid.

Conclusions

The results show several RNAs differentially enriched in the pull-down of phosphatidyl Inositol 4,5 bisphosphate coated beads. This method is helpful to screen lipid-binding RNA, which may have relevant biological functions. The method can be used with different lipids and comparison of pull-downs and can narrow the selection of RNAs that interact with a particular lipid for further studies.

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Abbreviations

PIP2:

Phosphatidylinositol 4, 5 bisphosphate

PI4P:

Phosphatidylinositol 4 phosphate

PA:

Phosphatidic acid

PIP3:

Phosphatidylinositol 3, 4, 5-trisphosphate

lncRNA:

Long non-coding RNA

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Acknowledgements

We would like to tank Pavel Kriz and Wilma Gonzalez for their technical help.

Author information

Authors and Affiliations

  1. Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México

    Andrea Bayona-Hernandez, Susana Guerra, Irma Angélica Jiménez-Ramirez & Enrique Castaño

  2. Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, Prague, 1083, 142 20, Czech Republic

    Martin Sztacho & Pavel Hozak

  3. Unidad de Biotecnologia, Centro de Investigación Científica de Yucatán, Chuburná de Hidalgo, Calle 43, Número 130, Mérida, Yucatán, CP 97205, México

    Luis Carlos Rodriguez-Zapata

  4. Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. Subsede Sureste, Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera Sierra Papacal-Chuburná-Puerto, Mérida, 97302, Yucatán, México

    Alejandro Pereira-Santana

  5. Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, 03940, México

    Alejandro Pereira-Santana

Authors
  1. Andrea Bayona-Hernandez
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  2. Susana Guerra
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  3. Irma Angélica Jiménez-Ramirez
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  4. Martin Sztacho
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  7. Alejandro Pereira-Santana
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  8. Enrique Castaño
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Contributions

AB, SG, AJ, and EC designed the experiments; AB, MS and EC performed the experiments with human; AB and SG performed the experiments with S. queretaroensis; AJ and EC performed the experiments with Yeast; AB and APS carried out the bioinformatics; PH and LC help with the data analysis and editing of the manuscript. AB, AJ, APS, and EC wrote the manuscript with the input of all the authors.

Corresponding author

Correspondence to Enrique Castaño.

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Ethics approval and consent to participate

This article does not contain any studies with any animals or human participants performed by any of the authors.

Grants

(Internship LTC19048 and LTC20024) and the project: BIOCEV – Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (CZ.1.05/1.1.00/02.0109), from the European Regional Development Fund. COST Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET CA19105 action). The Microscopy Centre was supported by the MEYS CR (LM2018129 Czech-BioImaging) and by the European Regional Development Fund-Project “Modernization and support of research activities of the national infrastructure for biological and medical imaging CzechBioImaging” (no. CZ.02.1.01/0.0/0.0/16_013/0001775) and by CONACYT grant FC2016/1572.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.

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Bayona-Hernandez, A., Guerra, S., Jiménez-Ramirez, I. et al. LIPRNAseq: a method to discover lipid interacting RNAs by sequencing. Mol Biol Rep 50, 6619–6626 (2023). https://doi.org/10.1007/s11033-023-08548-5

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  • DOI: https://doi.org/10.1007/s11033-023-08548-5

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