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.

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

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

Dirección de Cátedras Consejo Nacional de Ciencia y Tecnología Ciudad de México 03940 México

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

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

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The RNA-dependent association of phosphatidylinositol 4,5-bisphosphate with intrinsically disordered proteins contribute to nuclear compartmentalization